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Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle
Author(s) -
Sasaki Shinji,
Muraki Eiji,
Inoue Yoshinobu,
Suezawa Ryouhei,
Nikadori Hideki,
Yoshida Yuuichi,
Nariai Shouta,
Hideshima Ryoya,
Moriwaki Shiyunsuke,
Nakashima Ryotaro,
Uchiyama Katsuo,
Yoshinari Kanako,
Takeda Masayuki,
Kojima Takatoshi
Publication year - 2019
Publication title -
animal science journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.606
H-Index - 38
eISSN - 1740-0929
pISSN - 1344-3941
DOI - 10.1111/asj.13293
Subject(s) - single nucleotide polymorphism , genetics , biology , snp , genotype , snp genotyping , tag snp , allele frequency , molecular inversion probe , allele , snp array , mendelian inheritance , population , gene , medicine , environmental health
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.