Effects of Functional Polymorphisms on Beef Carcass Merit
To develop a resource to identify polymorphisms present in common beef cattle breeds, and relate those polymorphisms to phenotypic differences, low-coverage genomic sequence was obtained on 186 purebred bulls from 15 predominant breeds in the United States, and 84 crossbred sons of these bulls. These bulls were influential in the USMARC Germplasm evaluation population (GPE), enabling sequence-derived genotypes to be imputed throughout the population of individuals genotyped with the BovineHD (HD; n=1027) and BovineSNP50 (n=8697) platforms. Variants detected from these sequences were classified according to predicted effect on gene function, with 4,699 predicted to cause a loss of gene function (LOF); 66,484 non-synonymous (NS) SNP causing an amino acid change in the protein produced by a gene, and 59,092 which may have a role in gene regulation (REG), occurring in annotated non-coding RNA or regions immediately surrounding a gene. Imputed genotypes of 685 purebred genotyped grandsires in the GPE population (18 to 74 bulls per breed) were used to represent each breed to assess diversity and determine breed effects on carcass merit. Relative genetic distances between breeds were consistent regardless of the set of genotypes considered. Brahman was furthest from any other breed, and Hereford the most distant from any other taurine breed. Similar distances were obtained using HD and ND SNP. The mean between-breed distance estimated with REG variants was about 10% higher than HD or NS, and distances using LOF variants were about 30% lower. Heritability estimates from GBLUP considering records of 5990 genotyped carcasses and treating breeds as genetic groups, ranged from 0.49 for ribeye area to 0.59 for marbling score when using only HD genotypes. Similar estimates were obtained in independent analyses using NS and REG, but the LOF estimates were lower, between 0.29 and 0.32. In four-component analyses with different genomic relationship matrices for HD, NS, REG and LOF, 68% to 76% of additive variance was attributed to HD, and 2% or less to LOF. Contributions of both NS and REG were between 10% and 16% for carcass weight, marbling and fat thickness. For ribeye area, the REG component was 31% of additive variance, and NS was nil. The GBLUP breed solutions were consistent with breed differences estimated in previous analyses. USDA is an equal opportunity employer and provider.
Keywords: beef cattle, genomic prediction, functional polymorphisms