Developing an Efficient Reduced SNP panel for Low-Cost Genotyping in Beef Cattle

High-density SNP chip panels such as Illumina BovineSNP50 (50K) are still price prohibitive for many applications in beef cattle such as selection of replacement heifers on commercial farms. The objective of this study was to develop a low-density low-cost reduced SNP panel (RP) that could capture most of the predictive ability of a 50K panel for 13 important traits (birth, weaning, yearling and carcass weights; calving ease direct and maternal; fat thickness; marbling; milk; post-weaning average daily gain; ribeye muscle area; heifer pregnancy rate and stayability) in beef cattle. More than 15,000 animals from six cattle breeds (Black Angus, Gelbvieh, Hereford, Limousin, Red Angus and Simmental) genotyped with 50K were used to select 1,029 markers highly associated with target traits. Accuracies of direct genomic breeding values (DGV) were calculated within each of the six cattle breeds and for 3 independent validation populations using either 50K or RP. Accuracies of DGV obtained from RP were comparable with those obtained from 50K (>80% predictive ability of 50K) while the size of RP is  <2% of 50K. Including some additional randomly spaced markers (about 2,300 markers in total) improved the accuracies of DGV 6-9% further. These results offer promise for a low-cost low-density genotyping product in beef cattle.