Archive for Genomics

Can You Trust Genomic Evaluations? 7 Facts Exposed

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Tuesday, June 6th, 2017

Successful dairy cattle breeding is about using the facts available including the degree of trust that can be placed in the numbers. The facts used by breeders can vary all the way from in-herd observations, to show results, to including actual performance and genetic evaluation indexes. This article will deal with the genetic evaluation indexes that are based to a great extent on an animal’s DNA analysis. Often just referred to as ‘genomics.’ In this article, The Bullvine will cover details, from recently released studies and articles. We will look at how genomic evaluations are adding trustworthy information to the toolkit that breeders can use to advance their herds genetically.

1) Accuracy

Before there were genomic indexes, there were parent average genetic indexes (PA’s) for heifers that did not have their performance (production and type) records of for bulls that did not have daughters with a performance recorded. The prediction accuracy for PA’s was low, standing at 20-33%. Breeders knew that there would be a wide variation from the PA numbers, once performance data was added in.

In 2008, based on the study of the DNA profiles of daughters proven sires, genomic (genetic) indexes were published by genetic evaluation centers that used both pedigree performance information and an animal’s DNA profile. Immediately the accuracy of the genomic indexes doubled (60-65%) those for PA’s. Of course, this was lower than the accuracies for extensively daughter proven sires, but a significant step forward.

Alta Genetics has recently published an excellent article on the accuracy of genomic index predictions – “How genomic proofs hold up.” The study compares genomic indexes at the time of release as young sires and what their indexes are in April 2017.

The study reports:

Young sires released in 2010 2014 decreased by 171 vs. 52 in TPI and by 151 vs. 74 in NM$.
For the 1078 US A.I. Holstein bulls released in 2013, their April 2017 indexes decreased on average by 99 TPI and 103 NM$. The degrees of change for TPI were: 4% of bull lost more than 300 TPI points; 9% remain, in 2017, within 20 TPI points of their 2013 indexes; and 19% increased in TPI from their 2013 to 2017 indexes. For NM$: 2% on the bulls changes by more than 300 in NM$; 9% were within 20 NM$ in 2017 of their 2013 indexes, and 9% increased in their NM$ index.

Definitely, there was an increase in accuracy of prediction of genomic indexes from 2010 to 2017.

Take Home Message: With each passing year, breeders can place more and more trust in the accuracy of genomics indexes. As more animals have their DNA profile established and as more SNIP research is conducted breeders can expect to see further increases in accuracy of genomic indexes. Also, there will, in the future, be the publication for additional genomic indexes for specific fats and proteins, for lifetime performance and for health and fertility traits.

2) Improvement Rates

CDN has recently reported on a study “Analysis of Genetic Gains Realized Since Genomics.” This study compares two five-year time periods: (a) animals born (2004-2009) immediately prior to the existence of genomic evaluations; and (b) animals born (2011-2016) after genomic evaluations were available to breeders.

The rates vary by trait with the range in compared indexes being from a small improvement rate to over 500%. Note that in Holsteins the rate of genetic gain in protein %, lactation persistency (LP), daughter fertility (DF) and milking temperament (MTP) went from negative to positive. In Jerseys LP, MSP and daughter calving ability (DCA) went from negative to positive, yet metabolic disease resistance (MDR) went slightly negative. Similar rates of improved genetic gains were achieved by both Ayrshire and Brown Swiss breeds.

Take Home Message: Congratulations to the breeders for trusting and using the genomic index information to make faster rates of genetic improvement. A word of thanks goes out to the genetic evaluation centers all over the world for doing the research on and implementation of genomic indexes. The very significant increased rates of genetic gain may not be duplicated in the future for all traits as breeders are now selecting for many new economically important traits not previously evaluated and published.

3) Terminology

It is a known fact that the term ‘genomics’ has not always been interpreted correctly by everyone.

Over forty years ago, when genetic indexes were first published, frequently breeders thought of them as only being for production traits when they were available for both production and type traits. Today many people refer to genomic indexes as only being for production traits when they are available for production, type, fertility, health, other functional traits and total merit indexes (TPI, NM$, …).

Take Home Message: Interpret genomic indexes to be genetic indexes that include both pedigree and DNA profile information. Breeders can find genomically evaluated sires for all traits at all A.I. studs. Breeders can use one or all the genomic indexes as part of their herd’s breeding plan.

4) Inbreeding

Alta Genetics recently published an article, “Inbreeding: Manage it to Maximize Profit,” on sire options to limit the effects of inbreeding.

The article covers:

When selection is practiced in a population, it results in a concentration of good genes and thus inbreeding. So, inbreeding is a natural outcome of selecting the best and eliminating the rest.
Every 1% increase in inbreeding results in $22 – $24 less profit over a cow’s lifetime.
There is not a magic level of inbreeding to be avoided. The current average level of inbreeding in North American Holsteins is 7-8%.
A Midwest US study shows that superior inbred high genetic merit cows are more profitable than inferior genetic merit non-inbred cows.

The average inbreeding level of the top 25 NM$ (April ’17) daughter proven Holstein sires is 7.9% for genomic future inbreeding index (GFI). For the top 25 NM$ genomically evaluated sires the average GFI is 8.2%. Having genomic bulls with a higher level of inbreeding than proven sires is as expected when selection pressure is high, when generations are turned rapidly and when there is extensive focus placed on a single total merit indexes (NM$ or TPI or Pro$ or LPI or …).

Take Home Message: A.I. sire mating programs are designed to take into consideration the level of inbreeding of future progeny when a sire x dam is recommended. If a Holstein sire has a GFI of 9% or higher a breeder should require that that bull should have positive proof values for all of DPR, HCR, CCR, LIV, PL, SCC, immunity and calf wellness. Breeders should use and trust that inbreeding is being handled by sire mating programs.

5) Functional Traits

At the same time, as genomic evaluations became available, breeders started paying attention to a host of functional traits. These traits have economic significance and include milk quality, fertility, heifer, and cow health (immunity, wellness, disease resistance, livability, …), birthing, productive life and mobility. In the future, these functional traits will be expanded as on-farm data, and DNA profiling on animals are recorded and farm data is sent to data analysis centers. Noteworthy is the fact that animal wellness and welfare will be front and center for consumers of dairy products.

Take Home Message: Breeders can trust in the published genetic evaluations for functional traits as animal DNA profiles play a significant role in increasing the prediction accuracies from 15-25% to 60-70%. Functional trait improvement will require that breeders pay attention to both genetic and farm management.

6) Feed Efficiency

Feed accounts for 50-60% input costs for heifers and cows on dairy farms. Any gains that can be made by selecting genetically superior animals for their ability to convert feedstuffs to milk and meat have the potential for breeders to make more profit.

Research and data analysis are underway or nearing completion in many countries including US, Netherlands, and Canada on using DNA data combined with nutrition trial data to produce genomic indexes for feed efficiency. Other trials are underway to electronically capture on-farm data on feed intake, dry matter intake (DMI). It is a well-established fact that level of production is highly correlated to DMI.

CDAB has just published that “AGIL/USDA has demonstrated the feasibility of publishing national genomic evaluations for residual feed intake (RFI) based on the data generated by the 5-year national feed intake project funded by USDA National Institute of Food and Agriculture (NIFA), involving several research groups”. “The next step for CACB is to develop a proposal on how to collect data for use in genetic analysis for feed efficiency.”

Take Home Message: There will be genomic indexes for feed efficiency likely with 2-3 years. Once again breeders will have a tool they can trust into breed animals that return more profit.

7) Breeder Acceptance

A.I.’s are reporting that 60 to 90% of their semen sales are from genomically evaluated bulls. That fact on its own says that breeders purchasing larger volumes of semen are putting their trust in genomic evaluations. However, breeders wanting daughter proven sire proofs need to be given that option provided they are prepared to pay extra for their semen.

Take home message: Breeders check books tell the whole story – Genomic Evaluations are trusted.

The Bullvine Bottom Line

In less than a decade the use of DNA data in genetic evaluations has gone from unknown and not understood to a trusted source of very useful information. Having genomic indexes has given breeders the opportunity to advance their breeding programs, their herds, and their on-farm profits. Trust in information is important to dairy cattle breeders and they have and will continue, in the future, to place their trust in genomic indexes.

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Making progress on low heritability traits – Zoetis Webinar #7

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Friday, January 8th, 2016

Accelerating genetic improvement via genomic testing has been available to US dairy producers for more than five years. Until genomics became available, it was difficult to justify female selection of low heritability traits… the information was too low accuracy and slow from traditional methods. With the advent of genomic evaluations and the greatly improved accuracy it brings to genetic estimates, it’s important to re-evaluate long-held beliefs with the improved gains that can be made in low heritability traits.

The seventh installment of this video series covers “Making Genetic Progress on Low Heritability Traits”:

What does low heritability mean?
How do GPTA’s translate to real herd differences in low heritability traits?
Proof it works
Why some herds may see better results

Presenter

Dr. Weigel grew up in Iowa on the family farm (Weigeline Holsteins) and graduated from Iowa State University with a Degree in Dairy Science. He received both his M.S. and PhD from Virginia Tech, with his dissertation focusing on the prediction of genetic merit for lifetime profitability in Holsteins. Before joining the R&D group of Zoetis (formerly Pfizer Animal Health) in 1995, Dr. Weigel served as a post-doctoral fellow at the University of Guelph working on the implementation of Multiple Across Country Evaluations (MACE) for conformation traits of Holstein sires. Dr. Weigel’s current role with Zoetis is in Outcomes Research and he remains active as a breeder of Registered Holsteins.

Genomic Webinar Series

A webinar series developed by Zoetis and Holstein Association USA will be an educational resource for current and prospective CLARIFIDE® customers and Enlight™ users.

Through a series of online presentations dairy producers will be able to better understand:

How genomic testing works
How genetic improvement and genomics can benefit the future of their herd
How to utilize the data generated from genomic testing to make more effective management decisions.

The webinars will be moderated by The Bullvine with presentations by Zoetis or Holstein Association personnel. The Bullvine is an online source for dairy genetic and other industry happenings around the world, through their coverage via articles, videos and podcasts. Viewers will attend the presentation live at a specified time and date, and archived presentations will be accessible through other websites after each presentation.

The following webinars will take place from Noon Eastern time (9:00 a.m. Pacific time) as follows:

Topic/Title	Speaker	Date
An introduction to genomics	Cheryl Marti	July 8
Proving the technology works: How producers have benefited from using genomics	Dan Weigel	August 5
Using genomics testing strategies to accelerate genetic progress	David Erf	August 26
The economics of genomics	Cheryl Marti	October 7
Putting genomic results to work	Lindsey Worden	November 4
Moving Beyond Phenotype: genomics vs. size-based traits	David Erf	December 2
Making progress on low heritability traits	Dan Weigel	January 6

This webinar is proudly sponsored by:

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Categories : BullvineTV, Genomics

Putting Genomic Results to Work – ZOETIS Video #5

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Thursday, November 5th, 2015

To get the most from genomic testing the results have to be used to make decisions that have a positive impact on herd and genetic management. Matching herd data with animal identification and genomic data can be challenging without the right technology. Enlight is a program offered through the Holstein Association, USA to help CLARIFIDE users manage data for easier management decisions. In the fifth installment of this webinar series, Lindsey Worden, Holstein Association Director of Genetic Services, reviews ways to put your genomic results to work, including:

How the Enlight program offer solutions on how to benefit from the results of genomic testing.
Measuring the success of your genetic advancement program

Don’t miss this opportunity to learn more, and see how you can put genomics to work in your herd.

This webinar is proudly sponsored by:

Presenter

Lindsey Worden has worked as Holstein Association USA’s Executive Director of Holstein Genetic Services since October 2013. In her role, she oversees staff responsible for maintaining the Association’s genomic and genetic testing programs and software programs such as Red Book Plus/MultiMate, as well as other performance programs such as classification and production records products, providing guidance and direction for various Association initiatives. Worden was HAUSA’s project manager for the development of the Enlight™ genetic management tool, which was developed in collaboration with Zoetis, and now oversees the team responsible for supporting the product. Prior to her current responsibilities, she served as Holstein Association USA’s communications manager for more than 6 years. Worden is a graduate of the University of Wisconsin-Madison where she studied dairy science and life science communications and was an active member of the Association of Women in Agriculture, Badger Dairy Club and the dairy judging team. She has had a lifetime of involvement in the dairy industry and Registered Holsteins growing up on her family’s dairy operations in New York and New Mexico, and in her free time still enjoys helping out on her family’s Central New York dairy and working with her cattle. Worden works out of the Holstein Association USA headquarters in scenic Brattleboro, Vermont.

Genomic Webinar Series

A webinar series developed by Zoetis and Holstein Association USA will be an educational resource for current and prospective CLARIFIDE® customers and Enlight™ users.

Through a series of online presentations dairy producers will be able to better understand:

How genomic testing works
How genetic improvement and genomics can benefit the future of their herd
How to utilize the data generated from genomic testing to make more effective management decisions.

The following webinars will take place from Noon to 1:00 pm Eastern time (9:00 a.m. – 10:00 a.m. Pacific time) as follows:

Topic/Title	Speaker	Date
An introduction to genomics	Cheryl Marti	July 8
Proving the technology works: How producers have benefited from using genomics	Dan Weigel	August 5
Using genomics testing strategies to accelerate genetic progress	David Erf	August 26
The economics of genomics	Cheryl Marti	October 7
Putting genomic results to work	Lindsey Worden	November 4
Moving Beyond Phenotype: genomics vs. size-based traits	David Erf	December 2
Making progress on low heritability traits	Dan Weigel	January 6

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Categories : Genomics

The Economics of Genomics – Zoetis Webinar #4 Video

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Thursday, October 8th, 2015

You know genomic technology works better than other alternatives on your dairy. And you understand genetics are permanent, so decisions today impact results into multiple generations to come.

Many next ask, how do I know if it’s worth the investment? This topic will take a look at multiple ways genomic testing and selection can improve your profitability and efficiency, and in some scenarios, even your cash flow. Topics covered in this video are:

Improving profit and cash flow through strategic choices and selection
Improving profitability by using genomic test results versus using alternati
ves.
Other areas difficult to measure

Don’t miss this opportunity to learn more, and see real herd-modeled financials.

Presenter

Cheryl Marti is the U.S. Marketing Manager for Dairy Genetics and Reproductive Products for Zoetis. She received her B.S. from the University of Minnesota in Animal Sciences, her M.S. in Dairy Science (Genetics emphasis) at the University of Wisconsin – Madison, and her MBA from UW-Whitewater. Cheryl worked in the AI industry at ABS Global for over 11 years in many different capacities, including management, marketing, training and technical support of the Genetic Management System (a genetic mate assignment program), and also worked in the Sire Acquisition and Research areas. She joined Pfizer Animal Health, now Zoetis, in 2005, first as a Fresh Cow Reproduction Manager in the Great Lakes states and later as a Dairy Production Specialist in WI where she often worked with large dairies on genomics, reproduction, records analysis, and transition cows until mid-2014 when she moved into her current role. Her experiences include working with herds of all sizes across the U.S. and over a dozen countries on 6 continents. Cheryl’s passion for the dairy industry and genetics began at her family’s Registered Holstein farm in Sleepy Eye, MN, where she owns some cattle, and her sister and brother-in-law own and operate their family farm of 700 acres and a 160-cow dairy called “Olmar Farms.

This webinar is proudly sponsored by:

Genomic Webinar Series

A webinar series developed by Zoetis and Holstein Association USA will be an educational resource for current and prospective CLARIFIDE® customers and Enlight™ users.

Through a series of online presentations dairy producers will be able to better understand:

How genomic testing works
How genetic improvement and genomics can benefit the future of their herd
How to utilize the data generated from genomic testing to make more effective management decisions.

The following webinars will take place from Noon to 1:00 pm Eastern time (9:00 a.m. – 10:00 a.m. Pacific time) as follows:

Topic/Title	Speaker	Date
An introduction to genomics	Cheryl Marti	July 8
Proving the technology works: How producers have benefited from using genomics	Dan Weigel	August 5
Using genomics testing strategies to accelerate genetic progress	David Erf	August 26
The economics of genomics	Cheryl Marti	October 7
Putting genomic results to work	Lindsey Worden	November 4
Moving Beyond Phenotype: genomics vs. size-based traits	David Erf	December 2
Making progress on low heritability traits	Dan Weigel	January 6

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Categories : Genomics

Using Genomics as the Ticket to the Future

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Wednesday, June 24th, 2015

“Genomics has taken dairy cattle genetics to new heights.” Of course, there are breeders who agree and others who disagree with that statement. Regardless of our individual opinions, breeders definitely know more about the genetic make-up of the top animals than we did prior to 2008.

Let’s do an analysis on using and relying on genomics to achieve genetically improved dairy cattle in the future through increased accuracy, profitability, and genetic advancement.

Strengths

allows for reducing the effects of biases found in the phenotypic data used in genetic evaluations (accuracy)
can be used for both parentage verification and genetic indexing (accuracy)
increases the accuracy of genetic indexes for young bulls and genetically elite females (accuracy)
provides for enhanced accuracy when culling of heifers based on genetic indexes (accuracy)
allows for decreasing the generation intervals (rate of genetic advancement)
reduces the number of young bulls that need to be sampled. Each one costs $50,000. (profitability)
allows breeders to focus on replicating their best genetically indexed animals or families (genetic advancement)
can be used for decisions beyond genetics including in health and management (profitability)
fits a breeding model that uses genetic indexes and yields rapid genetic gain (genetic advancement)

Weaknesses

currently, not enough young females are being tested to know accurately the population average and ranges
adds to the cost for documenting animals
took some control out of the hands of breeders and breed associations
resulted in more friction amongst breeders
required that breeds incur the cost of education/awareness programs
does not fit a breeding model that uses show results or requires 90+% reliability for sires used

Opportunities

provides the opportunity for more on-farm profit including the need to raise fewer heifers (profitability)
reduces the loss that breeders incur when they get low-end heifers from low genetic merit unproven sires (profitability)
allows for breeders to implement new models for breeding and marketing (profitability)
results in a more rapid genetic improvement for both herds and breeds, at less cost (genetic advancement)
allows for the genetic evaluations for additional important traits (profitability and genetic advancement)
allows for the genetic evaluations for traits on which it is hard to capture field data (profitability and genetic improvement)
allows for the accuracy of comparison for animals originating from foreign sources (accuracy)
allows for re-structuring of or adding to services that breeders need (profitability)

Threats

The following threats are largely based on changes in the status quo.

devalues some animals previously considered elite and of some animals capable of winning at local shows
if not used wisely can result in increased levels of inbreeding
provides for breeders to discontinue participation in performance recording programs, yet they can make significant genetic improvement
could result in fewer A.I organizations and thereby potentially less choice for breeders
may require that a new genetic evaluation formula be developed

Where from here?

The position taken by breeders relative to genomic information very often depends on whether they see genomics as a threat or as an opportunity. It’s time to be positive. It’s impossible to turn back the clock. We need to stop the negativity on the topic of genomics or toward the people using that information. Breeders and industry stakeholders need to work nationally and internationally for collective benefit. With further research and development genomics will provide discerning breeders with information so they can achieve their breeding and profitability goals.

The Bullvine Bottom Line

The Bullvine strongly supports using genomic information. Although it is not the only tool, it is a very constructive one for improving the total genetic merit of dairy cattle. Progressive and pro-active breeds and breeders will use and further develop this tool.

The first webinar in the series to be held on Noon (EST) Wednesday July 8th 2015, and will focus on the basics of genomics to provide producers with a better understanding of the benefits of knowing more about their heifers. Click here to reserve your seat!

Smoking is good for you…and other facts dairy breeders should know

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Monday, June 1st, 2015

In the 1920’s and 30’s cigarette companies not only denied the health risks of smoking, they actually promoted them as a good thing, by putting up testimonials and stats about doctors who smoked. During the 1920s, Lucky Strike was the dominant cigarette brand. This brand, made by American Tobacco Company, was the first to use the image of a physician in its advertisements. “20,679 physicians say Luckies are less irritating,” its ads proclaimed. Of course many years later we are well aware of the health risks (480,000 people die prematurely each year in the US, due to smoking or being exposed to smoke). It’s flashbacks to this false advertising experience that dairy breeders are referencing when they distrust the use of genomics in dairy cattle breeding. They feel that it’s just the AI companies “forcing” genomics down their throats, in the same way that the tobacco companies “forced” smoking down the throats of millions, by using the weight of doctors’ credibility.

For a long time, physicians were the authority on health. Patients trusted their doctor’s education and expertise and, for the most part, followed their advice. When health concerns about cigarettes began to receive public attention in the 1930s, tobacco companies took preemptive action. They capitalised on people’s trust of physicians, to quell concerns about the dangers of smoking. Thus was born the use of doctors in cigarette advertisements. Executives at tobacco companies knew they had to take action to suppress the public’s fears about tobacco products.

When genomics was first introduced to the dairy cattle breeding world, it was controlled by the major artificial insemination companies. According to some breeders they “hammered” the benefits of genomics down their throats and left breeders almost no choice but to use high index genomic sires, as there were limited other options. The ironic thing is that high praise for the product is about where the similarities between the Tobacco industry and the dairy breeder world part ways.

Unlike cigarettes that were eventually exposed for their many alarming health risks despite the early endorsement, genomics had the opposite reaction – distrust. At the time, almost daily I was reading warnings in other “leading” dairy publications against using genomic sires. This pandered to the old school mentality that fosters breeder concern about using Genomics. Instead of basing their comments on facts, they used hearsay, conjecture and outright fear mongering to defend their negative comments. (Read more: The Genomic Bubble Has Burst?)

The facts are pretty clear. Genomics increases young sires’ reliability by 30% and 1st crop proven sires by 5%. In effect, that says that a young sire with a 50K genomic test and a proven sire will now have reliability comparable to an early 1st crop proven sire pre-genomics. This would indicate that, if you were willing to trust a 1st crop proof prior to the introduction of Genomics, you should now be ready to trust a genomic young sire from a proven sire as their reliabilities are very comparable. Furthermore, genetics marketing is also supporting this. Genomic young sires are set to outsell proven sires because most breeders are confident in the numbers and are making sound breeding decisions based on them. As we mentioned in our article Genomics – Lies, Miss-Truths and False Publications, genomically evaluated bulls with 65% reliable gLPIs, breeders can expect 95% of the time that their official proof will be within 400 LPI points (within about 10-15%). (Please note that this figure reflects the change in the CDN system). Yes, genomic young sires do, on average, drop below their original predicted values but, they are, on average, still higher than the current proven sires that they are competing with.

The interesting part is that, while promoting smoking was a “cash cow” for the Tobacco industry, the increased use of genomic young sires has actually caused problems for the AI companies, even though genomic sires now account for 50% of semen sales. This led me to propose that genomics will soon be used by 84% of dairy breeders in the world. (Read more: Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!) This is actually scary news for most AI companies. That is because the average genomic young sire produces about 20,000 doses of semen a year. That is about 10 to 20% of the semen production of a healthy proven sire. This means that instead of housing 1 proven sire, these companies now have to house four to nine extra young sires, in order to produce the same amount of semen. So while genomics was first expected to help these companies save money on bull housing, it has actually resulted in them having to increase their housing expenses.

Here at the Bullvine we think the facts about genomics speak for themselves:

Genomics is a Tool
On a daily basis, it drives me nuts to see the number of breeders who refer to Genomics as a selection tool. Genomics increases the reliability of individual traits and indexes. That’s it. The term “Genomics” is misused by many. They should be referring to “High Index” sires, meaning list toppers on the gTPI, gLPI, and other lists. This may seem like a minor thing. I am even guilty of it myself, from time to time. However, it’s really an enormous error when you consider it from a breeder viewpoint. Over the past week, I looked at more than 100 comments about Genomics from naysayers. Every single one of them would have been more accurate if they had used the term “High Index” actually than Genomics. Most of the reservations against Genomics have more to do with reservations about the use of high index sires. The debate between selecting for “High Index” or “Proven” pedigrees will go on for years to come. The point that many miss is that Genomics is a tool that can help both strategies. Since Genomics helps increase the accuracy of the indexes, it will help both approaches excel into the future.
The Numbers Don’t Lie
It’s always easy to quote a case-by-case example and find a few cases that help support a point of view. However, it takes consideration of the full spectrum to get a truly accurate assessment of how any program or any tool is working. This means that we can be 95% sure that the current top gLPI sire, RH Superman (gLPI of +3473), will be higher than +3000 LPI, once he has his official progeny proven index. That prediction is over 90% reliable, and that would make him among the top 3 active proven sires in Canada. In the US, sires like Delta (gTPI of +2691) will end up over +2300 gTPI placing him in the top 20. (Editor’s note: Prior to the regression to bring high genomic young sires closer to proven sires, sires like Extreme and Alta1stclass would have actually been higher than the current top proven sire). Yes, genomic young sires do on average drop below their original predicted values, but, they are on average still higher than the proven sires of that time.
Falling Numbers are not an Indicator of System Failure
Whether it’s young sires’ indexes dropping or semen prices going down, neither of these two events accurately predict the value of Genomics. You see Genomics is new to the industry and, with anything that is new, there is a period of figuring out how the “new world” will work. During that period, aggressive breeders and semen companies have sought to maximize revenues for themselves and the breeders they represent. This has meant testing the market to see exactly what should be the maximum revenue price for each animal or dose of semen. Simple economics teaches us that we need to test to find the point that maximizes revenue. That is either by selling at high prices and reduced quantities or selling at a medium prices and increasing quantities. Both are sound strategies. At times, due to exclusivity and extremely unique genetics, young sire semen has sold for up to $10,000 a dose and, with the removal of the exclusivity and with other sires coming out after the fact, that semen is now available at a significantly reduced price. (Read more: $10,000 a dose Polled Semen). The breeder who purchased this semen, Ri-Val-Re Holsteins from Michigan, actually made out very well with his investment, as he had a clear plan with the use of IVF to maximize his return. (Read more: Breeding R-Val-Re: Where looking good in the stall is just as important as looking good on paper) It has also led to other attempts and premium pricing or pricing models. This is not a failure of the system. This is progressive individuals trying to discover how the new system is going to work. Does it always return maximum profits?….No. However, does it help those individuals understand the new market and how they can operate to maximize efficiency in the future? ….Yes. Just because you are not able to justify these prices for your breeding program goals, does not mean that it will not work for others. The important thing is for you to understand your personal dairy genetic plan and goals and make sure you are constantly evaluating and improving them. (Read more: What’s the plan?). It is interesting to note that since the introduction of Genomics, the rate of genetic advancement has more than doubled. Coincidence? I don’t think so. Today more breeders can make more sound decisions. The industry, as a whole, is benefiting.

The Bullvine Bottom Line

Unlike cigarettes, where there is certainly no question left about the health risks of smoking, genomics and cigarettes are not interchangeable. There is significant proof that genomics does, in fact, provide good “health” for your dairy breeding program. To genomic detractors, I ask you “Where is your smoking gun”? Where is your proof that genomics does not work?

Not sure what all this hype about genomics is all about?
Want to learn what it is and what it means to your breeding program?
Download this free guide.

The Bullvine proves Genomics does not work!

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Wednesday, April 1st, 2015

April Fools. There are just those breeders who will never accept Genomics as a tool in their breeding toolbox. For those of you who have or are still need convincing on why to use genomics in your breeding strategy we offer the following articles:

Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.

Are You Making the Most of Genomic Information?

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Wednesday, March 25th, 2015

Much has been written about genomic indexes since they were introduced in 2008, yet one key ingredient has been ignored. That ingredient is how can a breeder use the genomic information to analyse and plan for the future breeding of their herd? To fill that need Holstein Association USA, and Zoetis joined forced to develop the Enlight service that any Holstein producer in the USA can benefit from using.

Let’s hear about Enlight from Lindsey Worden

Lindsey is the Executive Director of Genetics Services at Holstein USA and when listening to her speak about Enlight you can hear the enthusiasm in her voice. Enthusiasm for what a breeder using Enlight can do to advance their herd. As Lindsey says, the advancement can cover more than genetics. It extends to others areas including management, reproduction, health and in the future nutrition. That is a wide scope. For U.S. dairy people interested in learning the opportunities available, go to Holstein USA’s website to learn more.

Enlight Home Dashboard

One final matter that Lindsey emphasized to The Bullvine – “Enlight is a free tool for any dairy producer who is genomic testing their Holsteins through Holstein Association USA or Zoetis, using CLARIFIDE^®, a genomic testing product. Enlight is web-based, and has a direct connection to the Holstein Association USA herdbook database, so all animals in Enlight must also be in the Holstein herdbook”. It should be noted that a herd’s data contained in Enlight is proprietary to the herd owner and is not shared with others.

Worden Draws on Experience

Lindsey grew up on her family’s dairy farms in New York and New Mexico, and was active in 4-H and Holstein Junior programs, including dairy judging and showing. She followed that by studying Dairy Science and Life Science Communications at the University of Wisconsin-Madison. After college, she joined Holstein Association USA. That was over eight years ago, and she has filled a number of positions of increasing responsibility at Holstein USA. Lindsey is familiar with all facets of dairying from the small breeder’s herd, to the large commercial herd, to the show scene and to the international trade in genetics. She gives major credit to her parents for giving her and her brothers the opportunity to experience life, both on and off their farms. Lindsey attends many industry events and is always eager to speak with breeders to understand their positions, their concerns and their needs, and to explain Holstein USA services.

Enlight – Animal Snap shot

Working to Shared Benefit

In short, Enlight was developed in partnership by Zoetis and Holstein USA. They saw an opportunity to combine their collective strengths for the benefit of producers. It is novel in that a private company and a breeder not-for-profit association joined forces to provide a service, and refreshing to see that providing dairy people with a complete package is central to the service.

Excellent Uptake

Lindsey reported to The Bullvine that since July (2014) there have been over 600 herds enrolled in Enlight, and those users have genomic tested over 260,000 animals in total.

U.S. dairymen can expect to hear more about Enlight in 2015 as Holstein USA, in collaboration with Zoetis, will have this service as a focal point at meetings and in communications through out this year. It is interesting to hear the many different ways Enlight users are taking advantage of genomic information in their herds. Many begin with testing a few animals and eventually work up to testing most or all of the heifers born on their farm. Dairymen are using the information to make decisions about which animals will be parents to the next generation on the farm, making sure they are keeping and propagating the best genetics in their herds, and using the lower end genetics for recipients, or culling when they have excess animals to sell.

One important part of Enlight is that it is real-time. Enlight is refreshed every night, so whenever a dairyman registers a calf, or has new genomic or genetic information available, it can be viewed in Enlight. Since the service if free and web-based, users can run the analysis of their animal as often as they wish.

Enlight – Genetic Progress Graph

Expanded Service

For dairy farmers, linking all pieces of information on their animals together is important. Sandy-Valley Farms have been using Enlight for a few months now to capture their actual and genetic information in one place, to obtain genomic information instantaneously and to download information in Excel documents. And Danae Bauer of Sandy-Valley looks forward to using Enlight even more in the future as more options and screens are added to it. (Read more : PINE-TREE MONICA PLANETA IS THE NEW GENOMIC SUPER STAR MAKER, and DANAE BAUER: CAPTURING THE PASSION)

Holstein Association USA continues to see interest in genomic testing grow each year, and with the availability of Enlight to help producers make better use of their information, and a partnership with Zoetis, that trend is only expected to continue to increase. As more breeders are exposed to how using genomic information can improve their herds, more and more will adopt the technology and find benefit in keeping track of their genetics with Enlight.

The Bullvine Bottom Line

With many dairymen already using Enlight, there are many users that Holstein USA or Zoetis can direct interested producers to in order that they can hear a fellow dairy person describe the benefits as they see them. Enlight is definitely a win – win – win for producers – breed association – private service provider.

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Arm Chair Quarterbacks, Monday Night Football and Tuesday Morning Genomics

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Monday, March 9th, 2015

If you were the coach of an NFL football team, would you select your players based solely on looking at them or would you want to see their performance statistics, in order to decide how to assemble the best team possible? That is the question that Don Bennink (Read more: NORTH FLORIDA HOLSTEINS. Aggressive, Progressive and Profitable!!) asked at the recent genomics conference. (Read more. Genetics in the Age of Genomics – Seminar Recordings and Recap) While it’s a pretty simple question, it may forever change the way you make your mating decisions.

For generations, we have all been taught to look at a cow the same way, and that’s the way we continue to teach the next generation to look at dairy cows today. But just because that is the way it has always been done, does not mean that we have been doing it correctly. We all start out learning the parts of the dairy cow and have learned the same way as we always have on how to evaluate cows. In fact, one major publication did seven editions in a row about how to evaluate cows, and each one presented the same way it’s been done for generations. It doesn’t seem to matter that evaluating type or conformation has been proven not to be the most accurate way to determine longevity (Read more: She ain’t pretty she just milks that way).

For years, it has been assumed that, if a cow had “high type” and lots of production, she was the perfect cow. But we all know that perfect cows don’t always exist (Read more: The Perfect Holstein Cow). Nevertheless, we have bred for these two key areas: high type and lots of production. We totally disregarded that we did not make substantial gains in profitability. And, furthermore, herd life actually decreased, even though we all bought into to the theory that a high type cow is a long lasting cow. Unfortunately, actual performance data shows that, as we bred for this the cows were actually lasting less time than before. In fact mortality rates increased; conception decreased and the number of lactations that most cows lasted decreased.

Through the years, the use of high production and low fertility bulls has actually decreased overall herd conception rates. Don points out that when he “first started milking cows, and AI was in it’s infancy, farmers up and down the road, had a 60% conception rate. Today people brag if they have a 30% conception rate.” Don also points out that in 1996, 93.4% of the calves that were born in the US lived, (i.e. a 6.4% stillborn rate). In 2002, the stillborn rate increased to 11% (i.e. 89% lived) and by 2007, 14% of the dairy calves died at birth. It’s only in more recent years that the industry has acknowledged this trend and has started to put more emphasis on conception and the significant impact it has on profitability. The reason for this is we put so much emphasis on a two-year-old production that we were killing reproduction. That is because cows that get back in calf regularly drop in production because they have to use some of their energy to support the development of their calves. So the sires that gave the maximum amount of milk were also the sires who had the lowest conception rates. We all know that a cow that is milking hard is the hardest cow to get back in calf. No matter what their conformation.

The thing is that we have the systems and technology to make the changes we need to make for the future. As Don points out, we don’t need to go to the 125-year old technology of type evaluation to solve this problem. Instead of having to use theory to predict longevity, we can actually measure productive life through the actual length in months that cows last in herds compared to their herd mates. We don’t need type evaluation to guess who will last longer; we have the actual information. We have the ability to see just which cows will last longer, not from trying to figure out what type trait links best to longevity. We have actual longevity data, SCS, fertility, conception, still births, etc.

We are all armchair quarterbacks. We are all willing to second guess the mating decisions of others after the fact. The challenge is that, with the technology we have available today, we don’t have to do as much second guessing as in the past. Tools like genomics and new performance data such as DPR, Still Birth Rate, and Productive Life tell us everything we need to make an informed decision. Don asks, “Can you just pick the perfect team by just looking at your players? Or would it help to know which players have drug issues, which ones will end up in jail, which ones will last a full season, and which quarterbacks can actually complete a pass, or know how many sacks your linebackers have made in the past. As a coach, you want all this data to choose your team. Well we are not coaches we are dairy farmers, and we make our money milking cows. Don’t you want that data on your animals? Or are you just going to keep looking at them and think that you can guess which ones could perform?”

In today’s day and age, we not only have traits that are more directly connected to longevity than type evaluation, we also have genomic testing that can more accurately predict what sires and cows will last longer. Every Tuesday we now receive genomic predictions on animals. We don’t need to wait till for a quarterly classification visit, that may or may not catch a cow on her best day, to evaluate what we think from looking at her is the probability that she will last more lactations. We can actually get much more accurate data at a younger age on how long she will stay in the herd.

The Bullvine Bottom Line

Sometimes it can be hard to change the way we have always played the game. When something has been done for generations, there will always be those who are resistant to change. However, the industry has changed and the amount of information available today to make mating decisions is light years ahead of what it was just a few years ago. The game is changing, and you need to change what you base your breeding decisions on. . The best coaches and quarterbacks make their decisions based on performance data, not on hypothesis. Genomics has helped take away the guessing game. We can now know at a very young age, what the genetic potential of that calf is. We can make better decisions faster. In the past art and practical knowledge was what drove mating decisions. However, today’s breeding world calls for a different approach. It takes a level of focus and commitment, and it’s a business. It is just like football, where the coaches now use all the information possible to decide what players to put on the field and how to use those players for the big game on Monday nights. Tools like genomics have changed the game forever.

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Genomic Testing – Are You Missing Out?

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Thursday, August 21st, 2014

When The Bullvine mentions genomic testing to production oriented breeders, we frequently get the reaction “Oh, that’s just for herds that sell high priced animals. I focus on running a profitable milking operation. I don’t need to spend money on testing my animals.” Well, in fact, that is not an accurate assessment of the benefits available from using this tool at the present time. If you are among those not using genomics, Stop Procrastinating! It is a tool that everyone breeding their herd to improve it genetically should not be without.

Only Very Moderate Uptake – So Far

Currently, there is an 8% uptake of genomic testing of all Holstein heifer calves. The total is less in other breeds. We have barely scratched the surface. Half a century ago, official milk recording was at the same low level. Today it is recognized as a much-needed toll both on-farm and in the national herd. Obviously the question that breeders need answers to is ‘How will I benefit from genomic testing all my heifer calves?’

Known Benefits

Much has been written about benefits and opportunities available to breeders who are submitting samples for DNA testing. Those range from selecting the best mates for your females, … to parentage verification, … to how to manage your heifer herd, … to deciding which heifers to breed and which ones to cull or implant, … to polled or not polled, …to finding the genetic outlier of an individual mating, …to an aid in marketing heifers in sales.

Just recently Holstein USA and Zetas launched an exciting service called Enlight. Breeders that submit their samples to Zoetis can through Holstein USA’s website summarize and analyze their heifers for their genetic qualities. This is the first, and no doubt other breeds will establish similar services in the future. Breeding to get the genetics that work best for you and then managing them in the best way possible is definitely important.

At the industry level, genomic testing has also proven beneficial. Alta Genetics, a few years ago, working with large herds in the USA, parentage verified all young sire daughters. It was a significant step forward in accuracy of sire proofs so they could guarantee their product to their customers. Companies like Zoetis and Neogen initiated genomic testing services so they could help producers and also as complementary to their other products. A.I companies have been able to restrict their young sires sampled to only top genomically evaluated young sires, thereby saving millions for themselves by not sampling the bottom enders and millions for breeders that did not have to raise, calve in and milk the lower genetic merit daughters of the bottom end bulls. All of these benefits are leading to cost savings in the hundreds of millions of dollars.

However six years into using genomics we are only starting to reap the rewards.

Genomics Will Make the Future Brighter

Breeders often mention that they want sires to use and females in their herd that are superior to what is available today for traits that are difficult or impossible to measure. Here are some thoughts and facts that may help breeders to decide to use genomic testing so they can have animals that are even more profitable than their herd is today. It does however require that genomic testing becomes routine (Read more: Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!).

Heifers:

Investigation, at the farm level, is being done in beef heifers on growth rates, diets tailored to genotype, immunity to common diseases and age at first estrus. The results of those studies will be able to be applied to dairy heifers since little similar research is being conducted for dairy heifers. Already breeders can test for the genetically inferior heifers, so they do not need to be raised. Up to $500 per heifer in rearing cost could be saved by having the retained heifers calving by 22 months of age. Remember that it is age at first estrus that is important, for which we have very limited farm data. First breeding depends on a breeding actually occurring. With heifers genotyped and selected for first estrus significant savings will be possible.

Feed Efficiency:

Two major research projects, one in USA and The Netherlands and one in Australia and New Zealand, will identify the cows that are genetically more efficient at converting their feed to milk. Within a couple of years, we can expect to see reports relating genomic information to feed efficiency. This type of research is costly and not currently practical at the farm level, but using research herds this investigation is well underway. Reducing feed costs by 5-10% through genetic selection would result in many millions in savings. That is likely to be crucial to the dairy cattle breeding industry as dairy competes to feed a hungry world. (Read more: Feed Efficiency: The Money Saver and 15 Strength Sires That Will Still Fit In Your Stalls)

Inbreeding:

CDCB already makes available the inbreeding level of genomically tested animals based on their genomic results. No doubt further research results will provide numbers associated with inbreeding. Think about it. In the past the inbreeding level for two full sisters, based on pedigree, has been considered the same. However, by using their genomic profiles the level of inbreeding can be much more accurately known for each sister. A recent report from CDN, for the time period 2010 to 2013, shows that inbreeding rates are increasing not decreasing. Even though breeders are aware that inbreeding is a negative to future profit, they continue using fewer sire lines. More in-depth study of presence or absence of genes that negatively affect the viability of our cattle take time. Why do we always expect someone else to take responsibility for the level and rates of inbreeding? (Read more: 6 Steps to Understanding & Managing Inbreeding in Your Herd and Stop Talking About Inbreeding…)

Disease Resistance:

The list is long on diseases that breeders want their animals to be resistant to. Many research projects are underway to relate the genotype to particular types of mastitis, respiratory diseases, wasting diseases and even production limiting diseases like milk fever. CDN and Canadian milk recording agencies have been capturing field data for a number of years now on eight production limiting diseases. In time, the relationships between genetic lines and these diseases will be better-known. So that selection can be carried out to avoid problem bloodlines. When more animals are genomically tested, and bloodlines prone to diseases are identified great steps forward will be able to be made. It takes considerably more than 8% of the population genomically tested to move breeding for disease resistance to reality. (Read more: Genomics – Opportunity is Knocking)

Reproduction:

Failure to get animals to show good heats, to produce good oocytes and conceive when bred is the leading frustration on most dairy farms. The role that genetics plays in that frustration is now receiving attention by many researchers and organizations. In the past, the capturing of useful data to do genetic analysis relative to reproduction has been a significant problem. The relating of genomic results to reproduction holds out considerable hope. Early embryonic death, haplotypes that negatively impact reproduction, genetic difference between animals for cystic ovaries and many more are all areas of concern for breeders. Once again both genomic and on-farm data are needed to move forward. (Read more: 10 things dairies with great reproduction do right and Are Your Genetics Wasting Feed and Labor?)

Misconception:

I hear breeders say “Genomic indexes are just like production indexes.” However, that is not so. There are genomic indexes for production traits, conformation traits and management traits. Genomics is a dynamic science. It is best if breeders know not only the genomic values for the animals currently in their herds but also their ancestors. To build the genomic history for a herd necessitates that testing start as soon as possible. Genomics is a tool every breeder will benefit from using no matter what their selection goals are. (Read more: Better Decision Making by Using Technology and FACT VS. FANTASY: A Realistic Approach to Sire Selection)

In Another World

Outside the world of dairy cattle but totally related to DNA analysis, there is a study just under way in the United Kingdom, where 100,000 people with cancer or rare diseases are being genotyped to better understand people’s ability to avoid or resist cancer and disease. One of the terms used in the news release was that before there was DNA profiling this work would not have been possible. Relating that back to dairy cattle, if we do not have the DNA information for animals we will be limited in our ability to eliminate deleterious genes from our cattle.

Will Genomic Testing Pay?

The question for breeders appears to have been one of cost – benefit. “What will I get for the fifty dollar cost of doing a low-density test?” The fact is that, to date, milk producers have not taken the opportunity for more rapid genetic advancement by testing all their heifers. However, the tide is about to change. With new information coming out almost weekly on how the genetic (aka genomic) make-up of an animal relates to profitability, breeders without genomic information on their herd will not be in a position to know which sires to use or how to manage or feed their animals. Genomic testing needs to be viewed as an investment rather than a cost. Invest $50 shortly after birth to save hundreds over the cow’s lifetime.

The Bullvine Bottom Line

Every journey requires that a first step be taken. The first step is that breeders submit samples for DNA analysis. Every breeder will benefit by knowing the genomics of their herd. No doubt the cost of testing will come down as more breeders participate. Future success in dairying will require genomic testing, just as current success depends on capturing and using performance information. Are you prepared for using genomic information to assist in creating your future success in dairying?

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Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!

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Friday, August 1st, 2014

There are certainly breeders who are not fans of Genomics and the heavy use of high index genomic young sires. Yet genomic sires now account for 50% of semen sales. That leads me to propose that genomics will soon be used by 84% of the breeders in the world.

The reason for this has nothing to do with the merits of genomic sires versus proven sires. Rather it has to do with the historical patterns of adoption of new technologies. The theory behind this is called the Diffusion of Innovations. According to this theory, consumers differ in their readiness and willingness to adopt new technology. There are the innovators (2.5 percent of the population), the early adopters (13.5 percent), the early majority (34 percent), the late majority (34 percent), and the laggards (16 percent), who are also the people who still don’t have cell phones or who are not on Facebook.

As far as genomics goes, we have seen that it has followed this same pattern. When genomics was introduced, there was a small percentage of breeders who were so excited about the technology, or technology in general, which started using genomic sires instantly. These were the innovators in the dairy breeding marketplace. Since the information was not publically available and held by the A.I. centers, this uptake was very restricted. Then came the public introduction of genomics and the early adopters started using it. For a little while after that genomics seemed to stall. While there was 16% of the marketplace that was excited about Genomics and the possibilities that it held, the majority of breeders were not convinced. They had skepticism about whether genomics would work and if they should be using this new technology in their breeding programs. Regardless, the momentum started to grow.

Malcolm Gladwell describes this point, after early adoption, as “The Tipping Point” in his titled bestselling book of the same name. It’s at this point that it is determined whether something will spread like wildfire or sputter and fade into oblivion. Gladwell’s central argument is that there are actually a number of patterns and factors that are at play. They have an effect in virtually every influential trend, ranging from the spread of communicable diseases to the unprecedented popularity of a particular children’s television show. If you analyze the evolution of any significant phenomenon, Gladwell suggests, you will find that the processes involved are strikingly similar. Based on his in-depth research spanning a number of different fields, industries, and scholarly disciplines, Gladwell identifies three key factors that each play a role in determining whether a particular trend will “tip” into wide-scale popularity or fade. He calls them the Law of the Few, the Stickiness Factor, and the Power of Context.

The following is a closer look at each of these concepts and how they apply to what we have seen in the adoption of Genomics in the Dairy Breeding Industry:

The Law of the Few
Before the tipping point can be reached, a few key types of people must champion an idea, concept, or product, Gladwell describes these key types as Connectors, Salesmen and Mavens. If individuals representing all three of these groups endorse and advocate a new idea, it is much more likely that it will tip into exponential success. Regarding the use of genomics in the dairy breeding industry, these roles were filled by the large A.I. companies, their salespeople as respected high index breeders.
The Stickiness Factor
This refers to the unique quality that compels a phenomenon to “stick” in the minds of the public and then influences their future behavior. Gladwell defines the Stickiness Factor as the quality that compels people to pay close, sustained attention to a product, concept, or idea. In the dairy industry use of genomics, this was the allure of significantly more accurate genetic evaluations for young animals combined with the ability to dramatically accelerate breeding programs.
The Power of Context
This is enormously important in determining whether a particular phenomenon will tip into widespread popularity. Even minute changes in the environment can play a significant role in the likelihood of a given concept attaining the tipping point. If the environment or historical moment in which a trend is introduced is not right, it is not as likely that the tipping point will be attained. Clearly, in order for a trend to tip into massive popularity, large numbers of people need to embrace it. However, Gladwell points out that certain groups can often be uniquely helpful in achieving the tipping point. For genomics, commercial dairy producers were that group. When they started to adopt the use of genomic young sires that marked the point at which genomics fulfilled the three concepts and crossed the tipping point.

After the use of genomic young sires crossed the tipping point, the rate of adoption accelerated to the point where the limiting challenge was not consumer demand, but rather the ability of A.I. companies to supply the semen. Because young sires produce far less semen than mature proven sires, it is hard for A.I. companies to meet demand. This has actually led to an increase in the number of young sires being sampled compared to the number that was forecast when genomics was first introduced. A.I. companies have had to sample more sires than predicted in order to meet the growing demand. It has also led to a much shorter active use life span for sires than in the past.

The Polled Story

In looking at the three tipping point factors, when applied to the dairy industry, you can see why some trends may not have been adopted as quickly. An example of this is the use of polled sires. Polled sires have been around for years but have failed to gain significant traction until recently. (Read more: Polled Dairy Genetics: The Cold Hard Facts, From the Sidelines to the Headlines, Polled is Going Mainline! and Why Is Everyone So Horny For Polled?) That is because while polled certainly has the concept of the Law of the Few, it has not had the Power of Context. While there have been significant gains in quality of the polled sires available, adoption will not pass that tipping point until it meets the third concept that Gladwell highlights, which is the Power of Context. Until there is significant consumer demand that dairy cattle not be dehorned, the use of polled sires will not pass the tipping point. While there will certainly be polled sires in the top 10 genomic sires within 2-3 years, and proven sires in 5-6 years, polled semen will not account for more than 16% market share until it develops the Power of Context (consumer demand for animal treatment) needed to cross the tipping point. It’s for that reason that I think that widespread polled semen use will not really take off until 10-12 years from now. Until then, it will be the domain of the innovators and the early adopters and stay below 16% market share. In fact, I would argue that it has just recently crossed over in the past couple of years from the innovators to now include the early adopters.

The Bullvine Bottom Line

Throughout history, there have been many excellent examples of products or technologies that have failed for a variety of reasons. Genomics met resistance similar what was faced by artificial insemination in the early days. However, currently genomic usage has crossed the tipping point. It is now inevitable that soon 84% of the dairy breeding industry will be using genomic sires.

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The Genomic Roller Coaster – Hold on it’s going to be a bumpy ride

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Friday, July 11th, 2014

Since the very first genomic young sire lists were published in April of 2011, it certainly has been a very bumpy ride for the dairy breeding industry. Top sire lists are changing almost monthly. Contract sires seem to go cold even before breeders have a chance to breed their animals. This has many breeders feeling dizzy and asking “Does this genomic index thing really work?”

We here at the Bullvine decided to take a closer look. We took the Top 20 gTPI sires from April of 2011 and compared them to the Top 20 proven sires from April of 2014 to see who performed better over the past three years. The reason we are using the top 20 sires is that based on semen sales, most breeders, when using high index sires, prefer to stick to the very top of the list. Therefore, doing a comparison on the top 200 or even 100 sires would not be an accurate representation based on actual usage. The following is what we found.

TABLE 1 – Top Genomic Sires April 2011 to April 2014

The top 20 Genomic Sires from April 2011 dropped about 10% upon receiving their official daughter proofs in April 2014. Key areas that saw significant decline were DPR (57%), PTAF (31%), PTAM (27%), PL (24%) and PTAP (26%). This tells us that the genomic markers used in April 2011 for these traits were not as accurate as say SCS, SCE, DCE, UDC and PTAT, which saw less significant declines from April 2011 to April 2014.

TABLE 2 – Top Proven Sires April 2011 to April 2014

On average, the top proven sires from April 2011 held up pretty well on the April 2014 results seeing only 3% decline. Though interestingly we do see the same trend as in the genomic sires where the PL, DPR, PTAF lead the way with the greatest declines. Also of interest are the changes in ranking. In April 2014 the top three sires from this list were Badger-Bluff Fanny Freddie, Regancrest Altaiota, and Lotta-Hill Shottle 41 none of which were in the top 5 in April 2011’s top proven sire list.

TABLE 3 – Comparison of Top Genomic and Proven Sires from April 2011 (April 2014 values)

If you had used the top 20 genomic sires from April 2011 rather than using the top 20 proven sires from April 2011, you would have come out 3% ahead. More importantly let’s look at each sire did in the actual ranking.

TABLE 4 – Ranking of Top 20 Genomic and Top 20 Proven Sires from April 2011 in April 2014 values

Interestingly none of the top 7 sires in April 2014 were from the top 3 on the April 2011 Top Genomic or Top Proven Sires list. In fact, the top proven sire in April 2014 was Robust, who was 14^th on the Top 20 Genomic Sires in April 2011. The top Genomic Sire from April 2011, Shamrock, is actually in 17^th spot on this list. That is more than 200 points behind Robust, who in April 2011 was 169 TPI points behind Shamrock. That is a 370 point swing between these two sires. When you think about this from the effects it has on your breeding program, owners of daughters from Ladys-Manor Pl Shamrock, Mr Chassity Gold Chip, and Wabash-Way Explode who once thought they would have the next list toppers for sure. Now they find themselves (on average) behind daughters of Roylane Socra Robust, De-Su 521 Bookem, Sully Altameteor, RMW Armitage, Co-Op Upd Planet Yano, De-Su Observer, UFM-Dubs Sherac, and Vendairy Wonder. When they were making their mating decisions back in April 2011, breeders thought the first group would surely outperform the second.

Analysis reveals an even more alarming situation than this. What it shows us is that sires that were not even on the Radar back in April 2011, ended up outperforming the top 20 Genomic sires from April 2011. In fact, 4 of the 10 sires from April 2011 were not in the top 20 Genomic or Proven Sires in April 2011, and 25 of the top 30 proven sires from April 2014 were not on the top 20 Genomic or Proven Sires lists in April 2011.

TABLE 5 – Top 10 Proven Sires April 2014

TABLE 6 – Top 40 April 2014 Proven sires that were missed

While a few of these sires may not have been missed because they were about to receive their proven daughter proof shortly, the majority fall into a situation where they were just not as high ranking as the top Genomic sires from April 2011 but they held their values much better.

When looking at the 25 sires that were in the top 40 proven sires in April 2014 that did not find themselves in the top 20 Genomic or Proven Sires in April 2011, a strong trend starts to show itself. All of these sires were within 15% of the top genomic sire from April 2011, Roylane Socra Robust. This tells us is that you can’t only use the top 10 or 20 genomic sires, if you expect to have the best results in your breeding program. In fact, you need to consider sires that are within 15% of the top genomic sire. When you compare the top 20 Genomic Sires from April 2011 to these 25 sires you find the following:

TABLE 7 – Comparison of Top 20 Genomic Sires from April 2011 to Missed Sires

Applying this analysis to today’s breeding strategy shows us that we cannot just use the top 20 Genomic sires that are available, in order to have the best long term results. Instead, we need to use sires that fall within 15% of the top current genomic sire, Cogent Supershot, who has a current gTPI of +2625. That means all sires that are 2231 TPI currently could easily be in the top 10 proven sires in April 2017. That will be a list of sires that has over 600 bulls on it. Even if you remove the two proven sires (Robust and Dorcy) as well as those sires that are older and about to receive daughter proofs shortly, you are still left with over 500 genomic sires to choose from. That means that currently there are over 500 genomic sires that could be in the top 10 proven sires in April 2017.

The Bullvine Bottom Line

While many breeders battle to get their hands on the early release semen of the top 10 genomic sires, and A.I. units are putting extremely high prices on this semen, analysis of performance data from the top sires in April 2011 shows us that these sires are not necessarily going to outperform the other available sires. Breeders who used sires like Ladys-Manor Pl Shamrock, Mr Chassity Gold Chip and Wabash-Way Explode now find themselves behind sires such as Den-K Altagreatest, Pine-Tree Picardus, and Altaceasar. These were all sires that in April of 2011 were not even on most breeders’ radars. While genomic indices are an excellent tool for helping develop a short list of sires to use. Performance data shows us that sires that are within 15% of the genomic sires can still produce a top 10 sire. For your breeding program, this means that you need to take a look at all sires who are within 15% of the top sires and consider them for use. This will help you develop your own shortlist, and then using corrective mating tools like GPS (Read more: gPs– Genetic Profile Systems – Dairy Cattle Breeding Made Simple), will help you determine exactly which of these sires will perform best on a mating by mating basis. You can’t just use the top 20 Genomic Sires and expect to get ahead of everyone else. Past performance shows this just doesn’t work.

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The Genetic “SUPER COW” – Myth vs Reality

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Friday, February 28th, 2014

During the recent “Advancing Dairy Cattle Genetics: Genomics and Beyond”, Paul VanRaden with USDA’s Animal Improvement Programs Laboratory pointed out that “If we took the best haplotypes (genes) from all the cows genomic tested to date, we would have a cow at $7515 Net Merit”. That’s pretty spectacular considering the current top Sire on the $NM list is DE VOLMER DG SUPERSHOT at 1000 $NM.

Now to put that into perspective the current rate of gain is $80 per year. So in order to breed that $7515 animal it would take us 81 years to actually breed that animal. Therefore it raises the question whether such an animal is actually achievable and is there technology out there that could accelerate the process of getting that Super Cow.

The interesting fact here is the greatly accelerated rate of genetic gain since the introduction of genomics. This results for the most part from the greatly shortened generation interval. Females are now being used as bull mothers 18 months sooner than in the past (as yearlings vs mid 1^st lactation), and sires of sons are now being used 24 and sometime 36 months sooner than they were in the past. (Genomic indexes vs waiting for proven sires). The almost 40% increase in reliability of estimated transmitting ability has breeders and AI companies contracting and working with these elite animals at a significantly younger age.

An interesting comparison is found by taking the top 8 proven sires from April 2010 and comparing them to the top 8 genomic sires from April 2010 with their current daughter proofs. You see that the genomic sires are 99 $NM (704 vs 605) higher than the proven sires. These top genomic sires, that have been heavily used as sires of sons, are 16% higher than if we had used their proven counterparts from the same time.

This reminded me of a discussion stemming from an article we wrote over a year ago, “Are You Ready For Genetically Modified Cattle?”. We discussed about how many larger and larger corporations are entering the dairy genetics marketplace and the fact that technology is advancing at such a rate that some time in the not so distant future it will be possible to take the best haplotypes in the Holstein population and produce progeny that would have an estimated breeding value of $7515 as VanRaden proposes. But at this point it’s just like the “Perfect” Holstein Cow picture, it does not exist at this time. (Read more: The Perfect Holstein Cow)

Not only does the potential exists to produce high $NM progeny, but what about creating or developing traits that are not yet available in nature. Things like Epigenomics, Nutrigenomics and Transgenics will make this possible. (Read more: Forget Genomics – Epigenomics & Nutrigenomics are the Future)

The Bullvine Bottom Line

There is no question that great breeding has always been part art and part science. However as technology grows and new discoveries seem to happen almost monthly as opposed to yearly, the balance between art and science is starting to shift drastically. I often hear many breeders comment about the failures of genetic predictions in the past. That was when reliabilities were in the 30% and 40% range. As the systems are refined and biases removed, these rates are now approaching the 70% and 80% range. Given more time, there will come a point where we have over 90% reliable information for animals on the day that they are genomically tested. Add to this the ability to genetically preselect or even manipulate the embryo and there is no question that, before long, numbers like 7515 $NM will not seem to be so astronomical. They will be the expected.

Not sure what all this hype about genomics is all about?

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Forget Genomics – Epigenomics & Nutrigenomics are the Future

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Tuesday, January 14th, 2014

Two months ago I had one of those conversations. A friend said to me “you know Murray I am moving on from just simple genomics”. That perked my ears up and I listened more intently. “Yep I am now thinking about epigenomics”, he said. Well that was enough to set me off investigating what is out there that is beyond what our industry is currently considering and using when it comes to genomic. Relax a little, this may seem like rocket science today, but it is in tune with what our industry has always done in the past. We look to find more accurate ways of indentifying the elite animals. Then we figure out how knowing that information gives us ways to make dairy breeders and dairy farming more profitable.

Already Many Steps Too Far?

So now ‘epigenomics’ was pinned to my clipboard. But I didn’t get any further before I had a Master Breeder husband and wife corner me for half an hour and ‘inform’ me that “The Bullvine was leading the industry astray”. They stated to me that “they were from Missouri” and perhaps we should “still only be using the actually officially authenticated information – DHIR records and breed classification results – when it comes to selecting bulls and marketing females. They asked how can we know that the hair pulled and submitted for DNA testing actually came from said animal.” I have known this couple for almost forty years so I took the discussion on to a review great cows of the past and how they would not compare to the great show and brood cows of today. As we started to conclude our conversation the lady, who had been somewhat quiet during our sharing, commented “You (Murray) have a good point about how the genetic evaluation results over our lifetimes have resulted in the fact that we have far superior cows for both conformation and production, but our herd’s current biggest genetic problem is cows not getting back in calf. We just do not now get to have very many ten year old and older cows in our herd, liked we used to.” That gave me the opportunity to talk to them about genomics and having fairly reliable information, early in an animal’s life, on its genetic merit for reproductive traits.

The husband’s concluding comment warmed my heart. “Our grandson plans to come home to our family farm and he tells us that at university his professors are saying the information we have today on genomics is just the start. So don’t give up on us old guys. You folks at The Bullvine just keep giving us the facts and helping the industry do an even better job of breeding dairy cattle. We don’t own a computer but our family keep us quite up-to-date on what The Bullvine is writing about.” Obviously this couple are not as set in their ways as they led me to understand at the start of the conversation.

So if we have just scratched the surface, let’s delve a little deeper.

Epigenomics – What’s That?

By definition, epigenomics is the study of modification of the expression of the genetic material in a cell. Sounds rather out of the norm. Something can alter what the DNA says is the genetic merit of an animal? Let’s think that through a bit more.

As cattle breeders we can all think of times when three full sisters all had very similar performance. And I expect many of us can also remember situations where two of the sisters were very similar but the third sister just did not measure up to the other two. The question that breeders always ask is did the third one not get the good genes, or did she get the good genes but something inhibited her from being able to express them. I have even heard very knowledgeable breeders say that the third one will breed just a good as the other two. How they arrived at that conclusion I am not really certain. But I have seen it happen as they predicted.

Research in mice has shown that the diet of a sire can influence the gene expression of their progeny. So that fits under the definition of epigenomics. Dr. Jacques Chesnais of Semex feels that “there is a definite possibility that epigenomics plays as important role in adaption to the environment. In particular, in our industry, the way we feed and treat a cow in the early stage of pregnancy could affect the calf for a lifetime and therefore affect the future productivity of the herd.” Hearing that made me wonder if the recipient dams of ET calves may have an influence on how those calves pass on their genetics.

Leaders in the study of epigenomics in livestock Dr Marc-Andre Sirard and Dr Claude Robert, Laval University, are currently investigating how epigenomics applies to the bovine and in particular to female reproduction and embryo development. It will be interesting to follow their reports.

There is obviously much to be studied and learned about epigenomics in the bovine. Definitely traits like reproduction, health and immunity are ones that dairy breeders wish to know more about as they relates to inheritance.

So then – What is Nutrigenomics?

The second new kid-on-the-block, so to speak, is nutrigenomics. The study of the effects of foods and food constituents on gene expression. By definition “Nutrigenomics can be described as the influence of genetic variation on nutrition, by correlating gene expression or SNPs with a nutrient’s absorption, metabolism, elimination or biological effects.” Think about it. If we know the genetic make-up of our dairy cows we would be able to design their diets accordingly. Are there cows out there that can make better use of lower quality forages? Wouldn’t that be a boon for the economics of dairy farming. Especially given that feed costs are 52-58% of total dairy enterprise costs and low quality forages are less costly.

I asked two nutritional consultants about this. I got two very different responses. The first one said – “don’t bring that on too quickly I still have another ten to fifteen years in my working career”. The other consultant said “Well it would change my job but if it means dairy farming can be profitable and sustainable and if we can feed the hungry world – well bring it on”.

Expect Genetics to Play an Even Bigger Role in the Future

Investigation by Canadian Dairy Network (CDN) has predicted that, in stable milk pricing times and on milk production focused farms, half of the increased on-farm profits comes from increasing the genetic merit of sires and cows used to produce the next generation of females. With a better understanding and more definitive knowledge of epigenomics and nutrigenomics it could possibly be that 60+% of on-farm profits could be as a result of the genetics used.

From the DNA analysis using hair follicles, breeders now know with 50-70% accuracy the genetic merit of their animals for a host of important traits. Think what might be possible if by including epigenomics and nutrigenomics information. The accuracy levels could rise to 70-80%.

The Bullvine Bottom Line

The research phase of studying how epigenomics and nutrigenomics relate to the dairy cow is well underway. We can expect refinements to our genetic evaluation procedures based on what the research tells us. And in time breeders will have information so they can better breed, feed and manage their herds. Stay tuned to the Bullvine for more great insight into these two future changing technologies.

Not sure what all this hype about genomics is all about?

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The Genomic Bubble Has Burst?

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Friday, January 10th, 2014

Well that is what some would have you believe. They cite the decreased prices at the top sales, and that genomic young sires are no longer much higher on the list then their proven counterparts. (Read more: An Insider’s Guide to What Sells at the Big Dairy Cattle Auctions 2013) The truth is that, instead of just citing observations, true breeders are looking at the facts. For them, the facts show that Genomics is here to stay.

Almost daily I read warnings in other “leading” dairy publications against the use of genomic sires. This panders to the old school mentality that fosters breeder concern about using Genomics. Instead of basing their comments on facts, they use hearsay, conjecture and outright fear mongering to defend their comments.

Here at the Bullvine we have always worked to let the facts guide what we write. That is probably the biggest reason that we have been proponents of Genomics from the start. There are several key points that we think many breeders and our fellow media are missing. Let’s summarize them here to help put an end to nonsensical comments.

Genomics is a Tool
It drives me nuts on a daily basis the number of breeders who refer to Genomics as a selection tool. Genomics increases the reliability of individual traits and indexes. That’s it. The term “Genomics” is miss-used by many when they should be referring to “High Index” sires, meaning list toppers on the gTPI, gLPI and other lists. This may seem like a minor thing. I am even guilty of it myself from time to time. However, it’s really a huge error when you look at it from a breeder viewpoint. Over the past week, I looked at more than 100 comments about Genomics from naysayers. Every single one of them would have been more accurate if they had used the term “High Index” rather than Genomics. Most of the reservations against Genomics have more to do with the use high index sires. The debate between selecting for “High Index” or “Proven” pedigrees will go on for years to come. The thing that many miss is that Genomics is a tool that can help both strategies. Since Genomics helps increase the accuracy of the indexes in both strategies, it will help both strategies excel into the future.
The Numbers Don’t Lie
It’s always easy to state a case-by-case example and find a few cases that help prove any point. It takes a look at the full spectrum to truly get an accurate assessment on how any program or tool is working. The facts are pretty clear that Genomics increases young sire’s reliability by 30% and 1^st crop proven sires by 5%. In effect that says that a young sire with a 50K genomic test and a proven sire will now have reliability comparable to an early 1^st crop proven sire pre-genomics. This would indicate that if you were willing to trust a 1^st crop proof prior to the introduction of Genomics, you should now be willing to trust a genomic young sire with a proven sire as their reliabilities are very comparable. Furthermore, the genetics marketing is also supporting this. Genomic young sires are set to outsell proven sires as most breeders are confident in the numbers and are making sound breeding decisions based on them. As we mentioned in our article Genomics – Lies, Miss-Truths and False Publications, genomically evaluated bulls with 65% reliable gLPIs, breeders can expect 95% of the time that their official proof will be within 670 LPI points (within about 18-20%) (Please note that with change in Canadian LPI formula this number is more like 400 LPI points). This means that we can be 95% sure that the current top gLPI sire, SILVERRIDGE V EXTREME (gLPI of +3544), will be higher than +3000 LPI, once he has his official progeny proven index that is over 90% reliable and that would make him the top 3 active proven sire in Canada. In the US sires like ZAHBULLS ALTA1STCLASS (gTPI of +2598) will end up over +2200 gTPI placing him in the top 10. (Editor’s note: Prior to the regression to bring high genomic young sires closer to proven sires, sires like Extreme and Alta1stclass would have actually been higher than the current top proven sire). Yes genomic young sires do on average drop below their original predicted values, but, they are on average still higher than the proven sires of that time.
Falling Numbers are not an Indicator of System Failure
Whether it’s young sires indexes dropping or semen prices going down, neither of these two events accurately predict the status of Genomics. You see Genomics is new to the industry and, with anything that is new, there is a period of figuring out how the “new world” will work. During that period aggressive breeders and semen companies have sought to maximize revenues for themselves and the breeders they represent. This has meant testing the market to see just what is the maximum revenue price for each animal or dose of semen. Simple economics teaches us that we need to test that point that maximizes revenue, that is either sell at a high prices and reduced quantity or sell at a medium price at increased quantity. Both are sound strategies. At times due to exclusivity and extreme unique genetics, young sire semen has sold for $10,000 a dose and, with the removal of the exclusivity and other sires coming out after the fact, that semen is now available at a greatly reduced price. (Read more: $10,000 a dose Polled Semen). The breeder who purchased this semen, Ri-Val-Re Holsteins from Michigan, actually made out very well with his investment as he had a clear plan with the use of IVF to maximize his return. (Read more: Breeding R-Val-Re: Where looking good in the stall is just as important as looking good on paper) It has also led to other attempts and premium pricing or pricing models. This is not a failure of the system. This is progressive individuals trying to discover how the new system is going to work. Does it always return maximum profits?….No. But does it help those individuals understand the new market and how they can operate to maximize efficiency in the future? ….Yes. Just because you are not able to justify these prices for your breeding program goals, does not mean that it will not work for others. The big thing is for you to understand your genetic plan and goals and make sure you are constantly evaluating and improving them. (Read more: What’s the plan?). It is interesting to note that since the introduction of Genomics the rate of genetic advancement has more than doubled. Coincidence? I don’t think so. Since more breeders can make more sound decisions, the industry as a whole is benefiting.

The Bullvine Bottom Line

Genomics will not make every breeder an instant Master Breeder. Nor does it profess to. What it will do is help each breeder make sound breeding decisions based on the most accurate information available. There is still the need to have a breeding strategy the works for your specific management and financial goals. You cannot simply use the entire list topping sires and expect to end up with the greatest herd in the world. You need to take the time to choose the sires that work best for each specific mating and understand the issues of each cow or sire daughter group (i.e. inbreeding, strengths and weaknesses). That is exactly what great breeders of the past did. . They took the time to assess their animals and planned how to end up with the best progeny possible. That, and not Genomics, is what will lead to the greatest genetic advancement. Genomics is simply a tool that enables breeders to make improvement happen faster!

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Genomics – Opportunity is Knocking

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Thursday, November 28th, 2013

With less than a week until the December 03 index release day I am thinking what more do I want or need to learn about genomics in the world of dairy cattle breeding. I have friends that entirely use genomic information to breed and market while others are riding along and using higher indexing young sires but otherwise remain in the prove it to me “I am from Missouri camp”. Here at The Bullvine we have provided thoughts in the past on genomics (Read more: Genomics at Work – August 2013). Today we decided to further document some areas that we feel are important to watch for and questions we are searching for answers to so that you don’t miss this opportunity.

Verification

“Does it really work?” is the question most often asked. The verdict is still out for many breeders. (Read more: Is the Genomic System Really Working?, The Truth About Genomic Indexes – “show me” that they work! And What Happens If Genomics Doesn’t Work?)

Except for a few preliminary reports by a couple genetic evaluation centers little has been published verifying that using genomics actually works. Breeders need the truth and nothing but the truth based on scientific analysis. We can likely expect the report to say that it assists with increasing the rate of genetic advancement but that: i) on an individual animal basis it is not as accurate as a 99% reliable daughter proven A.I. bull; ii) for young bulls, heifers and cows it increases the accuracy of indexes ; iii) for traits for which we have limited farm data it is still too early to make an accurate assessment; and iv) it is in fact the most important step forward in breeding since we got broadly based proven sires. The message to our scientist and industry leaders is that breeders need to know the facts. The industry depends on breeders being successful. (Read more: CANADIAN BULL PROOFS – You’ve Got to Prove It to Use It!)

With the indexes of young animals today exceeding their older counterparts by a significant amount, breeders need to know the facts so they can decide on the extent to which they should use genomic information in their breeding plan (Read more: What’s the plan?).

Intensity of Use

It is well known that concern exists among all players, from breeders to scientists, on the increased rate of inbreeding. (Read more: Twenty Things Every Dairy Breeder Should Know About Inbreeding, 6 Steps to Understanding & Managing Inbreeding in Your Herd and INBREEDING: Does Genomics Affect the Balancing Act?)

A study of the sires of top ranking young animals shows the following:

Sires of top fifty August 2013 gTPI young bulls – Mogul (21); Uno (8); Supersire (7); McCutchen (3); Facebook (2); Lithium (2),..plus seven others
Sires of top fifty August 2013 NM$ young bulls – Mogul (13); Supersire (10); Uno (8); Robust (3); Shamrock (3); Epic (3); Lithium (2); Facebook (2); ..plus six others.
Sires of top fifty August 2013 gLPI young bulls – Mogul (17); Supersire (9), McCutchen (5); Bookem (5); Mixer (3); Epic (2); Lexor (2); Iota (2); ..plus five others.
Sires of top fifty gLPI heifers (Sept-Nov releases) – Supersire (11); McCutchen (6); Enforcer (5); Mogul (5); Liquid Gold (4); Munition (4); Morgan (3); Cashmoney (2); ..plus ten others

Even though most of these bulls are not themselves closely related it is concerning that only a few bulls come to the top on all these lists. 66% of the above lists are over 6.0% inbred and only one is below 5.0% inbred. Outcross sires (Read more: 12 Sires to Use in Order to Reduce Inbreeding and GOING OFF THE MAP: 14 Outcross Holstein Sires That Don’t Include GPS) has been recommended as a solution yet Oman, Planet, Shottle and Bolton are prominent is the ancestry of the bulls above. It is time that we stop worrying about inbreeding and start finding practical solutions. Do we need to designate breeding lines and then doing line crossing like is done in crops, poultry and swine? Why are A.I. organizations not using alternate sires of sons? Is it that those alternates do not come up as high on total merit index ranking lists? If that is the case should total merit index be the criteria used when selecting young bulls to be sampled or marketed. Should the inbreeding coefficient of every bull be a required number to be published? There are solutions but it takes effort and leadership to stop the runaway train.

Finding the Best

Breeders of very elite indexing animals want to know which bulls will ring the bell for them when they flush their top virgin heifers. Some of those breeders feel that there are certain sires more capable than others at leaving top of the list progeny? Put another way can two bulls be ranked the same for total merit but one leaves progeny that are very consistent for their genomic values while the other bull produces progeny that range more in value. Breeders are willing to gamble and use the bull that appears to be able to produce list toppers. Breeders are asking the question – have our scientists studied this and is their an answer to the question of why some families consistently throw the high outliers?

Which are the Future Parents

As well with more and more emphasis being given to management, health and fertility traits in dairy cattle selection the question becomes which are the young bulls or elite heifers for the future. Could it be that they should be 90%RK for Production and 99%RK for Durability and 99%Rk for Health & Fertility? Attention needs to be given to matter with a view to the needs for the next ten plus years. (Read more: Total Merit Indexes: Are they helping or hurting?, Does Your Breeding Program Save You Labor? and Are Your Genetics Wasting Feed and Labor?)

Health / Disease Resistance

No doubt we have only scratched the surface on what the DNA profile of an animal can tell use about an animal’s ability to remain healthy and disease free. Even though breeders would like to have the answers today, the absence of farm data to match to the DNA will likely mean that this area of breeding will be relatively inaccurate for some time into the future. That does not mean that we should not continue to study this area, it is just that we can not expect answers quickly.

Female Fertility

Here again we are dealing with an area where there is limited farm data, or the farm data is not in connected data bases that can be used to correlate female fertility with DNA profiles. Is there farm data out there that tells us when heifers reach puberty? No. Are there genetic differences in when heifers can be first bred? Likely but we do not know. To go even further what about female conception rates? Biologically up to 90% of the time a sperm fertilizes an egg, yet only 65% of heifers and 40% of cows in Holsteins actually become pregnant. The inability of a fertilized egg to implant is significant but knowing the genetics of that is still a long ways off. Maybe there is research in other species that might be useful for linking female fertility with DNA profiles.

Breeders who flush females know that to be financially successful a cow or heifer must give many viable embryos. And that there are differences amongst cow families in how many embryos produced. (Read more: What Comes First The Chicken Or The Egg? And Investing in Dairy Cattle Genetics – Think Outside the Box) One question yet to be answered is by using IVF on poor flushing families are we, in fact, hindering reproduction from a genetic perspective. Yes more questions than answers but remember that the most common reason for cows being culled is infertility. So we do not need bull dams being genetically inferior for reproduction.

Mobility

With lameness in dairy cattle being targeted as a big time problem in animal care circles, is it time that a mobility index be produced? Can we take our current DNA profiles and calculate such an index? It matters little that we know a host of traits about feet and legs when breeders are most concerned about a cow or heifer’s ability to move freely and comfortably in the environment is which she lives. (Read more: Cow Mobility: One Step Forward or Two Steps Back?)

Getting with the Program

Perhaps some of our ‘thought list’ will be possible in the next year or two. One thing we know is that for traits to be able to be evaluated we need more animals both recorded for performance and DNA profiled. Of immediate concern is that without broad based field data for calf and heifer performance we are limited in what we can accurately know about this important cost center. Any breeders not currently DNA profiling all their heifer calves are denying themselves future opportunities to advance their herds. Cost is frequently given as the reason for not DNA profiling, yet the cost is only about equal to officially milk recording a cow for a year. The information obtained can be used early in life including which heifers to keep, how to manage them and which sires to breed them to.

The Bullvine Bottom Line

Like almost everything else in genetic advancement, genomics does not have all the answers. It does not have 100% accuracy but it sure does shorten the generation interval in dairy cattle breeding. Opportunity knocks for the breeders that do profile their animals. And every month with new facts coming out on genomics, the opportunity for greater return on investment increases for participating breeders.

Not sure what all this hype about genomics is all about?

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Genomics – Lies, Miss-Truths and False Publications!

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Tuesday, October 15th, 2013

Recently I read the most disturbing Letter to the Editor that I have read in a long time. It was produced by lr Gerard Scheepens. The concerning part was that it was written by someone working for an A.I. company (K.I. Samen) and was published by a dairy publication (Holstein World) trying to pander to those who spend the most money with them instead of thinking about how accurate the letter was. In typical Bullvine fashion we decided to dispel the lies, miss-truths and false publications, so that you, the dedicated breeder, can see through the BS and understand what is actually happening.

Accurate Prediction or Wishing on a dream

In the article they make the following comment “Looking at the results of the genomic bulls with daughters in production you can see a devastating truth; nearly all of the bulls drop and drop a lot.” The funny part, but not surprising is that they don’t back up this “devastating truth” with numbers. Having painted a bleak picture, they just provide generalities and expect you to accept them as truth. As the Bullvine has published several times in the past (Read more: How Much Can You Trust Genomic Young Sires? and The Truth About Genomic Indexes – “show me” that they work!), genomically evaluated bulls with 65% reliable gLPIs, breeders can expect 95% of the time that their official proof will be within 670 LPI points (within about 18-20%) (Please note that with change in Canadian LPI formula this number is more like 400 LPI points). This means that we can be 95% sure that the current top gLPI sire, SILVERRIDGE V EXTREME, will be higher than +3173 LPI, once he has his official progeny proven index that is over 90% reliable and that would make him the highest active proven sire in Canada. Yes genomic young sires do on average drop below their original predicted values, but, they are on average still higher than the proven sires of that time. This clearly means that they are a better option than the proven bulls available at that time. It’s called genetic advancement.

Columbus disease

Didn’t Christopher Columbus colonize the new world? Wouldn’t America have been different if Columbus had not dared to try new things? If bold thinkers like Columbus had not set out to explore and try new things the world would still be reported to the editor as flat? You see in order to advance we have to try new things. The benefits of a technology such as genomics is that there are educated risks. They are not sure fire guaranteed, they are educated risks. Even using a 99% reliable sire will not give you the same exact result every time. Fear mongers who are afraid of change like to throw out things like bulls’ proofs dropping. Well, guess what people, so do proven bulls’ proofs. Those proofs just don’t get noticed as much and no one is using it to put fear into breeders for no reason other than personal profit. Mother always said that upon hearing outrageous criticism, “Always consider where it’s coming from!”

Equations

I don’t profess to be a mathematician or a geneticist, though there is one fact I know for sure. The more accurate the information you have to work from the more accurate the result. Genomics is not a perfect science, but it is more accurate than just parent averages alone. You think bull’s proofs drop now. Look what used to happen before the introduction of genomics. (Read more: Has Genomics Knocked Out the Hot House Herds? And The Hot House Effect on Sire Sampling). If someone runs a person over with a car, who is to blame? Is it the car manufacturer’s fault for making a machine that can go faster than we can walk and larger than a bike? Or is it the driver’s fault for using the machine in other than the intended way. You see genomics in itself is not solely to blame when the resulting calf does not live up to expectations. (Read more: Who’s to Blame? Why is there a lack of accountability in the Dairy Genetics Marketplace)

Real change is needed

In the published letter to the editor the author highlights the issue of inbreeding, something that has been an issue for a very long time. The thing is you need to put inbreeding into perspective. First data from the US reported that the current cost of inbreeding over an average cow’s lifetime was US$24. (Read more: INBREEDING: Does Genomics Affect the Balancing Act?) That means that a 1% reduction in progeny inbreeding (valued at around $5 per cow). But what if the genetics of that animal also means that their production will drop $10? Inbreeding needs to be kept in perspective. Inbreeding is only an issue when you don’t manage and account for it. (Read more: 6 Steps to Understanding & Managing Inbreeding in Your Herd and Twenty Things Every Dairy Breeder Should Know About Inbreeding) There are times when certain levels of inbreeding can work well. You just need to understand all the factors.

Sire and son

In the article it makes the point that “O Man has 253 sons with daughters tested in the US and only 5 of them score higher than him on Net Merit.” It is funny that for any point you can find one single stat that you might think (or hope) proves your point. In actual fact you need to look at performance over a whole population not case by case. It’s like saying 2% of the population died from the use of penicillin, what about the 98% of the population who are still living as a result of its use?

“150% more progress in what? for whom?”

The number of times the author of this article shows an inability to understand bull proofs is a major concern. In the article he makes the following comments “The top 10 NM bulls from August 2009 with daughters had an average of 702 NM. The top 10 NM genomic bulls without daughters had an average of 814. The genomic bulls without daughters had a 14% lead. In April 2013 the average of the bulls with daughter group dropped to 607 around 13.5%. However the genomic group fell to 515 NM which leads to a drop of 37%. Furthermore, the proven group, which was 106 NM behind now leads with 92 points NM. Where is the speed, and where is the progress?” Again there are two main issues here. First can I introduce you to something that is called a base change? Secondly, the author is again using a selective group versus the whole population. There are published results from across the whole population that shows that the actual rate of genetics advancement has increased rapidly with the use of genomics.

Cows are not pigs

Can pigs fly? The author’s point about how cows are not pigs is almost as irrelevant as the price of eggs in Winnipeg. Yes in pigs the female has a larger role in genetic advancement than the female in cattle (Though the use of IVF on top females in dairy cows is quickly changing that). The point the author makes is about how cows need to also reproduce in addition to produce. That is why we have traits like daughter fertility, calving ability, daughter calving ability, calving ease, maternal calving ease, daughter pregnancy rate, sire still birth and daughter still birth. This has nothing to do with genomics. It has to do with which traits we use to evaluate animals.

Variation is essential

“The new major impact bull always has an original pedigree”, according to the author of the letter. Really? Was Durham that unique (Elton x Chief Mark)? Shottle (Mtoto x Aerostar)? Goldwyn (James x Storm)? Man-O-Man (Justice x Aaron)? I think more time, research and education should be taken by the author. It is much needed before making comments that have no facts to back them up.

Reliability or accuracy?!?

For about 30 seconds I almost agreed with the author on this one point…then they fell off the rails and I was back to how off the mark this individual is. Yes bias is an issue (Read more: Preferential Treatment – The Bull Proof Killer). But then the author’s points fall off the train when he says “The accuracy of the breeding is way too low to take that kind of chance. Accuracy of the proof will become more important than the reliability of the proof.” That logic would then say that we never use an un-proven sire ever again. Then where would our genetic advancement be?

How to stop a runaway train?

And then the author himself slams the brakes on his own runaway line of reasoning! The author categorically states that as an industry we should “spend the money by improving the animal model, spend on better evaluations, less costly and more effectively.” The simple reply: Isn’t that exactly what genomics is designed to do? And is doing?

The Bullvine Bottom Line

Since launching the Bullvine we learned one thing, it’s not wise to spread falsehoods or inaccurate information. That is why whenever possible we have always put facts behind our points or when there are no facts available, such as in the case of dairy cattle pictures, we have gone to the effort ourselves so show how things are working. We don’t believe in treating our readers as if they have no brains by publishing falsehoods or misinformation. Instead we believe an educated breeder is the most valuable asset the dairy industry must have at this time. That is why each day we source, write and share the most educational content in the dairy industry. And we back it up with facts!

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Stop the Sale! Genomics, Chocolate and the Future of the Dairy Breeding Industry

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Friday, September 6th, 2013

“This cow is being stolen!” cries out Horace Backus, from the auctioneer’s box at the US National Convention sale. ‘A beautiful Jasper daughter with such a magnificent pedigree gets such a low offer – that is pure robbery!” adds Backus. Pounding his fists onto the podium, Backus has a point, since they are getting less than $5,000 for a very productive cow and moments earlier a very young calf sired by a genomic young sire sold for over $20,000. Here you have an animal already proving her profitability versus a calf that has nothing more to show for herself then a simple little test? I ask you ”Does the marketplace have it all wrong?”

Last week I was at our local county show (Read more: For Love of the Ring) and was talking with Doug Brown, owner of Browndale Specialty Sires. I have known Doug for over 30 years and have huge respect for him. One point that Doug made was related to the fact that at BSS they have 3 bulls in the top 100 LPI. This is a huge success for a breeding program that samples just a handful of bulls every year. And yet the conundrum, Doug says, is that they would be lucky if the three sires sold as much semen as the latest hot genomic sire. Again here we have a well proven and profitable commodity being outsold by a relatively unknown entity.

Can you have too much of a good thing?

Is genomics kind of like chocolate? Sure it’s great in small amounts when used correctly and it’s a great antioxidant. However regularly over-indulging in chocolate can result in significant weight gain, sugar complications and kidney problems from the high potassium.

Now anyone who has read the Bullvine with any regularity knows that we are strong proponents of genomics (Read more: Genomics at Work – August 2013, Genomics: Think Big Not Small and Stop Pissing On Genomics). But have we started to take things too far? We hear breeders starting to question if they should register their cattle anymore? (Read more: Why Do We Register?) Should we type classify anymore? (Read more: Is Type Classification Still Important? And Over-Scored and Over-Rated – Are we helping or hurting the dairy classification system?) and Should we only use Genomic Young Sires when making mating decisions? (Read more: How Much Can You Trust Genomic Young Sires? and Genomic Young Sires vs. Daughter Proven Sires: Which one is best for reliable genetic gain?) Have we overused a good thing?

Many times I have had the opportunity to talk with Ari Eckstein of Quality Holsteins (Read more: Quality Holsteins – Well-deserved Congratulations and Quality Cattle Look Good Every Day) and Ari has always reminded me that “Yes Andrew!” genomics is a useful tool and at Quality they do use high genomic test type sires, However, he reminds us “There is still a need to look at all the tools available when making breeding decisions that will result in generation after generation of proven cow families.” At Quality they use genomics kind of like a great pastry chef uses chocolate. It’s not the only thing tool they use and they use it as one ingredient. In other words, genomics should be only one part of many factors used to make complete a great breeding recipe.

The Bullvine Bottom Line

I think many breeders have emptied the kitchen cupboards and thrown out all the other ingredients, or tools, that they used to use when making their breeding and purchasing decisions and now are only using one. Even the likes of dark chocolate or Alba white truffles ($9,300 per kilo) are only great when they are used to enhance the tasting experience. Great breeding decisions come when we stop using just one tool and find the best way to apply specific strengths to specific goals. . When it comes to better breeding and the tools you use, genomics shouldn’t be the only one you use or be used as an all-in-one but it is definitely one to be reckoned with! Genomics for chocolate. Now that’s sweet!!

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8 Ways DNA PROFILING Your Whole Herd Will Improve Your Breeding Program

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Monday, April 15th, 2013

DNA profiling is a complimentary tool for the discerning breeder who is committed to genetic advancement for three reasons:

More accurate genetic selection
Increased profit
More effective management

Added to these three is the potential for breed advancement. Therefore, using DNA analysis is definitely a win-win-win situation.

Higher Quality Cattle – Better Genetic Selection

There are already the industry leading early adopters (5%) who quickly recognized the benefits of DNA profiling. Since the dairy industry ranks every animal in the world (Indexes), a new tool that is able to genetically rank every animal in your herd makes sense. The Bullvine has compiled the top 5 ways that DNA analysis can fine tune your selection decisions beyond the elementary keep, cull or sell.

Identify genetically superior heifers to maximize their value and use for extended reproductive work (ET)
Identify heifers to cull or use as embryo recipients
Identify heifers within a cow family that are more likely to be the ones to carry on the family
Identify AI or natural use sires that will assist in achieving a herd’s genetic plan
Identify heifers to be sold as herd replacements. As the overall genetics of your herd improves, even lower-end cull heifers will likely make good-quality replacement heifers when sold.

Progress is all about maximizing the potential of every animal. DNA profiling is an identification tool which not only provides the above five points – and perhaps more – but also has three other quick-to-appreciate advantages.

Provides a jump on genetic information well in advance of a bull being proven
Provides the best available index values for health and fertility traits
At the simplest level, provides verification of parentage.

If you’re still hesitating, ask yourself how often a new practice gives you eight ways to advance?

On Farm Profit Could Win by a Hair

Everyone can appreciate the financial incentive of raising the genetic level of your herd. Beyond that there are additional financial incentives from costs saved and revenue generated. The logistics of raising dairy animals is all about efficiently using space and resources. Heifer rearing costs are generally accepted between $2.75 and $3.25 per heifer per day. With DNA analysis at $45 to $60 per animal there is immediate payback. Do the calculations for a 100 cow herd? The revenue from and growing costs saved by selling the lowest four calves will more than pay for the testing of all female calves.

On Farm Management: Better timing – Identified culling

It isn’t only proactive elite breeders who focus on performance and added value. Even those who are most skeptical about trends perk up their ears when positive examples start piling up. Breeders with specific goals relating to high performance, long herd life, or top show type can appreciate a tool that helps accurately identify specific attributes. Furthermore, using DNA analysis to level out the peaks and valleys in freshening rates allows breeders to keep steady numbers in the calf hutches and heifer pens. More accurately identifying your own cattle makes it that much easier to market them to the specific needs of buyers. The genomic numbers become part of promoting animals in ads, social media and in the barn. Not only is it a genetic tool but a full-disclosure marketing tool, when the information is available to all buying and selling scenarios.

Industry Advancement: Pedigree accuracy – Breed purity

Much like requiring RFID tags for all animals, a DNA profile has the potential to add much to the breeding stock industry

– Will assist in improving low heritability traits: health and fertility

– Allows for a breed society to require that all males registered be DNA profiled

– Allows for a breeding company to require that all daughters in a sire’s proof be DNA profiled and parentage verified

– As more herds sample their females for genomics, expect the technology to become more accurate and cost-efficient

How & When – Determine Your Strategy

There is not one procedure or process that will work for all herds. Determine the simplest, most accurate steps available to you. The suggested best practice is testing every heifer calf at one day of age or by 30 days of age. Determine how the following choices could work for you.

– DNA profile as close to registration as possible. The sooner the better.

– Chose which panel. Low density unless for bulls for AI or top heifers to be sold

– Even if a breeder may not practice ET, the top 15% should be bred to the highest genomic sires for total index, type, production or health and fertility.

– The middle range should be bred using sexed semen

– The bottom 10% could be sold as embryo transfer recipients or bred to beef semen

Question for Breed Associations to Ponder

Is it in fact a good long term strategy to have DNA analysis remain optional or should it be mandatory some time in the future? __Optional? __Mandatory?

The Bullvine Bottom Line

DNA Profiling will allow the vast majority of breeders to sort, select and sell females according to their personal herd strategies and mate retained heifers for more rapid genetic progress. The benefits to individual breeders and the Holstein breed as a whole will be measureable. What are you waiting for?

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The Genetic Genius of Darwin, Mendel and Hunt – Genetic Transmission and the Holstein Cow

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Wednesday, February 27th, 2013

There is no question that when it comes to understanding what cows will transmit and what cows will not, it is an enigma wrapped in a conundrum. There is much that we don’t know and some would argue it is not meant to be known. The problem is, for those of us with a passion for breeding great dairy cattle, we want to know it all. For that I turn to the three greatest genetic geniuses in the history of the world, Darwin, Mendel and Hunt (No they are not a law firm).

Charles Robert Darwin He established that all species of life have descended over time from common ancestors, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection, in which the struggle for existence has a similar effect to the artificial selection involved in selective breeding.

Charles Darwin

Ask anyone in the world to name a geneticist and the first name that comes to mind has to be Charles Darwin. No better demonstration of Darwin’s theory of evolution exists in the world than in dairy cattle breeding. While there is no question that artificial selection and selective breeding exist on a daily basis, a cow’s ability to reproduce and produce milk leads to a natural level of selection that epitomizes Darwin’s theory. “The laws governing inheritance,” Darwin wrote, “are for the most part unknown.” Moreover, while many modern geneticists have theories about the tendencies of the modern Holstein cow, their genetic transmission pathways in large part remain a mystery to this day.

Gregor Mendel

Then along came Gregor Mendel who introduced the concept of “genes” to explain heritability. Mendel changed the whole way we look at breeding when he introduced the theory that the chromosome is the carrier of genetic traits. He also explained why a trait can disappear in one generation and reappear in the next and why these traits occur in a three-to-one ratio. One of Mendel’s disciples, three quarters of a century later, was Thomas B. Macaulay. Macaulay conducted his own studies, on his Mount Victoria Farms (Read more: Mount Victoria Farms – The art and science of great breeding).

Thomas Hunt Morgan

Then along came Hunt. Well, more specifically, Thomas Hunt Morgan, but my ego wouldn’t let this go as my name is Andrew Morgan Hunt (Read more about my ego: I’m Sorry But I’ve Had Just About Enough Of… ). In research that is now reproduced by grade 9 science students around the world, Morgan introduced the concept of X and Y-chromosomes. Morgan concluded that a female has two X chromosomes and that males have both X and Y-chromosomes. He also posited that the male of the species, because of the presence of the Y chromosome, transmits differently than the female.

To get a better understanding of this, let’s look at this from both sides of the story.

His side of the story (XY)

If you look at Holstein bulls throughout history you find four distinct patterns:

Great daughters but no legacy sons
These are the bulls that sired amazing brood cows but none of their sons were able to continue their genetic legacy. Examples are Hanover-Hill Triple Threat, Carlin-M Ivanhoe Bell, and Braedale Goldwyn. They all were able to sire brood cow daughters beyond compare, but no real sons to advance that genetic legacy. Why did these sires seem to produce better on the female side than that of the male? For that we need to turn to Morgan and his X and Y chromosome theory. Since the Y chromosome is the only one that is inherited solely via the paternal line, this leads some geneticists to believe that it carries little genetic information, and as a result a great sires genetic legacy rest more with his daughters than with his sons. Therefore, with this first group of sires it is thought that much of their genetics were transmitted on the X chromosome rather than the Y.
Great sons but not as many brood cows
Bulls that sired outstanding sons but never produced a top daughter. A couple of great examples of this are Montvic Rag Apple Sovereign, Maizefield Bellwood and O-Bee Manfred Justice. All of these sires have left outstanding sons, but are not found as often in the maternal sire stack of the great sires. There is no question as to their genetic contribution to the breed, but it was more as a sire of sons than their ability to leave an equal number of brood cows.
Sons and daughters both extraordinary
These are the sires that have gone down in history as the all-time greats. Sires like Johanna Rag Apple Pabst, Governor of Carnation, Montvic Chieftain, Wisconsin Admiral Burke Lad, A.B.C. Reflection Sovereign, Round Oak Rag Apple Elevation, Pawnee Farm Alrinda Chief, Walkway Chief Mark, Hanoverhill Starbuck, Madawaska Aerostar and Maughlin Storm. These are the bulls that not only displayed personal greatness but were also able to transmit both outstanding brood cows as well as legacy sons.
Sons and daughters that were inferior
Sons and daughters that are both below average. These bulls left inferior daughters and as a result were never even given the chance to produce sons. Bulls in this category are too numerous to mention and loads of their daughters go to the slaughterhouses every day. No explanation necessary other than a lack of genetic merit and here enters the need for genomics (Read more: The Truth About Genomic Indexes – “Show Me” That They Work).

Her side the story (XX)

The female side of the story uses the same four distinct groups.

Great daughters but no legacy sons
These are cows with outstanding female descendants but undistinguished males. Great examples of these are the cow families of Hanover Hill Papoose, Krull Broker Elegance and Plunshanski Chief Faith. They all were able to leave outstanding female descendants generation after generation, but were never really able to accomplish the same feat on the male side of the story.
Great sons but not as many brood cows
These are the cows with potent transmitting sons, but daughters who didn’t outperform the average. Examples of these are Wylamyna Tidy Kathleen (dam of Sir Bess Tidy and Sir Bess Ormsby Tidy Fobes) Lakefield Fobes Delight (dam of Lakefield Fond Hope, Lakefield Fond Delight Fobes and Carnation Royal Master) and Pawnee Farm Glenvue Beauty (dam of Pawnee Farm Arlinda Chief). All of these cows had outstanding maternal lines but for some reason were just not able to transmit that legacy through their daughters.
Sons and daughters both extraordinary
Among the females in this category are Glenridge Citation Roxy, Mil-R-Mor Roxette, Comestar Laurie Sheik, Braedale Gypsy Grand and Snow-N Denises Dellia.
Sons and daughters that were inferior
Cows who, in terms of influence, failed to produce anything worthwhile. Blame it on lack of genetics, bad breeding, improper management, or just bad luck, these cows just didn’t influence the breed. We have all seen examples.

The Bullvine Bottom Line

There has never been a clear explanation of why some bloodlines seem to transmit better through maternal lines, others through the paternal, and still others do well in both. Even genomics does not answer this. There are high genomic animals that still have these same tendencies. Maybe if we could genomic test the genes on each chromosome we might find the answers? Until then Genetic Transmission in the Holstein Cow will remain a mystery.

To read more about this get a copy of The Holstein History by Edward Morwick and read the chapter on Inheritance Patterns.

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Genomics: Think Big Not Small

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Wednesday, February 6th, 2013

Even though we are still in the early stages of genomic indexes, certain trends are already apparent. One issue that I have noticed is that too many breeders are using genomics to narrow down their sire usage to a few sires at the very top instead of using genomics to discover what sires not to use. Everyone likes to look at the top of the list to see what sires hold their rankings, however, the real power of genomics is actually in pointing out what sires not to use.

While there is no question that genomics has changed the way we look at indexes, there is one major issue that we are all guilty of. We focus only on those sires that are in the top 10 or so to make our sire selection decisions.

So let’s take a look at the current top 10 genomic sires and their TPI Scores:

Supersire 2530
Jabir 2515
Numero Uno 2497
Jacey 2493
Predestine 2491
Chevrolet 2490
Hunger 2488
Jetset 2484
Balisto 2483
Willpower 2476

You will notice that all these sires are within 54 TPI points of each other. That is a difference of less than 2%. The issue with this is that, according to CDN research, 95% of the time sires can vary by up to 20%, when comparing their genomic index to their eventual daughter proven evaluations (Read more: The truth about genomic indexes – “Show Me” They Work!). Applying that to the current list of sires and instead of looking at the top 10 sires you would instead need to look at all sires within 20% of the top sire, Supersire. Since Supersire is +2530 gPA TPI that means your short list would include all sires over 2000 TPI. Instead of 10 sires this means looking at the 1000 current sires.

Furthermore, genomics is not as much about identifying the top few sires you should be using, as it is about identifying the sires you should not be using. When you are looking at two full brothers and trying to decide which one to use or sample, if they are greater than 500 gTPI points apart you are better to use/sample the higher one. Or, if you can only afford to sample one of them then genomics would be a strong indicator of which one to sample. However, when they are much closer, genomics alone cannot make this decision with great accuracy.

For sires that are less than say 300 gTPI points apart you really cannot use their genomic total merit index numbers alone to make that mating decision. You are better to make a short list of sires that are within the 300 TPI points and then look for the sire that is the best corrective mating on your animal. Given how much sires change and how little difference there is in the top sires these days, you are far better making corrective mating your number one requirement and only using genomics to help determine your shortlist.

The Bullvine Bottom Line

Genomics is only as good as the way it is used. If we begin thinking that the top short list is the be all and end all for mating decisions, we start to muddy the waters. You cannot use the top 10 gPA TPI sires alone for your mating programs. Instead you are better to look at the top 1000 sires and find the sire that is the best corrective mating.

Everyone l points to the few select top genomic sires and then bemoans how much they change with each proof round and eventually to their daughter proof. Genomics works best on the macro level and not at the micro level. Due to current 65% reliabilities and a limited differential between top sires, a genomic total merit index cannot be relied upon for the final answer. Genomics is a Macro level tool and not a Micro tool. If you are limiting your mating decisions to the top few sires, you are also limiting your genetic improvement program.

Think big. Find the genomic sires that will deliver the specific improvements that your cows need!

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The Truth About Genomic Indexes – “show me” that they work!

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Thursday, January 31st, 2013

Genomic indexes have created both excitement and concern in the dairy industry. Some accept the science and the results while others are saying ‘Not so fast please! How can the accuracy be checked out?’ In the history of the dairy industry there has been 3 key issues that breeders took a strong stance for or against, artificial insemination, genetic indexes and now Genomics. With new traits being introduced and the world becoming more global there has certainly been loads of debate. While there has been many anecdotal comments about how and if it is working. In an effort to further answer this question (Read more – Is The Genomic System Really Working), the Bullvine went searching for information on how genomics is performing outside of North America and also how it is performing for health and fertility traits.

The German Genomic Experience

Dr Stephan Rensing from VIT (Genetic Evaluation & Research Centre) in Verden reported on genomics in dairy in German at the September 2102 ICAR Meeting (Read more – What the Experts Will Tell You About Who Is Winning The Genetic Improvement Race). His presentation was entitled “Two years of experience with genomics – how well does it work?” In Germany, like elsewhere, about 50% of the AI services are to young sires with both parent averages and genomic results.

In his report he mentions that with genomics results, known early in life, it totally changes the practices that breeders and A.I. organizations follow in selecting animals. Instead of selecting based on parent averages with low reliabilities followed by sampling, evaluating and then selecting the very best, both breeders and AI can now relatively accurately make selection decisions well before an animal is reproductively mature. He strongly recommends that selection be made based on all the information that is available on an animal at any point in time. That can be parent averages and genomic indexes or indexes that include parent averages, genomic evaluations and progeny performance data. Breeders have a new tool to increase accuracy and speed up the decision making.

The bottom line for Dr Rensing is that genomics is working very well in Germany.

In God We Trust, All others must bring data

Dr Rensing included in his study the 199 bulls in Germany that received their first official daughter proof in April 2011. He compared their December 2010 genomic indexes to their April 2012 proofs. The reason April 2012 (the 4^th proof run for the bulls) was chosen was because it allowed for more daughters, more data from each daughter and for daughters to be in their second lactation. Or in short, provided for more accuracy. Dr Rensing studied the correlations between the two sets of indexes and also how the very best sires performed. The very best sires are important as they are the ones returned to active AI service and used as the sires of sons.

12-2010 genomic proofs vs. 04-2012 daughter based proofs

For total merit (RZG) 95% of the bulls have an official daughter proven index within 0.6 standard deviation of their genomic index. That is very good. Much better than had been the case when bulls only had pedigree indexes when entered into A.I.. Note that the top 10% (twenty) of the bulls perform in a similar manner to all the other bulls. Showing that even the extreme sires had the same expected performance reliability as all the others sires. Something anecdotal comments in the past thought to be not true.

12-2010 genomic proofs vs.04-2012 daughter based proofs

When looking at production indexes (above) and conformation traits (below), again 95% of the bulls have a combined April 2012 index within 0.6 standard deviations of their December 2010 genomic index for both production and conformation. More evidence that there is a good relationship between genomic and official progeny proven indexes.

12-2010 genomic proofs vs.04-2012 daughter based proofs

The results from health traits (below) surprise to me. I had thought that there would be greater variation between genomic indexes and official progeny proven indexes for these lowly heritable traits. However it is less, almost half as much variation. After thinking about it, it stands to reason that for traits of lower heritability the genomic indexes are a giant step forward and will greatly assist in breeding for mastitis resistance, fertility and length of productive life. Since the Holstein breeding world is moving to breeding for these traits (Read more – Fact vs. Fantasy: A realistic approach to sire selection and From Fantasy to Reality: Top sires to address herd culling problems) genomic indexes will make that almost impossible job possible.

12-2010 genomic proofs vs. 04-2012 daughter based proofs

Comparing Top Canadian Genomic Bulls

To take this article one step further The Bullvine decided to study the current top five gLPI and compare them to each other.

Name	LPI	Prot	Conf	SCS	DF
MR LOOKOUT P ENFORCER-ET	3837	89	15	2.81	109
GENERVATIONS LIQUID GOLD	3607	87	14	2.84	102
MR CHARTROI ELOQUENT-ET	3507	91	13	2.81	97
MR LOOKOUT P EMBARGO-ET	3467	71	16	2.85	105
DE-SU DISTINCTION 11130-ET	3447	74	14	2.79	104

To start with we must say that these five bulls are all 99% Rank. Enforcer is the best for LPI and daughter fertility. However each other bull has his strength – for protein yield Eloquant is the best, for conformation Embargo is the best and for SCS score Distinction is the best. If you are using any or all of these bulls, first make sure they are strong where your herd needs improvement and then use corrective mating.

More CDN Research Underway

CDN is currently conducting research into confidence limits around the individual trait genomic indexes. Some time ago CDN did publish that for genomically evaluated bulls with 65% reliable gLPIs, breeders can except 95% of the time that their official proof will be within 670 LPI points (within about 18-20%). Meaning that we can be 95% sure that Enforcer will be higher than +3167 LPI once he has his official progeny proven index that is over 90% reliable. That would mean that at least 95% of the time Enforcer would end up with an official proof that would rank him #2 in Canada. That is the worst case.

Apply this to your breeding programs when looking at a genomic young sire you can take 670 LPI points or approximately 455 TPI points off their predicted index and they will achieve that number or higher 95% of the time. For example, take the #1 gPA TPI sire, Seagull-Bay Supersire, who has a current gPA TPI of +2530, you can be 95% certain that his daughter proof that is over 90% reliable will be at least +2075. That would place him in the top 43 sires in the US (220 points behind current proven leader Freddie). Remember that is 95% of the time he would be there at least. Not a bad worst case scenario.

The Bullvine Bottomline

Genomic indexes are a great tool that allows breeders around the world to more accurately select from within the animals that do not have an official sire proof or cow index. It is true they are not as accurate as indexes that include actual cow or progeny performance information for production and conformation traits. However they are significantly better than parent averages and a great addition to the breeder’s tool kit when it comes to selecting for health and fertility. They are here to stay, they will be used by discerning breeders and yes they will be improved on over time.

Not sure what all this hype about genomics is all about?

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How Genomics is Killing the Dairy Cattle Breeding Industry

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Wednesday, October 10th, 2012

There is no question that the introduction of genomics to the dairy cattle industry has greatly accelerated the rate of genetic advancement (Read – The Genomic Advancement Rate – The Battle for Genetic Supremacy) and could kill the seed stock industry as we know it. Read on.

The Introduction

When artificial insemination companies first started using genomics to help identify which bulls had the genetics to excel and which bulls didn’t, it had the following effects

The number of young bulls needing to be sampled decreased.	The cost of procurement went up slightly since their are capped leases and actually less risk. Some bulls where still purchased outright
Bull sampling costs decreased due to needing to sample less bulls and not having to pay as many incentives.	Average semen price has increased greatly. As young sire semen prices have gone from being paid to use it, to costing as much as a daughter proven sire
Due to the increase in average semen price revenues have gone up sharply	With increased revenue (young sire semen price) and decreased expenses (cost of sampling) profits have gone up significantly

What will happen in March 2013

As of March 2013, breeders will have the ability to test their own bulls before negotiating the deal with the A.I. company, resulting in a much greater negotiating position for bull breeders. The estimated effects are as follows:

The number of young sires sampled will not change	The cost to actually sample a sire will stay low
With open ended leases and increased competition the cost of procurement could go way up and could even hit the $1M mark per proven bull.	Semen sales price will not change
Revenue will stay the same	With greatly increased procurement expenses profits will decrease drastically

How Will A.I. Companies React?

There are not substantial enough profit margins in the A.I. industry to support such a change in profitability. As a result, A.I. companies will be forced to do the following:

Increase semen price
Since they now have greater expenses, A.I. companies will be forced to increase price. As demonstrated in many other industries, the market will not respond favourably to this and ultimately will drive prices back down.
END RESULT: No change
Cap contracts
So if A.I. companies cannot increase revenues they will have to try and cut their costs. The procurement of sires will become the major expense they will look to control. One way to do this will be to cap bull contracts. However, as the NHL has shown us, even if they could introduce a cap, some members will break that rule and other breeders will not stand for it.
END RESULT: No change
Produce their own product line
If A.I. companies cannot buy the bulls at a cheaper price, then they will have to go and buy females and produce their own product. This will lead to cheaper acquisition costs. A.I. companies can now buy the females for $50,000 to $250,000 and only need to have that female produce one son. That will still be cheaper than leasing the sire on an open lease. This also allows them to have greater control of their bloodlines, accelerate their genetic advancement and develop their own distinctive product.
END RESULT: Cheaper product development costs and a distinctive product.

What does this mean to the average seed stock producer?

For the initial stage, when A.I. companies are buying into the female side, prices will rise. Once they have the base genetics, they will not need to buy any more and they will stop buying. (Read – Should A.I. Companies Own Females and Select Sires v.s. Semex – A Contrast In Cooperatives)

If you look at the current substantial increase in the prices of genomic heifers, you will notice that it is the current seed stock breeders who are buying and trying to get ahead. The money for this is not coming as much from the female side as it is from the current or future revenue potential from the semen lease deals. These people will be out of the market as more and more A.I. companies STOP leasing from these bull breeders because they are now producing their own genetics.

This will leave the seed stock breeder with a product or cattle that do not top the lists like they used to. Also, now the A.I. companies will not release their new high genomic sires until they have mated them on all their own females first. This will give A.I. companies a substantial advantage in generating list toppers. Bull breeders, on the other hand, will not have the lease deals that they currently enjoy, so they will not have any revenues from the sale of high index animals.

I believe that the show market will survive, since they are not as dependent on genetic advancement alone since they use a combination of genetics, management and chance. This is something I will explain further in a future article.

The Bullvine Bottom Line

The introduction of genomics first started off by generating greater profits for A.I. companies. Currently it is contributing to greater sales for seed stock producers. Ultimately it will lead to decreasing profits for A.I. companies and they will seek to regain control. The only way to do that will be to control product development —-it will either be do that or go broke. This will lead to the industry becoming dominated by whatever players are able to build the largest self-contained genetic pool and advance their genetics ahead of everyone else’s.

What can the average seed stock producer do? (Watch for the answer in a future article.)

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Does Genomics Belong in The Show Ring?

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Friday, October 5th, 2012

In our recent article about the 7 Sires to Use In Order To Breed The Next World Dairy Expo Champion we highlighted six test sires and one proven sire as the best sires to use in order to breed the next generation of great show cattle. The response to this article has been insane. First from a readership perspective we had over 10,000 people reading the article in the first 2 days alone. Of even greater interest were the reactions that breeders had to this article (over 200 comments on Facebook, Twitter and our website). Many breeders felt that genomics had nothing to do with the show ring. Instead they felt that it was more important to stick to proven sires when mating their top type cattle.

Ignorance Is Not the Answer

This actually demonstrated to me that awareness of what genomics is and how to use it is desperately needed. Far too many breeders confuse genomics with the index system. Genomics is not a kin to Holstein USA’s TPI formula or the Canadian LPI formula. Rather, it is tool to use in order to predict each sires ability to transmit a certain trait.

Given that the genetic information for every animal is contained in its DNA, technology now makes it possible to predict a sire’s ability to transmit certain characteristics to their progeny. It has nothing to do with the relative weights or importance of one trait over another. Rather it is solely about a sire’s ability to transmit that specific trait. How you use that information and what weights you put on some traits over others is entirely up to you.

Less Science more Cow Talk

So that is all fine and good. It sounds very scientific but what does it mean at the show ring level? Let me take a stab at that in “show speak.” It doesn’t take much to know that some show cows are “managed” into greatness and others are bred for it. We have all seen the ones that on the average day look like they are a lucky to be “all-barn” let alone “all-world.” Those cows are the ones that I call managed into greatness. Then there are those other cows that have the complete package. They come from a strong type pedigree that and are sired by a sire who has proven to deliver top show cattle. These are the cattle that are bred to be great.

EASTSIDE LEWISDALE GOLD MISSY EX-95-CAN

A great example of this is last year’s World Dairy Expo Supreme Champion, EASTSIDE LEWISDALE GOLD MISSY EX-95-CAN. Missy comes from a strong type sire stack with a dam that has sired 35 daughters all have scored GP+, with 33 of them being VG+. No doubt that Missy’s dam, STADACONA OUTSIDE ABEL VG-88-4YR-CAN 29* is great at breading type cattle. In addition to that if you look at Missy’s own genomic test you will notice that she scores well above breed averages for type traits.

Another great example of a show cow that also has the genomic test to back it up are MD-DELIGHT DURHAM ATLEE EX-92-4YR-USA DOM GMD 2*. Of course, we all know Atlee as the All-American Sr. 3yr from 2005 where she also won Reserve Intermediate Champion at WDE. However, we also know Atlee as the dam of the top type sire MAPLE-DOWNS-I G W ATWOOD EX-90-4YR-USA. If you look at Atwood’s CDN type proof you see the following.

	Conformation	Mammary System	Feet & Legs	Dairy Strength	Rump
Official Proof	18	16	14	15	3
DGV	19	16	14	15	2
Parent Average	17	15	11	13	8
Estimated Daughter Performance	18	15	15	15	3

What you will notice is that his genomic test is the closest to his actual daughter performance. Rather than looking at the sires in his pedigree, or the performance of his maternal line (which by the way is one of the strongest type pedigrees in the world today), it’s his genomic test that would have accurately predicted that his rumps would not have been as strong as expected, and that his feet and legs would be better than expected. This is very valuable insight, when trying to breed the next great show cow.

So how does that help me breed a great one?

It’s great that we can show that genomics validates what we already know about sires like Atwood and great show cows like Missy and Atlee. However, how can we use that to help us to breed the next great show cow? To answer that question let’s take at two high genomic test type sires, MR ATWOOD BROKAW and CANYON-BREEZE AT AIRLIFT.

MR ATWOOD BROKAW

MR ATWOOD BROKAW is the Atwood son of REGANCREST MAC BIKASA VG-87-2YR-USA. In Brokaw you combine the two greatest type families in the breed today. No question that from all angles Brokaw has it all.

	Conformation	Mammary System	Feet & Legs	Dairy Strength	Rump
Official Proof	20	17	9	18	7
DGV	22	19	9	21	7
Parent Average	15	14	10	11	4

What we notice from his genomic test is that we can expect Brokaw to be far greater at transmitting dairy strength than his pedigree would indicate.

CANYON-BREEZE AT AIRLIFT

Then there is CANYON-BREEZE AT AIRLIFT the Atwood son from the same family as CANYON-BREEZE ALLEN.

	Conformation	Mammary System	Feet & Legs	Dairy Strength	Rump
Official Proof	17	12	18	16	16
DGV	19	12	21	18	21
Parent Average	15	12	11	13	4

What we notice here is that Airlift will sire rumps that are light years better than his pedigree would indicate while needing to be cautious on his mammary systems. Something that anyone who use enough Allen in their herd would attest to. What genomics does is it gives us this insight light years sooner that waiting for 100’s of daughters to help prove it out. That can be all the edge you need in breeding the next great show cow.

Do you think this is all hogwash?

Well let’s take a look at the current undisputed show ring champion BRAEDALE GOLDWYN GP-84-8YR-CAN EXTRA’05 GM’12. Here is a sire that by his own conformation would have never been considered potential for greatness in the show ring. A sire that by his maternal line of high classifying cattle had no great show history to them at all. So let’s look at the numbers:

	Conformation	Mammary System	Feet & Legs	Dairy Strength	Rump
Official Proof	12	11	13	7	3
DGV	10	9	13	6	4
Parent Average	5	5	-1	4	2
Estimated Daughter Performance	14	13	13	8	3

As you can see by the numbers, Goldwyn’s direct genomic values would have predicted his type prowess long before anyone would have suspected it. This is especially true in regards to feet & legs. Something no one would have expected from a James son.

The Bullvine Bottom Line

We all know that to win in the show ring it takes more than just great genetics. It takes genetics, management, and luck. Slacking on any parts of these means that you have to go “outside” the rules in order to make things happen. Instead of putting yourself in that precarious position, stick to what has been proven to work and use the best genomic sires available.

Not sure what all this hype about genomics is all about?

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7 Reasons Why You Shouldn’t Use Sires with DGV’s lower than Their Parent Averages

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Friday, August 31st, 2012

In our recent article, Is the Genomic System Really Working? we pointed out that the early numbers indicate that the genomic system is a 27.1% improvement over the old system. In taking a closer look, we also noticed an interesting trend that sires with LPI DGV’s (Direct Genomic Values) lower than their parent average actually did a nose dive, when they added daughter information.

In God we trust. All others must bring data

Now some of you would say that the system is already putting too much weight on DGV’s and that it is too early. I get that. However, here are some actual facts from the most recent proof round (August 2012) for you to consider. (Again please note we use the CDN system as a result of being able to have access to the genomic information on it.):

For the sires who dropped more than 200 GLPI points from their genomic parent average index to their official proof, 96% (25/26) of them had DGV LPI’s lower than their parent averages. Note that 118 bulls received official proofs in the CDN system in August 2012.
For sires with DGV’s higher than PA’s, 33% (11/33) actually increased their LPI ratings with the addition of daughter data.
When we take a look at the 5 sires who took the biggest jump with the addition of daughter information when compared to their parent average (COMESTAR LAUTREC, L-RIDGEVIEW NOAK-ET, GEN-I-BEQ BRAWLER, OCONNORS JAY, FAVREAUTIERE GRIZZLY) we notice that they on average had DGV LPI’s that were on average 536 LPI points higher than their parent averages.
Conversely when we look at the 5 sires who dropped the most (BIG TIME WILTON, STANTONS BRAKE, EXPRESS DOLSUNN, STANTONS UNLIMITED, WEST PORT BRUTUS) we notice that on average they have DGV LPI values over 1000 points lower than that of their parent averages.
When you take the top 5 sires with the highest DGV LPI values (GEN-I-BEQ BRAWLER, OCONNORS JAY, MORSAN BORIS, EXPRESS BOLLY, COMESTAR LAUTREC) they on average had an increase of 151 LPI points with the addition of daughter information.
Of the 33 sires that increased with the addition of daughter information 30 of them had DGV’s higher than their parent averages. That compares to only 3 of the 83 sires who dropped having DGV LPI’s higher that their parent averages.
So then it comes to the question, “what if a sire has high genomic values but they are just below his parent averages?” To answer that, we looked at the sires that had GPA LPI’s of over 2000 and DGV’s lower than their parent averages (ARDROSS STERLING, STANTONS UNLIMITED, and STANTONS BRAKE).They dropped by an average of 787 points with the addition of daughter information. Conversely those sires that where over 2000 GPA LPI points and had DGV’s higher than their PA’s (GEN-I-BEQ BRAWLER and MORSAN BORIS) actually increased by an average of 134 over their GPA LPI values.

The Bullvine Bottom Line

While the numbers are still early, the facts clearly indicate the merits of only using sires who have DGV’s higher than their parent average. No matter how high they are. Breeders need to have access to the DGV LPI values for the young sires they help sample for breeding companies.

Not sure what all this hype about genomics is all about?

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Is the Genomic System Really Working?

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Friday, August 24th, 2012

With Genomic sampled sires starting to get proofs, many breeders are finding themselves asking, “Is genomics really working?” Since it takes about 36 months for a sire to be sampled this is the first round we can start to evaluate the genomic system since its release in August 2009. To answer that question we decided to take a close look at how the system is working and if there are any early trends indicating if it is or not.

New Release Sire Performance over the past 2 Years

Probably this first place to look is how the young sire sampling programs are working proof round over proof round. (Due to the access of information, we are using the CDN system for this analysis).

Round	# of New Release	Average LPI*	# >2000 LPI
10-Aug	129	981	6
10-Dec	138	1013	7
11-Apr	133	996	6
11-Aug	127	1007	5
11-Nov	115	1041	7
12-Apr	111	957	2
12-Aug	119	981	3

*not base adjusted

Let`s start with the good news. The breed has been advancing when factoring in the base change. Now the not so good news, when compared to previous rounds at delivering top sires the numbers are not so pretty. As you can see by the table above, the last two proof rounds have not been so favorable for genetic advancement). We see the lowest average LPI from the sire sampling programs, with also the lowest number of elite sires being proven. This caused us great concern about the merits of the genomic system at delivering top sires and so we decided to look even deeper.

What’s going wrong? Or Right?

To get a better understanding of just why this last round was the 2nd lowest performing round in the past years (only behind Apr 2012) we decided to look at the group of young sires receiving proofs this round and discover whether it`s the system or how we`re using it.

In order to determine this we figured it would be best to compare the old system, top 10 parent average LPI (PA LPI) sires to the Top 10 Genomic sires (GPA LPI) and see how they stacked up. For the record her are the two groups.

TOP 10 PA LPI	TOP 10 GPA LPI
ARDROSS STERLING	GEN-I-BEQ BRAWLER
STANTONS BRAKE	OCONNORS JAY
MORSAN BORIS	MORSAN BORIS
STANTONS UNLIMITED	EXPRESS BOLLY
GEN-I-BEQ BRAWLER	COMESTAR LAUTREC
VELTHUIS S V B SAMPSON	ARDROSS STERLING
VELTHUIS SONAR	WALLACEVIEW PATTON
COMESTAR LAUTHIERY	DE-SU BURNISH-ET
GEN-I-BEQ LAVAL	BRYHILL LOYAL
STANTONS VISION	HARTLINE FOWLER-ET

The results are as follows:

	PA LPI	GPA LPI	Official LPI
TOP 10 PA LPI	1995	1720	606
Top 10 GPA LPI	1806	1968	2033

As you can see from the table above the GPA LPI sires outperformed the PA LPI sires by 27.1% indicating that the GPA system is a better indicator of estimated performance than the old PA system. In actuality, the top 10 GPA LPI sires actually increased their numbers by 3%, contrary to the expected drop. Even all 119 sires only averaged a drop of 89 points (9%) contrary to some other stats showing sires drop upwards of 20% from GPA LPI to the official LPI proof.

It’s also important to note that with an average official LPI proof of 2033 (445 points for base change) would have this group rank #5 behind the August 2009 proof round behind (Shottle, Justice, Goldwyn and Ashlar) with BRAWLER’s base adjusted proof (3083=2638+445) falling behind Shottle’s August 2009 proof of 3873.

So if it’s Not the System, What Is the Problem?

As the analysis of the PA LPI system vs. the GPA LPI system above indicates the issue is not the system. So then the question becomes, is it how we are using the system? Or are we just going through a lull? That question is tricky to answer. If we look at a longer period trend using currently available data from CDN we see that the two proof rounds before this period where even lower performing than the last two proof rounds.

Round	# of New Release	Average LPI	# >2000 LPI
10-Jan	135	738	1
10-Mar	130	686	1

It may also be that as an industry we are still very much learning how to use the Genomics system and sire selection practices have to adjust for these changes. When we look at the PA LPI list vs. the GPA LPI list we see two herds whose sires on average drop between 400 and 600 LPI points. Can we say hot house effect? (to read more Has Genomics Knocked Out Hot House Herds?)

The Bullvine Bottom Line

It is still early to weigh the success or failure of Genomics. The early indicators show that it is a 27.1% improvement over the old PA system. There is still much room for refinement and education on both the breeder side and the sire sampling side!

Not sure what all this hype about genomics is all about?

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The Effect Genomics Has On The August New Release Sires

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Friday, August 17th, 2012

With the recent proof release, breeders now have the opportunity to start seeing the effect of genomics has on the top new proven sire proofs. Thanks to the Canadian System and CDN (Canadian Dairy Network) we can even take one-step further and get a better appreciation of how genomics actually is affecting sire proofs.

The Process

In an effort to better understand these effects The Bullvine took a look a closer look at the top 5 new release sires. We looked at their official proofs, DGVs (Direct Genomic Values) and PAs (Parent Average). We also calculated what the sire’s current YS (Young Sire) index would have been (based on the CDN formula of 65% DGV and 35% PA) to see what their current index would have been without daughter information. We then took each of these parts and compared them to each other. The results are as follows.

GEN-I-BEQ BRAWLER

Trait	GLPI	Milk	Fat	Protein	%F	%P	Conf
Official	2638	1307	67	55	0.18	0.10	13
DGV	2605	1289	66	55	0.18	0.10	12
DGV Diff	33	18	1	0	0.00	0.00	1
PA	2003	1484	74	44	0.20	-0.04	9
PA Diff	635	-177	-7	12	-0.02	0.14	4
YS	2394	1357	69	51	0.19	0.05	11
YS Diff	244	-50	-2	4	-0.01	0.05	2

What stands out in BRAWLER’s official proof is that he actually outperforms his DGV and parent average indexes. While the general expectation has always been that high genomic sires will drop, with the addition of daughter information, BRAWLER is a high genomic sire that actually increased his values. Note that his official values for protein, conformation and LPI significantly exceed his PA values. One of the interesting points on BRAWLER is that his official conformation score is higher than both his DGV and PA values. It appears that so far his daughters are performing much better than his parent average or DGVs predicted, especially in mammary traits.

COYNE-FARMS DORCY

Trait	GLPI	Milk	Fat	Protein	%F	%P	Conf
Official	2305	1670	45	48	-0.17	-0.05	12
DGV	2726	1730	50	52	-0.14	-0.05	14
DGV Diff	-421	-60	-5	-4	-0.03	0.00	-2
PA	2016	1399	62	42	0.10	-0.04	9
PA Diff	290	271	-17	7	-0.27	-0.02	3
YS	2477	1614	54	48	-0.06	-0.04	12
YS Diff	-172	56	-9	0	-0.11	-0.01	0

While BRAWLER’s PA and DGV actually held him back, we see the exact opposite effect for DORCY. NOTE: Due to the need for DGV’s we have had to look at US proven bulls on the CDN system. DORCY posts outstanding DGV values, but so far his daughters are falling short of those values, especially for fat, udders and legs. In fact, his DGV’s actually elevate his proof, by our estimate, by almost 30%. While these early daughters (65) may not be a complete indication of where his proof will end up, current daughter values would predict that we should see declines in these traits.

OCONNORS JAY

Trait	GLPI	Milk	Fat	Protein	%F	%P	Conf
Official	2305	1419	63	75	0.10	0.24	10
DGV	2291	1465	65	77	0.09	0.24	10
DGV Diff	14	-46	-2	-2	0.01	0.00	0
PA	1710	1190	45	49	0.05	0.09	10
PA Diff	596	229	19	27	0.05	0.15	0
YS	2087	1369	58	67	0.08	0.19	10
YS Diff	218	50	5	8	0.02	0.05	0

While BRAWLER’S official proof is higher and DORCY’S is lower than their DGVs, JAY’S official proof is bang on. The biggest difference between his young sire proof and his official proof is that his parent averages are actually much lower than his DGVs and daughter information.

WABASH-WAY EXPLODE

Trait	GLPI	Milk	Fat	Protein	%F	%P	Conf
Official	2183	2042	49	58	-0.26	-0.07	12
DGV	2333	1917	50	56	-0.22	-0.04	14
DGV Diff	-150	125	-1	2	-0.04	-0.03	-2
PA	2127	1910	65	55	-0.06	-0.06	10
PA Diff	56	132	-16	3	-0.20	-0.01	2
YS	2261	1915	55	56	-0.16	-0.05	13
YS Diff	-78	127	-6	2	-0.10	-0.02	-1

EXPLODE joins his fellow US proven DORCY in finding it hard to live up to his high DGV values. Similar to DORCY, EXPLODE’s daughters are lower than his DGV’s for feet and legs, as well as rump and protein. However, so far his daughters are proving to be much more durable than his DGV did predict over his parent average.

MORSAN BORIS

Trait	GLPI	Milk	Fat	Protein	%F	%P	Conf
Official	2171	796	68	45	0.38	0.17	12
DGV	2207	778	67	44	0.39	0.17	11
DGV Diff	-36	18	1	1	-0.01	0.00	1
PA	2035	963	57	46	0.22	0.13	12
PA Diff	137	-167	11	-1	0.17	0.04	1
YS	2147	843	64	45	0.33	0.16	11
YS Diff	24	-47	5	0	0.05	0.01	1

Much like the other Canadian proven sires, BORIS’s DGV values are bang on, with only a slight variation where his daughters are currently outperforming predictions for feet and legs.

Interesting Note

When we applied the same analysis to Co-Op Bosside Massey, we see that his daughter information was much higher than both his parent average and DGVs, hence explaining with the addition of more daughters Massey’s proof increasing.

The Bullvine Bottom Line

While most of the early top genomics sires are still awaiting proofs, this analysis of a small group shows some interesting trends. First it shows that there may be differences from country to country in the accuracy of predictions (Editors note: As we have now crunched over 200 US sires we see that this is no longer the case, these two are more an anomaly than the standard. Watch for the results of this number crunching in a future Bullvine post). It also shows that, at least in the Canadian case, the DGV values are a much better indicator of potential than the old PA system predictions. This could be because genomics so far has been able to limit the effects of hot house herds (read Has Genomics Knocked Out Hot House Herds). In looking at the differentials for these five sires, we see that DG Values vary by 6% from official LPI Proofs, while their PA’s vary by 15%. This is in line with CDN’s prediction of a 5% accuracy gain, as a result of using genomics for calculating first crop proven sire proofs. Furthermore, it shows that with daughter information added top genomics sires, can actually outperform their high parent average and DGV predictions.

For more information check out our Genetic Evaluation Resource Center.

Genetic Evaluations – Why the Sky Is Not Falling

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Wednesday, August 8th, 2012

As more and more early high genomic young sires are getting their daughter proofs in next week, I am sure we are going to hear that the sky is falling. And yes, while there is much certainty that the bulls may drop, that in no way indicates that genomics does not work.

As early proofs have indicated, the large majority of genomic sires will drop. But that should not have everyone running for the hills. Instead, what you should do is look at 2 key metrics: 1) How they compare to the proven sires that where available at the same time as the breeding 2) The percentage that are returned to service.

Why genomic bulls may drop

While critics would say that any drop is not acceptable, that just shows that they do not understand how the system works. There are other reasons that bulls may drop that most breeders may not consider; here are a few reasons:

Hot House Effect
While we all would like to believe that the system is faultless, that is just not the case. It’s important to remember that proofs are first and foremost based on herd variation and genetic gain over their parents. So if a genomic sire is used on a dam who maybe lost a teat, or was sick as a calf and did not develop to her full genetic potential, this will have a huge advantage for the genomic sire. Same is true if breeders are looking to work that system. By that, I mean they are going to have other genomic cattle in the herd that do not receive the same level of attention as the families that they are working to have succeeded. (read more here: Has Genomics Knocked Out The Hot House Effect)
Higher Quality Dams
In the past, young sires were used on G and the odd time a GP dam, but never on your high scoring 2yr olds. But with genomics, we see sires being used on VG 2 yr olds. Unless the progeny can score higher than the dam (not account for herd variance), it will be next to impossible for that bull to receive a positive type proof, let alone one that will allow them to be a breed leader. However, the potential for these sires to have the exact opposite effect is very possible, for instance, they were used on a VG-87 2yr old and her resulting progeny ending up a GP-80 2yr old. The sire will actually receive a much lower type score as a result. In reality, it is better to compare and note the similarities between a genomic sires daughter proof to a 2^nd crop proof of the past.
System Improvements
As mentioned in the hot house bullet above, the system is not perfect. These early proofs are based on the best educated guess that the geneticist could do given the data provided. As more data is available it will be possible to refine the system. The most useful data they will get will be these early genomic sires with daughter proofs. This will allow them to see how effects such as being used on higher quality dams will have and how they can adjust the system to account for this.

Does it matter?

The critics will say that the AI companies could care less if the bulls drop. They have sold so much semen on these young sires at such high rates that they have already made their profit. And yes, this is partly true. There is no question that a high genomic young sire will probably become a significant profit as compared to the past when they were a $50,000 investment. And then there is still the issue of credibility. It does not take long or many sires killing pedigrees before the clients of these AI companies will start losing business. The other part of the equation is that often these same AI companies have used these sires as sires of sons in their own programs, resulting in a significant risk for their programs and future profits as well.

The Bullvine Bottom Line

What breeders need to remember is, yes, genomic sires may drop. But instead of running around like Chicken Little announcing the sky is falling, what they need to do is compare those same sires to the proven sires that were at the top of list at the time when they made the breeding decision. From a systems perspective, it is better to look at what percentage of these genomic young sires are return to service. This will indicate if the system is working or not.

Not sure what all this hype about genomics is all about?

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What Happens If Genomics Doesn’t Work?

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Friday, July 27th, 2012

There has be so much talk lately, The Bullvine included, about how much the dairy breeding world has changed since the introduction of Genomics, that it has me thinking, “What if genomics doesn’t pan out. What if it doesn’t work as well as predicted?”

History is full of trends and inventions that the world thought would be amazing that in the end seemed nothing more than hype. In recent history there has been foursquare (location based social network) and the Snuggie that, due to great marketing and an audience starved for something new, saw immediate rapid growth but lacked staying power. Are genomics no better than the Snuggie?

While I must admit, I am sure there has been way more research and development behind genomics than there was behind the Snuggie, there are some significant areas that we have had to assume as musts that may turn out to bite us in the butt. Such as:

Not a Perfect Science
Because genomics are so new, this means that we have to operate on a number of assumptions. As time goes on and more and more animals are tested, I am sure the accuracy will improve.
Limited Data
While the ability to have genetic evaluations and recording systems provides genomics the ability to more accurately predict genetics merit far ahead of genomics in other animals or humans, it’s still in its infancy. As more and more cattle are tested there will be more and more data to work from providing geneticists with greater accuracy in the systems they produce.
Hot House Effect
While even we have written about how genomics has removed the hothouse effect (Has Genomics Knocked Out Hot House Herds?), does it really mean that it has been removed, or maybe it has just changed the game? Maybe “shady” breeders just need to think of new ways to work the new system.

Is It Genomics or Is It You?

History is littered with wide scale aversion to new, disruptive technologies. Thomas Edison turned down the radio because it had no commercial value; Western Union turned down the telephone because management thought ‘it will never be more than a toy’. Can you believe that Thomas J. Watson Sr., founder and head of IBM, turned down the computer; and Kodak turned down the Xerox copier. This makes me think of how many old school breeders are pissing on genomics (Old School Dairy Breeders – STOP PISSING ON GENOMICS) maybe more because of fear of change, than anything else.

May be you should also stop listening to the radio, talking on the telephone or taking pictures? Now tell me how many cattle you’ll be marketing?

The Bullvine Bottom Line

There are no guarantees in life (well, I guess I should say with the exceptions of death, taxes) and genomics is no different. Genomics is not a perfect science, yet. However, it does have a very sound scientific basis that, as time goes on, can be refined and enhanced. For those who are afraid of genomics I ask you, are you afraid of genomics, or are you afraid of change?

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GENOMIC HEIFERS: Understanding who is on top

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Tuesday, July 17th, 2012

Adding genomics to genetic evaluations brings more attention to young heifers. There is increased accuracy to heifer indexes and new population benchmarks. Even more significant are the Direct Genetic Values (DGVs) that are generated from the DNA results. As you will see, the the very top heifers increase their genetic indexes significantly, while their full sisters, without high DGVs are not on the list. The DGV value makes the difference.

The Bullvine continually receives the question, “Why are the top heifers at the top?” In order to assist the industry to better know how high is great, the Bullvine has done an analysis of the top 25 Canadian Holstein heifers published in April 2012 by Canadian Dairy Network.

What do the average for the Top 25 look like?

[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/07/genomic-heifers.csv” icons=”false”]

This is a truly exceptional group. What other Top 25 female list would be able to boast of an average value of 192 kg. for fat plus protein and 13 for conformation on their Parent Average Genetic Indexes? And look at their DGVs. They are even higher at 203 kgs. for fat plus protein and 13.8 for conformation.

Digging Deeper

Average numbers are a good place to start, but there are additional facts that can assist us in understanding the Top 25.

21 were less than 1 year of age and 4 were over 12 months of age. Obviously, the heifers on this list are young.
The prominent cow families represented on this list are: Lila Z (24%); Lead Mae (24%); Gypsy Grand (16%) and Laurie Sheik (8%).
The heifers’ sires are 48% daughter proven bulls and 52% genomic young sires.
The heifers’ dams are 40% with performance of their own and 60% with PA GLPIs only.
96% of the heifers have DGVs higher than their PA GLPI.
The most significant fact is that the top 25 heifers on average have DGVs 228 LPI points higher than their PA GLPI. They are what are commonly referred to as high outliers. Most of these heifers have full sisters who are not as high for DGV. Previously, they would have been considered equals.

In future articles, The Bullvine will be bringing forward ideas on the genetic needs of dairy cattle and strategies to use in selecting and breeding.

THE BULLVINE BOTTOM LINE

When deciding to invest in a high genomics heifer, it is important to study both the heifer’s PA GLPI and her DGV. Although 25 may be too small a group to depend on for everything. Nevertheless from this small snapshot we get a clearer picture of the potential that genomics and DGVs provide. The Bullvine is excited to provide this perspective on an ongoing basis.

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Old School Dairy Breeders – Stop Pissing On Genomics

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Monday, July 16th, 2012

Recently as part of our weekend humor series we published the picture seen at the right. In publishing the image we knew we would get a reaction, but we were surprised at the way breeders interpreted it. While we intended to show how old school breeders are dissing on genomics, but instead it seemed to become a rallying cry for old school dairy breeders.

The conversation that has stemmed from it has been very interesting. As you can see, there are still many breeders who don’t totally understand the merits of using top genomic young sires. In an effort to help educate, or maybe just bang my head against the wall, we have prepared the following details. .

Proven vs. Young Sire – Who wins in the long run?

Let’s take a comparison of the top 10 Genomics Young Sires vs. the Top 10 Proven sires from the April 2012 proof run. Of course we all know that the genomic young sires will have higher breeding values, but we need to account for the expected drop. Our analysis of the NAAB genomic sires’ proofs vs. their later daughter proven proofs currently shows a 13.8% drop on TPI. (Note: we are actually tracking the drop on LPI sires, TPI sires and PLI sires, and so far we see them dropping 9.7%, 13.8%, and 13.5% respectively.)

The following table shows where the current top genomic sires would rank compared to the proven sires options available currently.

[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/07/PROVENVSGENOMIC.csv” icons=”true”]

What Does This Mean?

What you notice is that three of the top current genomic young sires (Numero Uno, Supersire, and McCutchen) would all rank among the top 10 proven sires. In fact, 25 of the top 50 sires would be genomic young sires. This is not to say that they will all drop the 13.8% that the average sire has already. They could drop more or less. However, what it does show is that these young genomic sires have a much higher predictability than in the past. You can now use a group of these young sires with much greater confidence than in the past.

The Bullvine Bottom Line

Are all the top genomic sires, going to end up on the top of the proven sires list, when they have daughter progeny? No, of course not. But what we have been finding is that only about 10% of them drop off the top list, and many of them hold pretty strong. We have even found some genomic sires that actually go up with daughter information. What it does mean? Use genomic sires that are within 10% of the top sires. If they have GTPI values of 2,300 or greater, you will end up ahead of where you would have been, if you had not used any genomic sires at all. Just remember this is an average. The movement will not be exactly the same for all sires, hence the need to spread out your young sire usage.

For all those old school breeders, who are pissing on genomics, well what can I say? I don’t expect to change your mind. However, it is foolish to piss on something that you don’t understand. Might I recommend that you read our free guide – The Dairy Breeders “No BS” Guide to Genomics.

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GENOMICS: Big Dollar Opportunities are Adding Up

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Wednesday, July 11th, 2012

Is the glass half-full or half empty? The comment is often heard that genomics has yet to prove itself. When index breeding for production traits came on the scene forty years ago, it too was seen as the new kid on the block. In response, The Bullvine has decided to compile a list of points could be considered significant dollar opportunities Please note that these dollar values are derived from the Canadian situation but the general principles can be applied elsewhere.

Sample Only the Best Young Sires

Eliminating the need to sample the bottom 60% of 550 young sires (all breeds) will save the Canadian industry $16.5 M per year. Add to that, eliminating the loss that producers bear when they must cull daughters of low genetic merit young sires and it is over $20M in savings by genomically testing all young sires and only sampling the top sires.

Turning Generations

Generation interval is extremely important in determining the rate of genetic advancement in a population of food producing livestock. Shortening the generation interval, by using genomics to more accurately identify the top heifers and young bulls, will decrease the generation interval by one year, when 30% of the population is bred to young genomically tested young sires. That will increase the rate of genetic advancement by 25% per year. However the rate of usage of genomically tested young sires is fast approaching 50% which equates to a reduction in generation interval of two years. This results in a 60% gain in genetic advancement. Research has shown that that 60% gain is worth $30M annually for the traits that are currently included in the LPI formula.

Increased Accuracy

When considering the accuracy, with which we know the breeding values of the animal in a population, there are many points to consider:

Conducting a low density panel test on all heifer calves in a population of cows has a cost. It also has the benefit of having a totally accurate herdbook, no wrong assignments of parents and these help in genetic evaluations.
Knowing the genomic values for all females means that those genetic merit females can be used as recipients or can be fattened and sold for meat.

Identifying the elite females in a population greatly enhances the rewards that can be reaped from using only the best as dams of the next generation. Putting a dollar value on increased accuracy on the female side of a population is not easy to do but by The Bullvine’s calculation it would yield $20M per year in net terms for Canada’s dairy farmers.

Beyond Canada there are great populations of dairy cattle that contribute to the advancement of the genetic merit of dairy cattle everywhere. Knowing the genomic values of these animals will greatly help North America advance their populations, especially for breeds with numerically smaller numbers.

Traits under Selection

As The Bullvine has reported (read Is Your Breeding Strategy a Field of Dreams) selecting for traits beyond milk, fat, protein, SCC and conformation will become possible with the use of genomics. Already The Bullvine has learned from our followers that they look forward to knowing in genetic terms details for feed efficiency, production limiting disease resistance, calf health and liveability, reproduction traits and more. Putting an industry dollar value on knowing the growth of those additional traits is not possible at this time. But it will be quite a significant number.

Inbreeding

This article will not spend time addressing inbreeding as it has been addressed previously in The Bullvine (read Inbreeding: Does Genomics Affect The Balancing Act). Suffice to say at this time inbreeding can be handled when selection uses genomic values. Not previously mentioned by the Bullvine on inbreeding is the fact that in dairy cattle populations beyond Holsteins there is considerable benefit to using genomics to select semen and embryos from outside a country’s borders.

The Bullvine Bottom Line

So far in this article, The Bullvine has been able to identify over $70M to $100M in annual benefit to Canadian dairy breeders alone from the use of genomics. That means $10,000 annually for each and every breeder. So is the glass half full or half empty when it comes to using genomics? How do you see it?

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Dairy Cattle Genomics: Have we taken it too far?

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Thursday, July 5th, 2012

When you look at the top 10 GTPI heifers you see that 9 of them are from heifers themselves with only one coming from a scored and milk producing dam. In addition 9 of them are from one sire (Shamrock), which instead of widening the genetic pool is actually shrinking it. Looking at the top GLPI list reveals that three out of every four in the top 100 are from un-calved heifers. While, on paper, cutting the genetic interval makes sense (read The Genomic Advancement Race – The Battle for Genetic Supremacy), long term, have breeders and AI companies started to take it too far?

In the new genomic world the previous gold standard of a proven sire stack and string of VG+ is no longer required. In any given pedigree you can now find GP cattle (read Is Good Plus Good Enough) or sires that you never have heard of.

Does Classification Even Matter?

While GP-84-2YR used to be the kiss of death for many marketing and genetic programs, genomics has changed the game. With genomics, we are seeing many GP 83 or 84 cows used as dams that would have never been touched before. While many will increase in score later in life, others do not, and yet that does not seem to be as big a factor. Many A.I. companies and breeders are more concerned about their genomic values than that of the actual classification scores.

There could be many reasons why that potential bull mother did not score very good. It could be management, it could be an accident that happened. Also, it could be that she is just not that good. It brings into question the relevance of classification. While the index system relies on having a large data set in order to map the genomes to the potential performance of each trait, it has me thinking do we need to score cattle anymore or can we just use their genomic values? Then I snap back to reality and realize that it’s one thing to look good on paper and another to deliver in reality.

Have We Forgotten Sire stack?

At one time, if there was a non -known sire in the pedigree, A.I. would not touch it. The marketability of that pedigree was next to nothing. No matter what the classification score was, or what the family was behind that animal, sire stack carried significant weight. Now I find myself having to do as much homework on the sire of the new top young sires, as I do on the young sires themselves. That may be because most of them are still young sires themselves. However, it is also because a young sire that did not turn out can still sometimes be better than a previous Top 10 proven sire.

For example, let’s say the proven sire has a TPI of 2300 at the time of mating and the young sire being used as sire of sons has a TPI of 2900. By the time the resulting progeny is being sampled the proven sire may have a TPI of 1750, and the young sire that was being used as a sire of sons may have a TPI of 1850. While that young sire may not be a list topper anymore, he is still higher than the proven sire that could have been used at the time.

The Bullvine Bottom Line

The dairy cattle industry has seen more change in the selection of parents in the past four years than at in any other period in its history. Genomics has changed the name of the game, and while many breeders have been apprehensive in embracing it, others have taken it and are running full force. I would not be surprised to see more significance in the future put on Direct Genomic Values (DGV’s) than on the weighted GLPI or GTPI. With everything that is new, there is a learning curve and, as we discover how to use this tool better, I am sure we will find better ways to apply the information. However, there is no question that genomics is here to stay and it is greatly changing the rate of genetic gain.

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Will there ever be another distinct bloodline?

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Wednesday, June 20th, 2012

Before the recent Kueffner Kows at Cowtown Sale Horace Backus, commented that he had never seen anything like it in all his years! “The quality of every animal and the homebred breeding was just so good. Just before the sale started, I took a moment to walk through one of the lines of cows while it was quiet and everyone was already gathered in the tent. I stood looking at a line of maybe 40 animals, and thought I was standing at Madison seeing that many great cows all together.” These comments reminded me of the ones he made before the 1998 Hanover Hill Dispersal where Horace said, “In the history of the Holstein Breed, there have only been four or five herds that have created a distinct blood herd. Today we are selling a distinct bloodline herd.” This got me think will there ever be another distinct bloodline herd?

Over the years, the marketplace has changed greatly. The improvements in technology have been incredible. It is now easier than ever to market, compare and transport your genetics to anywhere in the world. To get a better understanding how each of these will play into the potential of having another distinct bloodline, we decided to take a closer look at each one.

Marketing to the World

In the era of Hanover Hill era buyers did come in person from around the world. The world has changed greatly with the Internet. I often wonder what a great marketer like Peter Heffering would have done in today’s time. The ability to market to a much larger audience through the internet and Facebook is expanding the marketplace. You are no longer just selling to the person next door or in the same country or the few who are able to travel to buy. You are often selling to people half way around the world. And more importantly than where they are, is how quickly and easily you can reach them. You no longer have to run magazine ads in each country’s major breed magazine. Today you simply post a quick smartphone picture, or better yet video, on your Facebook page and share it with the world.

Cross Country Comparisons

One of the things that contributed greatly to each country or region having its own distinct bloodlines was that the ability to compare performance data on in each country presented challenges. In previous generations, it was hard enough getting everyone to talk in the same units (ex. Lbs. vs. kgs.) let alone the fact that they had different methods of evaluating things. Then came Interbull and MACE proofs. That started to open up the marketplace, but for some the confidence in the MACE system was not there and for the most part most countries still had regionalized breeding and evaluating systems. Then came genomics that has given breeders around the world the confidence no matter where the bull was proven to use him on their cattle. We now see that there is no longer a negative stigma in North America on foreign proven bulls. Moreover, many of the great international cow families are gaining significant respect in the North American marketplace, especially as sons of these cattle have proven themselves well on the North American genetic base.

Transportation of Genetics

All the great marketing and evaluation systems in the world mean nothing if you cannot get the genetics to the consumers. Artificial insemination had a drastic impact on the ability of breeders to develop distinct bloodlines. Instead of just running your own breeding program where you sell the odd breeding bull, artificial insemination meant that when you sold that bull to an AI center, he would now be able to reach the world market. With AI companies also becoming less regional or country focused and more world focused, that meant you could sell a bull in Chicoutimi Quebec and his semen could be used in Kamifurano Japan. Breeders no longer had to develop their own bloodlines and could draw on the best bloodlines from around the world. Furthermore, as embryo transfer technology advanced you could also import and export embryos and further accelerate your breeding programs.

The Bullvine Bottom Line

Today breeding herds like De-Su limit the amount of genetics they sell and AI organizations like Select Sires are entering the female animal ownership side in order to develop a distinct product in the marketplace. Nevertheless, I truly feel that with the overall changes in the global marketplace we have a much more level playing field through evaluation systems and technology and, therefore, it is highly unlikely that we will see the achievement of a distinct bloodline at the level reached by Hanover Hill.

Show Cows: All Type and NO Action?

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Thursday, June 14th, 2012

The June 12^th sale of RAINYRIDGE TALENT BARBARA EX-95 for $230,000 has me asking if she is really worth it. For years, there has been a stigma around the cows that win the big shows that they are all fake and don’t pack genetic punch. After all, we know how hard it is for a show cow to produce the next generation show winner. Using a genetics perspective, we decided to see what these show cows offer besides their good looks! (i.e. Which ones have the brains to go with the good looks.)

We looked at the All-Canadian and All-American winners and the reserve and honorable mentions and here is what we found.

All-American’s

The 2011 All-American’s average an outstanding 92 points, but more importantly, they also average over 1500 TPI points and on average have 6 generations of VG or EX dams in their pedigree.

Notable standouts include:

PINELAND GOLDWYN TIDBIT VG-89-3YR

PINELAND GOLDWYN TIDBIT
With a TPI of 1800 Tidbit leads the way when it comes to the 2011 class. This reserve All-American Sr. 2yr old is backed by an outstanding 11 generations of VG or EX. Bred by Pineland Farms of New Gloucester ME, Tidbit is now owned by Ferme Pierre Boulet. This Goldwyn has a strong type sire stack that has shown an ability to consistently produce impressive records.

GARAY ALEXANDER DESTINY VG-89-2YR

GARAY ALEXANDER DESTINY
Following close behind Tidbit is the All-American Fall Milking Yearling GARAY ALEXANDER DESTINY. Destiny is backed by five generations of VG & EX cows back to the great SNOW-N DENISES DELLIA EX-95-2E-USA GMD DOM.

RAINYRIDGE TALENT BARBARA EX-95

RAINYRIDGE TALENT BARBARA
The HHM All-American Aged Cow in 2011 packs strong genetic punch for new owners River Valley Jerseys of Tremont, IL. Bred for strong type back to one of the greatest show cows of all time RAINYRIDGE TONY BEAUTY EX-5E-CAN 9*, Barbara already has three VG daughters. It’s no wonder that one of the greatest cattleman of this generation (Kueffner) and the type-breeding specialists (ST JACOBS ABC) took such interest in her, I am sure there are great things to come for her new owners.

All-Canadian’s

Maybe it’s the different rules for scoring 2yr olds in Canada, but the Class of 2011 averages a strong 91 points which is slightly less than their US counterparts. Similar to their US contemporaries they have an average of six generations VG or EX behind them. They average 1199 LPI points (91% Rk. For LPI.) It is worth noting that this places them in the top 10% of the population!

WILLOWHOLME GOLDWYN JESSICA EX-94-CAN

WILLOWHOLME GOLDWYN JESSICA
Leading the way on the Canadian side is WILLOWHOLME GOLDWYN JESSICA. The honorable mention 5 year old has an LPI of over 2000 points. This 4^th generation VG or EX Goldwyn daughter has average production numbers, but gets her LPI points from high conformation and strong durability scores.

EASTSIDE LEWISDALE GOLD MISSY EX-95-CAN

EASTSIDE LEWISDALE GOLD MISSY
The 2011 Supreme Champion from WDE and the Royal Winter Fair, has substance to her good looks. Her Outside Dam (STADACONA OUTSIDE ABEL), was a 2011 Canadian cow of the year nominee and has 100% of her daughters GP+ or better. Missy herself already has a VG-87-2yr old daughter by Dolman. Currently on an extensive flushing program, Missy’s genetic prowess is just beginning.

JACOBS GOLDWYN BRITANY EX-95-CAN

JACOBS GOLDWYN BRITANY
The reserve all Canadian 4yr old completes 7 generations of VG or EX. Much like Jessica, Britany gets much of her 1881 LPI points from her +17 conformation score. Bred for type, Brittany’s dam, JACOBS JASPER BEST VG-88 4*, has 100% of her nine daughters GP or better.

The Bullvine Bottom Line

At the end of the day, all dairy cows, including show cows, need to be genomically tested. While none of these show cows we have talked about will top the GLPI or GTPI list, they do have the credentials to produce the next generation of great ones.. Some will. Some won`t. So, are show cows all type and no action? Certainly not! But success is in the selection.

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What Will The Cow of The Future Look Like?

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Wednesday, June 13th, 2012

Will she score 95 points? Will she produce 40,000lbs per year? Will the cow of the future be polled? Will she produce less methane gas? In the future, consumer demand will shape everything about dairy farming, including what the dairy cow will look like. Dairy consumption in emerging economies is rising fast. In China alone it will triple by 2020. As rice-paddies turn to pasture, breeder goals and ultimately the makeup of the modern dairy cow will change.

Over the past decade in North America, total milk production has increased in concert with the increased demand for dairy products from growing populations and increasing exports. This increase in production was achieved without increasing cow numbers, which have held steady, or slightly decreased, for nearly two decades. Production efficiency has therefore increased substantially with average production currently at 21,000 lbs. per cow per year.

While many things have contributed to the gain in production efficiency, one key area has been genetics. One of the biggest changes in the genetics market has been the use of genomics. Genomics has brought greatly increased reliability to estimated breeding values and is drastically decreasing the interval between generations (To read more check out The Genomic Advancement Race – The Battle for Genetic Supremacy). The next steps will be health traits and profitability and not just the ones that we are currently evaluating. We are getting ready to delve into better understanding of reproductive issues such as which cows are more efficient at converting feed to milk production (To read more check out Holstein vs. Jersey: Which Breed is More Profitable). Also rising on the priority list will be disease resistance (to read more check out Your Cattle Are Under Attack) and ultimately which cows are the healthiest, trouble free and most profitable.

As the revered management guru, Peter Drucker, says, “You cannot improve what you cannot measure.” Even though the dairy industry has a great system for evaluation production and conformation, there is much needed improvement in the areas of profitability and herd health. These areas were once thought to be low heritability however, with genomics, traits such as somatic cell, and immune response can greatly impacted at the genomic level. With Pfizer a company very focused on animal health now offering genomic testing, it’s only a matter of time before there is greater measurement in these areas.

This first steps in any effective improvement program requires accurate measurement. While many conformation traits and overall production traits are measured intensely when you look at overall measurement of cow –by-cow profitability, there are some major gaps. One of the biggest is accurate feed conversion metrics. While there have been studies by breed vs. breed comparison, there is a much greater need to take this analysis to the cow by cow and ultimately the genetics evaluation level.

The other day I was talking with a human geneticist about the use of genomics and ultimately the ability for genomic manipulation of a population. One of the key things he pointed out to me was how the dairy cattle industry really has the ability to lead the way when it comes to genomic advancements. Not because of the ethics issues, which we will leave for another forum, but rather because the dairy industry already has such a system in place for evaluation of the progeny. This ability to measure the exact effects of the manipulation will greatly accelerate the advancement process.

The Bottom Line

Over the years we have started to see less emphasis on stature, and increased focus on feet and legs and mammary systems. The cow of the future, will not just be about their conformation, but rather their ability to efficiently convert feed and their resistance to disease. With companies with the size and resources of Pfizer or their newly formed Zeotis entering the marketplace offering genomic tests, and maybe ultimately genomically modified cattle, the future may come much quicker than most breeders expect. So what will the cow of the future look like? We do not know exactly, but she will no doubt be the one that returns the most profit to her owners. All this will be driven by consumer demand.

Not sure what all this hype about genomics is all about?

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INBREEDING: Does Genomics Affect the Balancing Act?

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Tuesday, May 29th, 2012

If you are like many of us you are alternately amazed, overwhelmed and confused by the barrage of information that is fed to you through your breed organizations, cattle committees and industry publications. As part of The Bullvine`s commitment to be an informative and understandable resource for cattle breeders, I have spent considerable time trying to get my non-scientific head around the 2011 paper in the Journal of Dairy Science entitled, “Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information.” Was it worth the bother? Yes. Definitely.

What You Don’t Know Can Hurt You

We can all agree that Genomic information is a tremendous breakthrough for cattle breeding. With all the potential, it didn’t take long for the concern to arise that greater rates of genetic gain could lead to higher annual rates of inbreeding. My wild imagination skipped to a picture of everyone breeding to the top bulls and ending up with a single family. Even if that seems outrageous, it is definitely possible that generation intervals could be halved through taking advantage of the accurate GEBV’s available at birth and this could increase the inbreeding per year. Therefore, I definitely wanted to find out from this paper published by Pryce, Hayes and Goddard in Australia on how genomic information offers possibilities to control the level of progeny inbreeding.

Concern: Are we moving from homogenized milk to homozygous cows?

Let’s take a look at the indicators that might lead us to believe the answer is, “Yes!”

Genomic predictions are both cost effective and highly accurate. Therefore there is the very definite potential to accelerate the rate of genetic gain beyond that achieved through progeny testing.
Shorter generation intervals could result in large numbers of animals who are similar in genetic makeup due to the sires used.
It’s human nature to aim for the best. The uptake of genomics has been beyond anything previously predicted or imagined. Not only is the playing field being leveled it is being dramatically narrowed down.

Strategies to Control the Rate of Inbreeding

An important part of this Australian study was to evaluate the effect of the three strategies tested on the homozygosity of deleterious recessives. In other words, what can breeders do to limit the potential for negative effects of inbreeding? Before, we go further, it is interesting to note, that these researchers referenced more than twenty other research papers. The focus on this subject is concentrated and that can only be good for the eventual outcome for breeder decision making.

The main limitation of comparing methods to predict progeny inbreeding is that, at this time, there is no best practice for measuring inbreeding. Pedigree is flawed by errors and gaps and often, particularly in commercial herds, the depth of pedigree. Genomic relationships calculated using SNP data could have errors from incorrect identification of samples.

The goal of these researchers was to compare 3 strategies for controlling progeny inbreeding in mating plans:

Pedigree inbreeding coefficients
Genomic relationships
Shared runs of homozygosity.

The Good News Is….

I know this all sounds very complex, but relax there is good news. The study found that both genomic relationships and pedigree relationships were successful strategies to control the rate of inbreeding under genomic selection. They also concluded that using genomic relationships instead of pedigree relationships “appears to be better at constraining genomic inbreeding under genomic selection.” The unique part of their study was that they went a step further and proposed “using runs of homozygosity to control the rate of inbreeding.”

Again I know sounds very complex. So let’s try and break it down. One of the underlying processes of inbreeding is that it increases the frequency of both favorable and deleterious homozygotes. ROH stands for run of homozygosity. If the occurrence of deleterious homozygotes is more likely to arise as a consequence of recent inbreeding (which is the potential of heavy use of genomics) then strategies to minimize ROH could be a way of reducing them. A novel approach, don’t you agree?

What did they do?

In the research simulation they used 300 cows with 20 sires available for mating, replicated 50 times. Each of the 300 individuals allocated as dams were matched to 1 of 20 sires to maximize genetic merit minus the penalty for estimated progeny inbreeding and given the restriction that the sire could not be mated to more than 10% of the cows. In the discussion part of the paper, which, of course, is the easiest part to understand they offer this: “The results presented here show that using A GRM instead of pedigree in a mating plan is an effective way to reduce the expected inbreeding in progeny, with minimal effect on the genetic gain for the inbreeding objective.” The breeding objective in Australia is expressed as APR and in Canada it is LPI and in the US is TPI.

What can YOU do Today?

Before we go on to look at the financial aspect of this discussion, you should refer to the Genomic Evaluation Details which are available from CDN (Canadian Dairy Network) or from your breed association. In the CDN report there is a column that gives the percentage inbreeding (%ING) numbers for the Sire; Dam and MGS. In general it could be agreed that 0-8 is good; 8 to 10 is okay: 11 to 14 watch and 15 or more take action.

What is the Dollar Difference of Inbreeding?

Inbreeding affects profitability by adversely affecting traits related to fitness and production. Data from the US reported that the current cost of inbreeding over an average cow’s lifetime was US$24. For this study a conservative value of $5 per year was used as the economic value per 1% increase in inbreeding. “These results demonstrate that using GRM information, a 1% reduction in progeny inbreeding (valued at around $5 per cow) can be made with very little compromise in the overall breeding objective. These results and the availability of low-cost, low –density genotyping make it attractive to apply mating plans that use genomic information in commercial herds.”

By itself this economic benefit does not currently justify the investment in whole herd genotyping, if one considers that pedigree information is free and appears to do a pretty good job of controlling inbreeding, However, it may be economically worthwhile for dairy farmers to invest in whole-herd low-density genotyping in conjunction with other uses of genotyping. Examples could include confirming parentage, selecting the best heifer calves to keep as herd replacements, managing genetic defects, flushing and selling high-value pedigree stock. These researchers conclude: “Based on our calculations the value of genotyping to control inbreeding could be worth between $5 and $10 per cow.” You do the math.

THE BULLVINE BOTTOM LINE

So this is my untrained, non-scientific understanding of this single paper on a subject that is growing faster than gossip on a grapevine. Having said that, it is each dairy breeder’s job to be informed. Use your network to find out who has the best answers to this question because when it comes down to the affect of inbreeding on YOUR breeding bottom line it’s YOUR money!

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It’s in her genes…..

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Wednesday, May 16th, 2012

There is no question that strong maternal bloodlines are the foundation of any good breeding program. But what top female possesses the best bloodlines and what bloodlines are the ones to watch in the future? In order to determine this, we looked at the top GPTI, GLPI, Polled, and Red cows and heifers. The following is our analysis.

Top GTPI Cows

Leading the way is LADYS-MANOR PL SHAKIRA VG-85 2YR-USA is also a full sister to the #1 Genomic Sire in the breed, Ladys-Manor Shamrock. She and her full sister LADYS-MANOR PL SHANDRA-ET VG-85-2YR-USA, who is #4 on the list, are from the seventh generation bull mother, Ladys-Manor Ruby D Shawn. The most impressive sire stack on the list (#6) goes to SULLY PLANET MONTANA-ET whose sire stack of Planet x Shottle x Justice x BW Marshall leads the way. Montana is also the most genomically gifted on the list, just slightly edging out the extremely popular genomic bull mother Shakira and AMMON-PEACHEY SHAUNA-ET.

[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/05/GTPI-Cows.csv” icons=”true”]

Top Genomic LPI (GLPI) Cows

Planet daughters dominate the list occupying the top 17 spots and 23 of the top 25. Topping the list is COMESTAR LAUTAMIRE PLANET who is from the Laurie Sheik family. She combines a solid sire stack and genomic values with a maternal power that is the Laurie Sheik’s trademark. The most impressive sire stack on the list goes to the SULLY SHOTTLE MAY daughter SULLY PLANET 935-ET VG-86-2YR-CAN who combines Planet x Shottle x Oman x BW Marshall. When it comes to genomically gifted, none can top ALEXERIN OMAN 993. This Justice daughter has DGV LPI of +3395, which is almost 2000 LPI points higher than her parent average.

[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/05/Genomic-LPI-GLPI-Cow.csv” icons=”true”]

Top GTPI *RC and R&W Females USA

Setting the pace is KHW SHAMROCK ARALYN. This Shamrock daughter is from the popular RC bull dam KHW Goldwyn Aiko VG-89-USA and is among 6 Shamrock daughters to top the list. In fact, the top three spots are all trace back to Kamps-Hollow Altitude-ET EX-95-USA 2E DOM, who has had every bull she put into stud return to active service and is also the dam of the 2010 World Red Holstein Champion, KHW Regiment Apple-Red. This family has dominated the Red and White scene, demonstrating that they can get it done in the show ring as well as with genomics. The genomic leader of the list is CURR-VALE OBSERVER DELTA-ET. This Observer daughter traces back to Pineyvale Outside Apple another cow family that has it all, type, numbers and red factor. The strongest sire stack on the list belongs to MD-HARMONY SMRK CHRIS V1-E, Shamrock X Gold Chris X Shottle.
[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/05/GTPI-RC-and-RW-Females-USA.csv” icons=”true”]

Top GTPI Polled Females USA

There seems to be nothing more popular these days than polled genetics (read They’re Sold On Polled) and, with that, the demand for genetics from chart topper VER-HAGES TNT SABLE-P-ET could not be higher. This daughter from the Glen-Drummond Splendor family possesses an impressive sire stack – Shamrock x Lawn Boy x Lou – with strong genomic values. The only member of the list to surpass Sable-P for genomics is HICKORYMEA MANOMAN OPINE-P who also poses the most impressive sire stack on the: list Man-O-Man x Shottle x Bosco.
[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/05/GTPI-Polled-Females-USA.csv” icons=”true”]

Top Genomic Females in the U.S.

Shamrock daughters dominate the list with 18 daughters of the top 25 being sired by this outstanding son of Ladys-Manor Ruby D Shawn. Leading the way is a pair of Shamrock full sisters from the Genomic powerhouse herd De-Su. In the number one spot is DE-SU 1438-ET followed by DE-SU 1439-ET at #2 and not to be forgotten is DE-SU 1451-ET who is #6 on the list all from the popular genomic family Clear-Echo Hershl D Rac-822. In fact it’s 1451 that possesses the highest genomic values in the family. This family has proven to be genomic giants and, with these members topping the list, demand just continues to grow. Of interesting note is the 4 animals on the list owned by Select Sires (S-S-I SHAMROCK MENNA7392-ET, S-S-I SHAMROCK MAGIC7368-ET, S-S-I MOGUL MAYHEM 7963-ET, S-S-I SNOW MALENA 7514-ET) demonstrating this AI center’s strong desire to produce their own genetics (for more read Should A.I. Companies Own Females).
[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/05/Top-Genomic-Females-in-the-US.csv” icons=”true”]

Top GLPI Heifers

Similar to the US list, the CDN list is also topped by a pair of full sisters, Velthuis SG Snow Event and Velthuis S G Snow Evening. These Snowman daughters are from the Whittier-Farms Lead Mae family who has 6 daughters in the top 25. Event and Evening are from the extremely popular bull mother Calbrett Planet Eve VG-CAN-2YR. In fact, it’s interesting to note that 16 of the top 25 females come from three main families, (Lead Mae, Lila Z and Gypsy Grand). The Event and Evening sire stack of SNOWMAN X PLANET X SHOTTLE is also the highest on the list. With a DGV LPI of 4406, the split embryo sisters Event and Evening are also the highest genomic females on the list.
[csv2table source=”https://www.thebullvine.com/wp-content/uploads/2012/05/Top-GLPI-Heifers.csv” icons=”true”]

The Bullvine Bottom Line

No matter how you look at it, when marketing top females, it comes down to their genes. Whether you are looking at LPI or TPI, genomics has put the spotlight on the females that truly have the best genes.

For more information check out The Bullvine Bull Book or our Genetic Evaluation Resource Center.

What the Experts Won’t Tell You about the Future of the A.I. Industry

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Friday, April 27th, 2012

Having grown up working with the Canadian Association of Animal Breeders, to working directly with some of the largest A.I. centers in the world, to running our own genetic programs that had many top LPI cattle, I have had the opportunity to learn the semen sales and marketing world from a variety of perspectives. From this frontline view I have never seen as much change as the A. I. industry is now experiencing with Genomics. With all these changes, the question becomes “What does the future hold for the AI industry?”

Genetic Advantage

It used to be that every artificial insemination center could claim an advantage in a certain product offering. Semex would claim a type advantage that over the years converted to a longevity value, in order to appeal to the much larger commercial market, instead of just elite breeders looking for the next great show cattle. ABS global added product lines and partnerships such as Judges Choice to counter moves such as Semex’s and included strong type offering to their very commercial product line. Every AI center jockeyed back and forth to show how their genetic product offering was different. Even when they overlapped, they would claim greater reliability or stability based on the country or system of origin.

Then along came genomics and wiped all that out.

Today when you look at all the major A.I. centers products, you could take the name and stud code off and you would be hard pressed to notice any difference. They all try to offer a complete product line. Moreover, with the reliability, and ability to take the system or country of origin out of it, they all have pretty reliable product. This almost completely eliminates any genetic advantage that any A.I. center has.

It has been very interesting to watch companies like Select Sires take to owning top bloodlines in a big way (to read more check out Should A.I. Companies Own Females?). This may be the only way that A.I. companies can differentiate their genetic advantage. Buy owning the top females these genetics companies (at this point, they are no longer just an A.I. company), are able to develop distinct bloodlines that none of their competitors can have. This is only going to change more when breeders have full access to genomic information in 2013 and may start to sample and prove their own sires.

Think about it. I remember back when I was working with GenerVations, and Champion hit as #1 in Canada. We marketed the heck out of the fact that he was the best in Canada. We relied on the world’s confidence in the Canadian system to promote that this new, small A.I. center had a reliable product. We blasted that message around the world making sure everyone knew that GenerVations had the #1 in the world. Because we all knew that there was about a 2-3 year window before competitors would have their own Champion sons, or he would no longer be the top bull. Today we are looking at an even smaller window of opportunity. . With new genomics bulls coming out pretty much monthly, things can change in a heartbeat. The Select Sires program at least gives them 8 months advantage on the sires and total control over the dams (since they own them). This gives them the ability to offer their customers a distinct advantage by doing business with them. Some may look at it negatively and yet, from a purely business perspective, it makes total sense. In the end, it will look like a very shrewd investment in a market in which it so is hard to differentiate yourself.

Service vs. Price

Therefore, when you can no longer differentiate your company on product, it only leaves you two other options, service, and price. You are either going to become the Wal-Mart of the A.I. world or you are going to become Nordstroms’s. Both can exist in the same market place you just have to become extremely great at what makes you different.

If you want to become the Wal-Mart of the A.I. world, you are going to offer the lowest price for a very commercial product. This means you need to have your production facilities running super efficiently and your overhead at a bare minimum. This position plays extremely well to commercial producers who are looking for the lowest costs possible. For years, companies like ABS, Alta Genetics, and Select have battled very aggressively. Since most of these companies more or less were just selling a commodity, there really was not any brand loyalty. Since most large herds did their own insemination work, they eliminated the close link that is developed between producer and the A.I. center through the regular visits by the technicians doing the insemination work. While the major A.I. companies tried to lock in that connection again by offering mating programs and other services, since they all were pretty much the same and, often, not used by producers, they were only able to gain marginal difference. And like the Wal-Mart model, margins are tight and profits are slim.

Therefore, if you cannot compete on product and you cannot compete on price, that only leaves service. With the majority of the marketplace doing their own insemination, A.I. companies have to look outside the scope of traditional marketplace to provide services. While this has been the case for many years in the commercial marketplace, it is also fast becoming the case in the entire marketplace. While you may be able to get a slight premium when you have the #1 bull, otherwise you will live and die by the quality of service you offer your customers. We have already seen this happen. Many A.I. companies have gone to offering many non-genetic products in order to become a complete service organization, rather than just a supplier of genetics.

Also of interest, is how the roles of sales and sire analysts have also changed. While many have called the modern sire analyst a glorified tail hair puller, they are now becoming more of a breeding advisor mixed with a negotiation specialist. This is exactly what they have to do. They can provide insight to breeders about the daughters of the top mating sires and maybe a little insight that his proof will not tell you. Even more so, they are now the chief negotiator for their A.I. center. If I were a GM of an A.I. company, I would invest heavily in negotiation and relationship building training for these individuals. Realistically, unless you run a program like Select Sires, this will be your only way to get the top sires from many breeders.

The Bottom Line

Like most mature market places, there is little room for grey areas when it comes to the future of the A.I. industry and where the major A.I. companies position themselves. It will take strong action now either to develop very aggressive genetic programs like Select Sires has, or you will need to decide if you are going to be the lowest cost provider or offer the greatest service. And yes, I know there are many small micro A.I. companies that will be able to turn a profit. I get that, they are able to keep their overhead so low that they will be able to offer a niche product to small segments of the market place. However, when it comes to the big players, they need to ask themselves, “Am I going to get aggressive and develop distinct bloodlines?” “Are we going to be the lowest price provider?” Alternatively, “Are we going to become legendary for the quality of our service?” Anything that is a smorgasbord of these will only end in extinction in the end. Don’t think so? Look what happened to your local hardware store, when Home Depot moved in, or the independent grocer, when Wal-Mart put up one of their super centers in the same community. Where do you shop today? Who will be your provider tomorrow?

What do you think? Comment below our join the discussion on our facebook page.

Has Genomics Knocked Out Hot House Herds?

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Tuesday, March 27th, 2012

For years there has been an unspoken awareness that some herds appeared to be able to “work the genetic indexing system.” These herds clearly understood how genetic indexing systems work in their country and how to manipulate the composition of their herd in order to achieve the highest ranking possible for some top members of the herd. It was possible to pick these herds out, they had top females and even though they had many sons sampled out of them, seldom were able to produce a top ranking sire, especially for total merit. This scenario played out in all major countries that use the BLUP (Best Linear Unbiased Prediction) system. Fast forward to the top total merit rankings since genomic testing has become available. At first glance it appears there might be a lot less of those animals on the list. The question is: “Has genomics knocked out all of these animals from the top lists?”

How It Was Done In The Past

First it is necessary to understand what was happening in the past. Since indexing calculations are based on the variance compared to herd and genetic base, the greater the difference the greater the gain or loss in the result. Putting that into practice takes two areas: conformation and production evaluations. The following is a breakdown on how both were done.

Conformation

In order to get maximum results from their genetics programs, many top programs needed to have their top cattle score significantly higher than the other animals scored that same day. While many people deemed these herds “Hot Houses”, in reality they are just working the BLUP system to get maximum results. Since the calculations also took into account the genetics of the other animals scored, these “hot house” herds needed to have daughters of high type bulls that would score lower than the selected cattle that were typically sired by bulls with lesser conformation scores. For example, you have a low value cow sired by a +14 conformation sire that goes 79 points, and a high conformation cow sired by a +6 conformation sire that goes 86 points. This would provide the selected cow with the greatest difference over the expected value and have significant improvement in their EBV for conformation and thereby in their overall total merit.

It’s in these herds that you may have seen a “good group” and a “bad group” of the herd, with a corresponding difference in management and presentation of the groups. While it’s normal in any herd to have the high value or “family favorites” get some level of preferential treatment, these herds took it to a new level. While this sounds bad, in reality it was necessary in order to achieve top rankings. For the classifier visit the good group was show ready and the bad group was ready to head for beef. (Though if you read “Tom Byers: It’s Classified” you realize that this really does not make that big a difference for the professional classifier).

In contrast to the “hot house” herds who try to have a high herd average score (for example the average 2yr old score of 83+ points) find it very hard to get high indexing conformation females. With very little difference in scores from the top to bottom of the herd, there is less herd variance, contributing to a lowering of their overall rankings. Since these herds where not a cross section representation of the breed population and BLUP treats them as if there were, these cattle actually get somewhat penalized for being a member of a great herd.

In order to have maximum impact, herds wanting to have high index’s needed to have maximum within herd variance. This meant that they have to have a true cross section of the breed present in their herd, as opposed to just the best of the best, like many of these breeders would have liked. It’s also for these reasons why niche type sire sampling programs need to be used in all types of herds not just high conformation breeding programs.

Production

The story is not that different on the production side. Here the comparisons are for milk, fat and protein yields on a within test day basis. Adjustments are made for a cow’s age, lactation number, stage of lactation, month / season…etc.

In order to maximize the increase in production genetic evaluations, these “hot house” herds needed to have underperforming daughters of high production sires, that were being out produced by the selected females that were typically sired by more balanced sire who’s production index may not be as high. In Canada, this is where you would see females with very high (i.e. +200 and more) BCA deviations. Sometimes you would see deviations that were greater than even their herd average BCA. You ask yourself “How could one cow on the same feed, same treatment, same exact program, produce twice as much milk as another cow?” While it sounds unrealistic, it was necessary in order to gain maximum results. All breeders have seen cows that can out produce herd mates by 30, 40 even 50%, but when you see them doing more than double (100%) it raises questions in the minds of people with practical cow sense. Hence why some herds are stamped as “Hot House’s.”

How Genomics Has Changed Things

With the introduction of genomic evaluations in August 2009, the effects that any “hot house” efforts can have has been reduced in the genetic indexing systems. This is because for young cows in first or second lactation, the relative weighting for Direct Genomic Value (DGV) compared to traditional Estimated Breeding Values (EBV) is roughly 55:45 (Source: Canadian Dairy Network). What that means is that if a “hot house” cow would have had a 300 point jump from these types of efforts, they now would only see a 165 point jump. While it would still have an effect, genomics has greatly decreased the “hot house” effect. Remember that the female family members of each cow are being re-evaluated as well. Additionally those females formerly lower on the listings, but that were in herds where practices are normal, could now move up the genetic index rankings.

The other factor that Genomics has brought into play is that, if a particular animal is not gifted with the best genomics her parents had to offer, she will also see a significant drop. So let’s say that a cow has an EBV-PA of +2500 LPI or TPI, but her genomic panel comes back with a LPI or TPI value of +1500. That cow would see a drop of about 450 points. Dropping her to an LPI or TPI of +2050. This takes her from being near the top of the list to almost out of consideration. All this is outside the control of any on-farm practices. It’s for these reasons I am sure that some owners now get nervous when opening their genomic results letters. This single test can have the biggest effect on the genetic profitability of any cow. It can even have a greater effect than the classification. With GLPI’s and GTPI’s now over 60% reliable, adding animal performance information now has much less influence than in the past.

The Bullvine Bottom Line

The great news is that genetic indexes that contain animal genomic information are not as influenced by preferential treatment or herd variance as traditional genetic indexes are. Since genomic values are based on evaluations of thousands of cattle in many different herds, in many different environments, and in different countries, the ability of a “hot house” to greatly change results has been significantly diminished. That is not to say it has been totally removed. Remember that 45% of the new GLPI formula is still based on an animal’s performance compared to contemporaries. Therefore, these efforts will still have an effect. It is for these reasons that you see some previously prominent cows and cow families are now absent from the top female lists. Am I saying that these cattle may not be great investment? No, what I am saying is consider these factors when making your purchase decision. Do your homework before selecting, breeding, merchandising or buying. GLPI’s, GTPI’s and DVG’s will help you make more informed decisions, but remember they are just a tool.

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Archive for Genomics

1) Accuracy

2) Improvement Rates

3) Terminology

4) Inbreeding

5) Functional Traits

6) Feed Efficiency

7) Breeder Acceptance

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Presenter

Genomic Webinar Series

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Genomic Webinar Series

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Genomic Webinar Series

Strengths

Weaknesses

Opportunities

Threats

Where from here?

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Let’s hear about Enlight from Lindsey Worden

Worden Draws on Experience

Working to Shared Benefit

Excellent Uptake

Expanded Service

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Only Very Moderate Uptake – So Far

Known Benefits

Genomics Will Make the Future Brighter

Heifers:

Feed Efficiency:

Inbreeding:

Disease Resistance:

Reproduction:

Misconception:

In Another World

Will Genomic Testing Pay?

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The Polled Story

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TABLE 1 – Top Genomic Sires April 2011 to April 2014

TABLE 2 – Top Proven Sires April 2011 to April 2014

TABLE 3 – Comparison of Top Genomic and Proven Sires from April 2011 (April 2014 values)

TABLE 4 – Ranking of Top 20 Genomic and Top 20 Proven Sires from April 2011 in April 2014 values

TABLE 5 – Top 10 Proven Sires April 2014

TABLE 6 – Top 40 April 2014 Proven sires that were missed

TABLE 7 – Comparison of Top 20 Genomic Sires from April 2011 to Missed Sires

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Already Many Steps Too Far?

Epigenomics – What’s That?

So then – What is Nutrigenomics?

Expect Genetics to Play an Even Bigger Role in the Future

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Verification

Intensity of Use

Finding the Best

Which are the Future Parents

Health / Disease Resistance

Female Fertility

Mobility

Getting with the Program

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