Genomics

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Archive for Genomics – Page 3

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.

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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!

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

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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?

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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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Should A.I. Companies Own Females?

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Friday, March 23rd, 2012

The debate is back! While Artificial Insemination companies have owned females for many years, with recent dominance by some AI breeding programs on the TOP GTPI list in the US and the upcoming ability for breeders to sample their own bulls, the debate is at the forefront again!

Lessons from the Past

Over the years there have actually been many examples, with mixed results when A.I. companies have owned their own female bloodlines.

AltaGenetics
Back in 2001 Alta Genetics caused considerable stir when they planned to take their embryo program and convert it into a 1000 elite females test herd to have sires sampled through 100 contracted progeny test herds. While the program had many supporters from the genetic advancement side, it was seen as very risky and ultimately was put on hold when Alta purchased Network Genetics. The herd was then dispersed to farms owned by Alta in Canada and Holland and in four independent herds in the U.S.
GenerVations
GenerVations is probably a great example of an A.I. program that has had a lot of success owning their own female bloodlines. Starting with Albert Cormier’s part ownership of Skys-The-Limit Claire where he was able to maximize profits from both sides, thanks to Champion. Continued by GenerVations part ownership of Lylehaven Lila Z, owning female bloodlines has been what enables GenerVations to compete on a global scale. Not being able to have a large sampling program, GenerVations has had to focus on potency rather than volume. Selecting on the very top bloodlines and putting all your eggs in a few baskets means GenerVations has to take a larger risk than the big A.I. companies. Owning top females has helped them manage the risk.
Genex CRI
The Genex CRI Genesis program has been around since 1989. While heavily focused on top Index cattle they have been able to achieve success on the female side with such cattle as MS Pride Plnt Tasket 788-ET who tops TPI and Lifetime Net Merit lists. On the male side, the Genex program has proven to be very stable in their bull program. The 54 Co-op prefix bulls averaged a mere $1 drop in Lifetime Net Merit (LNM) as they transitioned from genomic-only genetic evaluations in August 2010 to daughter-proven genetic evaluations in December 2011 (minimum of 40 daughters). The average change among the 1,879 bulls industry wide over the same time period was a $22 decrease.
St. Jacobs ABC
While the St. Jacobs ABC’s Judges Choice program has been around for many years marketed in partnership with ABS Global. They have more recently entered into the ownership of top female bloodlines with the purchase of Ashlyn, Hezbollah, and Barbara. Choosing to focus on established show cattle has meant that the Judges Choice program has been focused on young sire sales with sires achieve proven status being an added bonus.
Select Sires
Probably the A.I. Company making the biggest waves today is Select Sires. Select has been very aggressive in the ownership of top genomic females to the point that on the December Top 200 Genomic Female list they owned 18% of the top 50 new genomics heifers in the US. With Ladys-Manor PL Shamrock and others, Select Sires is investing heavily in ownership of top genomics females in order to produce the next generation of top TPI Sires.

The Genomic Game Changer

The biggest reason this issue is coming up again is because genomics is changing the prominence of industry sires with no daughter proof data, and virgin heifers are now in heavy demand as for contract matings. Genomics has deceased the risk to such a level that it can be very economically viable for these A.I. companies to invest in top bloodlines and increase their genetic advancement rate faster than their competition. By being able to control the matings on these top females and use top (often unproven ) genomic sires on these virgin heifers they will be able to greatly increase their rate of advancement over their competition, and in fact fast than even top breeders. That is because they will have access to their own top genomics young sires sooner. They can use them on contract matings far faster than any breeder can. This gives them a distinct competitive advantage over both other A.I. companies and over breeders.

The Question of Ownership

A.I. companies owning females seems to be a very touchy issue for many breeders. While many of these companies are perfectly within their rights legally, it comes down to a question of public perception. Many companies, such as Semex, have taken a very vocal position that they do not own females. Given that Semex is a member owned co-operative, it’s understandable that they do not want to be in competition with their breeders, many of whom are the top suppliers of sires to many A.I. companies worldwide. However, Select Sires is also a federation of nine farmer-owned-and-controlled cooperatives. You could not have two more extremely opposite positions from two very similarly owned companies.

The Bullvine Bottom Line

Genomics has changed the breeding world. However, it has also created a wild wild west environment where both breeders and A.I. companies are figuring out what the new world will look like. Will A.I. companies be nothing more than service companies that deliver genetics from many sources (much like a Wal-Mart) where they are more based on quality of service and customer experience than the genetics they have to offer? Will more and more top breeders try to increase their own profits and sample their own sires? (Watch www.thebullvine.com for articles on these issues coming shortly) The important thing to note is that some A.I. companies have taken early steps to control the source and supply top genetic animals to their customers. The world is changing and so will the inter-relationship between breeders and A.I. companies, in many cases they are no longer just a customer they are now a competitor.

What do you think? Leave your comments in the box below.

The Genomic Advancement Race – The Battle for Genetic Supremacy

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Tuesday, February 28th, 2012

In the race to have the next great sire, there comes a point where you have to ask have we taken it too far. Analysis performed by Holstein International of the 33 popular genomics bulls of 2009 showed that only one has managed to maintain his breeding value: O-Style. Even with those facts, why are so many A.I. companies now basing 70%, 80%, and 100% of their genetic programs on genomic sires?

Partly due to the “shortage” of new daughter proven sires of sons, and partly due to the increased confidence in genomics since it started in 2009 the percentage of breeding programs that are using genomic sires has increased from 40% to 50% on a global basis. Moreover, just like a great outlier sire, the difference between the AI’s is substantial. With Accelerated Genetics, Genex-CRI and Alta Genetics all sampling over 90% genomics sires.

So why are these studs putting so much weight in genomics? Do they know something the rest of us don’t? Have they just gone cuckoo?

In reality is actual goes back to the genetic advancement formula that has been around for many years.

Let’s take a close look at each piece of this equation and the effect genomics has.

Accuracy

The effect that genomics has on accuracy is very significant. According to CDN the average gain in accuracy in LPI due to Genomics is as follows:

Sub-Group for Holstein Breed	Average LPI Reliability (%)
Sub-Group for Holstein Breed	Traditional	Genomics	Gain	Direct Genomic Value (DGV) Weight
50K Young Bulls and Heifers (Born 2008-2011)	37	66	29	64%
3K Heifers (Born 2008-2011)	35	61	26	64%
Younger Cows in 1st or 2nd Lactation (50k)	54	70	16	56%
Foreign Cows with MACE in Canada	43	68	25	61%
1st Crop Proven Sires in Canada	85	89	11	54%
Foreign Sires with MACE in Canada	70	81	11	54%

Selection Intensity

In the past AI companies would have sample multiple sires from the same cross, and try multiple crosses to find out which one was the genetically gifted. That does not even take into account the need to sample from a larger portion of the top females to discover which ones where genetically gifted and which ones where “artificial” in their breeding values. With genomics, they can pre-screen these sires and crosses to see which ones will have the highest chance of producing the next top-selling sire and which ones did not get the best their parents had to offer.

By eliminating the need to sample such a large number of sires, allows the AI companies to focus on a more intense core group of sires, and push the limits on genetics advancement

Genetic Variability

This is one area than many breeders do not pay enough attention to. Certain traits, such as Milk Yield, Protein Yield, and stature are much more heritable than others (i.e. Rump and Feet & Legs). What this means is, if you spent all your time breeding for feet and legs, you will see less overall genetic gain than say focusing on production traits. That is why production sires will typically offer the greatest genetic gain, since most type traits have a much lower heritability. It’s also why breeders always need to be conscious of production when building your breeding program and don’t mate for low heritability traits.

The following is Holstein heritability estimates used for genetic evaluations in Canada

Production Traits

Milk Yield 43%
Fat Yield 34%
Protein Yield 40%
Fat Percentage 50%
Protein Percentage 50%

Functional Traits

Somatic Cell Score 27%
Lactation Persistency 40%
Herd Life 10%
Calving Ability 6%
Daughter Calving Ability 6%
Milking Speed 21%
Milking Temperament 13%
Daughter Fertility 7%

Major Type Traits

Conformation 26%
Rump 15%
Mammary System 25%
Dairy Strength 36%

Time

In order to cut down the genetic intervals many AI companies are now using genomic sires themselves as sires of sons. This means that there are sires of sons that don’t have any daughter information yet. The company taking this to the extreme is Alta Genetics. Their breeding program is made up by no less than 70% of genomic bulls that are sired by genomic bulls. The greater you can cut down the interval from the birth of the parent to the birth of the progeny the greater the average genetic gain per year.Yes, you will run the risk of sires that drop, but overall on a large breeding program you will come out ahead.

The Bullvine Bottom Line

Many AI companies, especially in North America, are pushing the edge with genomics to maximize annual genetic gain. While they will run the risk of a sire not turning out, or dropping significantly from his pre-proven prediction, when you look at the net result over the generations of their whole breeding program they will come out way ahead. By leveraging the effect Genomics has on accuracy, selection intensity, focusing on highly heritable traits, and making the interval between generations as low as possible, these studs stand the greatest chance of consistently producing the best genetics available.

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

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Not Sure Which Genomic Young Sire To Use?

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Friday, February 24th, 2012

If you are like many, this whole genomics thing can be very confusing. While it might be just simplest to pick the top five genomic young sires. Who knows what could happen. In order to get some clarity on just what young sires you should use we took a deeper look at the top 50 genomic young sires available in Canada and here is what we found.

GLPI vs Parent Average

In the past most would have just simply used the top parent average young sires and gone from there. It’s interesting to see that only one of the top GPA LPI sires (DE-SU PHOENIX 588-ET) would have even been considered a top LPI sire before genomics.

GPA LPI	PA-LPI
DE-SU PHOENIX 588-ET	GEN-I-BEQ LAVAMAN
GENERVATIONS LEXOR	COMESTAR LOBSTER
CABON FERNAND	COMESTAR LAUTAMARCUS
MISTY SPRINGS NUMBER ONE	DE-SU PHOENIX 588-ET
COOKIECUTTER HEFTY-ET	STE ODILE RIMOUSKI

Genomically Gifted

With DE-SU PHOENIX 588-ET jumping to the top of the list, we then wanted to see just who else has been genomically gifted with the best genes his parents have to offer. What we found was the following:

Sire	GPA LPI	PA – LPI	Difference	Direct Genomic Value
CABON FERNAND	3239	2492	747	3655
DE-SU ALTAROGERS-ET	2816	2159	657	3167
COOKIECUTTER HEFTY-ET	3211	2591	620	3211
DE-SU ALTAMELHOR-ET	3013	2413	600	3296
SHEEKNOLL ALTAVITTEK	2905	2307	598	3291

Bitch Slapped With the Ugly Stick

Since we took the time to see who was gifted we thought it would be equally important to see what bulls full-out of the ugly tree and hit every branch on the way down. Here is what we found:

Sire	GPA LPI	PA LPI	Difference	Direct Genomic Value
COMESTAR LAUTAMARCUS	2879	3020	-141	2806
GIBBS M-M DENALLI-ET	2913	2909	4	2847
COMESTAR LOBSTER	3048	3020	28	3094
GEN-I-BEQ LAVAMAN	3116	3070	46	3317
GENERVATIONS LINGO	2938	2888	50	2899

(Please note: this does not mean they are totally ugly they are just not as pretty as the could have been)

When in Doubt Go To Sire Stack

One thing I have learned from your tried and true breeders, is whether you are breeding for index or showing, nothing beats a good sire stack. With that in mind we prepared a 4 generation sire stack of each sire and here is the cream of the crop.

Sire	Sire Stack	Sire Stack Index
DE-SU PIERRE 649-ET	Planet x Bolton x Shottle x Justice	2638
PIROLO SOLEMIO-ET	Man-O-Man x Goldwyn x Justice x Jacko Besn	2617
GENERVATIONS ENSIGN	Man-O-Man x Baxter x Shottle x Justice	2582
ESPOIR	Man-O-Man x Goldwyn x Champion x Jesther	2573
GALLAIS FEELING	Man-O-Man x Bolton x Shottle x Trent	2565

Girl Power

The following are the bulls that are getting it done from a strong female (dam) side of their pedigree.

Sire	GPA LPI	Sire Stack Index	Difference
MAPEL WOOD BREWMASTER	3046	1955	1091
MISTY SPRINGS SUPERSONIC	2827	1760	1067
DE-SU ALTAMELHOR-ET	3013	2084	929
LESPEREE GLOBAL	3009	2099	910
MISTY SPRINGS NUMBER ONE	3220	2331	889

The Bottom Line

Depending on your propensity for risk you can take those sires that are the extreme genomically, such as CABON FERNAND or DE-SU ALTAROGERS-ET, or you can go for the sire with great blood lines, such as DE-SU PIERRE 649-ET and PIROLO SOLEMIO-ET. But as my wife tells me every day, behind every good man is a great woman, so maybe you try MAPEL WOOD BREWMASTER or MISTY SPRINGS SUPERSONIC.

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

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Archive for Genomics – Page 3

All-American’s

All-Canadian’s

The Bullvine Bottom Line

Other posts you might like:

The Bottom Line

Other posts you might like:

What You Don’t Know Can Hurt You

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

Strategies to Control the Rate of Inbreeding

The Good News Is….

What did they do?

What can YOU do Today?

What is the Dollar Difference of Inbreeding?

THE BULLVINE BOTTOM LINE

Other posts you might like:

Top GTPI Cows

Top Genomic LPI (GLPI) Cows

Top GTPI *RC and R&W Females USA

Top GTPI Polled Females USA

Top Genomic Females in the U.S.

Top GLPI Heifers

The Bullvine Bottom Line

Other posts you might like:

Genetic Advantage

Service vs. Price

The Bottom Line

Other posts you might like:

How It Was Done In The Past

Conformation

Production

How Genomics Has Changed Things

The Bullvine Bottom Line

Other posts you might like:

Lessons from the Past

The Genomic Game Changer

The Question of Ownership

The Bullvine Bottom Line

Other posts you might like:

Accuracy

Selection Intensity

Genetic Variability

Time

The Bullvine Bottom Line

Other posts you might like:

GLPI vs Parent Average

Genomically Gifted

Bitch Slapped With the Ugly Stick

When in Doubt Go To Sire Stack

Girl Power

The Bottom Line

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