Development of a custom SNP chip for dairy and beef cattle breeding, parentage and research

Abstract

Genomics is currently being utilized for genetic evaluations, parentage verification and screening for lethal recessives, congenital disorders and other mutations with large effects on performance in cattle populations. However, many of these analyses are routinely undertaken independently and on different platforms. The objective of the current paper is to describe the development of a low cost custom genotyping panel to service all of these requirements for both dairy and beef cattle breeding industries. In total, 9,973 variants were successfully added to the commercially available Illumina low density genotyping platform (6,909 SNPs) and included 5,500 SNPs to aid imputation to high density genotypes, 2,176 SNPs to facilitate imputation to microsatellite genotypes, 424 variants for major gene effects and 1,873 variants of research interest. A total of 9,852 cattle were genotyped between March to August 2013 with a median animal call rate of 0.989 and < 5% of animals genotyped below 0.95. Illumina SNP call rates, i.e. present on the LD, 50K or HD panels, were high with over 99.4% of SNPs with call rates ≥ 0.95. Non Illumina SNPs, i.e. novel to an Illumina platform, had lower SNP call rates with 87.6% at ≥ 0.95. For parentage verification, for the 2,891 cattle with sires without SNP genotypes and requiring imputation to microsatellite genotypes the imputation accuracy was 96%. Carriers of lethal recessive conditions, brachyspina and complex vertebral malformation, were detected in the Holstein-Friesian population at 2% and 4%, respectively. In addition, congenital disorders citrullinaemia, osteopetrosis and syndactyly were identified at low frequencies (< 1%). Variants in the Myostatin gene, nt821, F94L and Q204X were segregating in Angus, Belgian Blue, Charolais, Limousine and Simmental populations. Development of the custom genotyping platform servicing these requirements will provide a valuable ‘one-step’ tool to service current and, due to its ongoing development, future needs of both dairy and beef cattle industries.