Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes

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 D 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.