The purpose of this research was to determine whether or not utilizing a cow’s parents’ genotypes for imputing single nucleotide polymorphisms (SNPs) affected the calculation of genomic inbreeding coefficients. The imputation genotypes of 68,127 Italian Holstein dairy cows were examined using a variety of genotyping methods. Genomic inbreeding coefficients were calculated using four PLINK v1.9 estimators, two genomic relationship matrix (grm)-based estimators, and one run of homozygosity (ROH; FROH) estimator. When at least one of the parents was genotyped, the findings revealed consistently high genomic inbreeding coefficients. However, skewed genomic inbreeding coefficients were seen in cows genotyped with MD SNP panels whose SNPs were poorly represented in the chosen imputation SNP data set and did not have their parents genotyped, in contrast to what was predicted based on actual genotype data. For cows genotyped with MD, the estimators Fhat1, Fhat2, and Fgrm gave greater genomic inbreeding coefficients, even when both parents and the maternal grandsire were genotyped. Overall, FROH was the strongest estimator, followed by F and Fhat3.
Word genome single nucleotide polymorphisms (SNPs) are frequently employed in cattle breeding programs throughout the globe to estimate genomic breeding values, as well as genome-wide association studies, population genetics, and determining realized homozygosity and inbreeding. Breeding businesses may cut genotyping costs by genotyping a small number of core animals with HD SNP panels and a large number of LD/HD animals, then projecting them to HD genotypes or a set of predetermined SNPs.
Imputation success in dairy cattle breeding is determined by three major factors: the relationship between core animals genotyped in HD and those to be imputed from LD/MD to HD, the distribution along the genome and the number of SNPs in the LD/MD panels, and the linkage disequilibrium between SNPs in the LD/MD and HD. Although there are strategies for achieving high imputation accuracy, variability in genomic estimations based on imputed SNP data is to be anticipated.
This work expands on recent findings on whole genome imputation SNP-based genomic inbreeding coefficients (FSNP) in dairy cattle. Extreme genomic inbreeding coefficients might be the outcome of imputation, particularly in cows genotyped with MD SNP panels with just a handful of their SNPs included in the final imputation SNP data. The goal of this research was to see whether significant genomic inbreeding coefficients in cows genotyped with MD SNP panels that had few of their SNPs included in the final imputation SNP data might be attributed to not having their parents genotyped during the imputation process.
Whole genome SNP data is frequently imputed in dairy cow breeding, which may significantly decrease genotyping costs. However, there may be cows with incorrect imputation owing to the lack of genotyped parents. The findings revealed that whole genome SNP inbreeding coefficients might be skewed for cows who did not have parents or maternal grandparents genotyped and were also genotyped with an SNP panel with low representation of its SNPs on the chosen imputation SNP data.
