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.

中文翻译：

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日本黑牛的牛单核苷酸多态性阵列中掩埋的SNP的基因型和等位基因频率。

单核苷酸多态性（SNP）阵列被广泛用于牛育种的遗传和基因组分析。因此，从SNP阵列获得的数据已在全国范围内大规模积累。商业SNP阵列在染色体上/基因组上的位置上包含大量未分配的SNP。这些SNP在随后的分析中被排除在外。值得注意的是，未分配位置的SNP或“埋没的SNP”包括一些与遗传疾病相关的标记。在这项研究中，我们使用基本的局部比对搜索工具针对周围序列确定了掩埋SNP的位置，并根据基因组位置表征了动物在线孟德尔遗传中SNP与遗传疾病之间的关系。我们确定了285个埋藏的SNP在基因组上的位置，并调查了5955例日本黑牛中这些SNP的基因型和等位基因频率。在人群中发现了11个与遗传病相关的SNP，其中包含5个埋藏的SNP，其风险等位基因频率范围为0.00008396至0.46。这些结果表明，牛SNP阵列中的埋入SNP可用于从日本黑牛的大规模累积SNP基因型数据中鉴定与遗传疾病的关联。