Abstract
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.
Highlights
A reference genome is a DNA database, assembled as a representative of species’ nucleotide sequence
The post-filtration variants were visualised using the Venn diagram (Fig 2) showing the numbers of SNPs common between all possible breed combinations. 23,113 of filtered SNPs were common to each breed, which indicated a polymorphism characteristic to Domino lineage, but monomorphic in the other breeds
Considering pairwise breed comparisons, the highest numbers of SNPs specific only for a combination of two breeds was identified for Jersey-Fleckvieh (19,060) and for Jersey-Brown Swiss (18,006) combinations, the latter may have been expected provided phenotypic similarities between both breeds as well as a similar milk production performance
Summary
A reference genome is a DNA database, assembled as a representative of species’ nucleotide sequence. It is based on genomic sequences from many individuals and, as a result, it is universal for the species. We must be aware of the fact that it represents genetic diversity averaged over the polymorphisms represented in DNA of donor(s) genomes. It should be borne in mind that most species are represented by distinctive breeds with. Breed-specific single nucleotide polymorphisms in Bos taurus
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