Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland.
Institute of Animal Breeding, Balice, Poland.
PLoS One. 2018 Jun 1;13(6):e0198419. doi: 10.1371/journal.pone.0198419. eCollection 2018.
In Bos taurus the universality of the reference genome is biased towards genetic variation represented by only two related individuals representing the same Hereford breed. Therefore, results of genetic analyses based on this reference may not be reliable. The 1000 Bull Genomes resource allows for identification of breed-specific polymorphisms and for the construction of breed-specific reference genomes. Whole-genome sequences or 936 bulls allowed us to construct seven breed specific reference genomes of Bos taurus for Angus, Brown Swiss, Fleckvieh, Hereford, Jersey, Limousin and Simmental. In order to identify breed-specific variants all detected SNPs were filtered within-breed to satisfy criteria of the number of missing genotypes not higher than 7% and the alternative allele frequency equal to unity. The highest number of breed-specific SNPs was identified for Jersey (130,070) and the lowest-for the Simmental breed (197). Such breed-specific polymorphisms were annotated to coding regions overlapping with 78 genes in Angus, 140 in Brown Swiss, 132 in Fleckvieh, 100 in Hereford, 643 in Jersey, 10 in Limousin and no genes in Simmental. For most of the breeds, the majority of breed-specific variants from coding regions was synonymous. However, most of Fleckvieh-specific and Hereford-specific polymorphisms were missense mutations. Since the identified variants are characteristic for the analysed breeds, they form the basis of phenotypic differences observed between them, which result from different breeding programmes. Breed-specific reference genomes can enhance the accuracy of SNP driven inferences such as Genome-wide Association Studies or SNP genotype imputation.
在牛属中，参考基因组的普遍性偏向于仅由两个代表相同海弗德品种的相关个体所代表的遗传变异。因此，基于该参考基因组的遗传分析结果可能不可靠。1000 头公牛基因组资源允许鉴定品种特异性多态性，并构建品种特异性参考基因组。全基因组序列或 936 头公牛允许我们构建了七个牛属的品种特异性参考基因组，包括安格斯牛、瑞士褐牛、弗莱维赫牛、海弗德牛、泽西牛、利木赞牛和西门塔尔牛。为了鉴定品种特异性变体，所有检测到的 SNP 都在品种内进行过滤，以满足缺失基因型数不高于 7%且替代等位基因频率等于 1 的标准。泽西牛（130070 个）的品种特异性 SNP 数量最多，西门塔尔牛（197 个）的数量最少。这些品种特异性多态性被注释到与安格斯牛的 78 个基因、瑞士褐牛的 140 个基因、弗莱维赫牛的 132 个基因、海弗德牛的 100 个基因、泽西牛的 643 个基因、利木赞牛的 10 个基因以及西门塔尔牛的基因重叠的编码区域。对于大多数品种来说，来自编码区域的大多数品种特异性变体都是同义突变。然而，大多数弗莱维赫牛特异性和海弗德牛特异性多态性是错义突变。由于所鉴定的变体是分析品种的特征，它们构成了它们之间观察到的表型差异的基础，这是由于不同的繁殖计划造成的。品种特异性参考基因组可以提高 SNP 驱动推断的准确性，例如全基因组关联研究或 SNP 基因型推断。
