Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle

Abstract

Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position‐unassigned SNPs, or “buried SNPs” include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.

Online Mendelian Inheritance in Animals (OMIA): a record of advances in animal genetics, freely available on the Internet for 25 years

“…Looking to the future, OMIA has considerable potential to help in resolving ‘buried SNPs’ (Sasaki et al . 2019) and variants of unknown significance. In the latter case, for example, it would be feasible for OMIA to include the relevant information about the 5667 single‐locus human disorders documented in OMIM, any one of which could occur in any animal species, and for which, currently, only a small fraction (no more than 6%) have been reported in any OMIA species.…”

Estimated Breeding Values of Aberdeen-Angus Cattle Breed

“…Such genes are usually called target genes and are considered DNA markers of breeding traits of agricultural animals. The introduction of these markers into breeding work makes it possible to use information about the hereditary potential of the selected animals and increases the accuracy of assessment and selection efficiency (Sasaki et al, 2019;Tsuchida et al, 2010).…”