Population genetic copy number variation of CHKB, KLF6, GPC1 and CHRM3 genes in Chinese domestic yak (Bos grunniens) breeds

Abstract Single nucleotide polymorphisms (SNPs) are common markers used for population genetics studies. Recently, copy number variations (CNVs) have been used to study genetic and phenotypic diversity within and among populations. Therefore, studies of the genetics of CNVs are important in the context of understanding evolutionary changes and genomic selection based upon genetic and phenotypic variation. The aim of this study was to analyse the distribution of the choline kinase beta (CHKB), Krüpple-like factor 6 (KLF6), glypican 1(GPC1) and cholinergic receptor muscarinic 3 (CHRM3) genes in five representative Chinese domestic yak breeds. The data generated by qPCR was transformed into log2 ratio and analysed using GraphPad (PRISM). The results show that the CNVs of CHKB, KLF6, and GPC1 genes presented more copy number losses in Tianzhu, Gannan and Plateau yak populations compared with the Datong and polled yak having relatively more copy number gains. However, the CHRM3 CNV showed more copy number gains in five yak populations. Therefore, these results indicate that there are relatively more copy number losses (deletion) in the yak populations; supporting the hypothesis that log2 ratio is more powerful at detecting loss than gain in copy number types. Taken together, these data provide information on the application genome CNVs in population genetics and suggest that the CNVs of the genes could exert a significant effect on phenotypic differences in yak populations.