Study on Paternal Genetic Diversity of Cattle (Bos taurus) in Qinghai-Tibet Plateau
YAN Hui-Xuan1, YAO Ting-Ting1, CAO Yi-Fan1, LI Xin-Yi1, CIREN Luo-Bu2, SUOLANG Qu-Ji2, NIMA Cang-Jue2, DANZENG Luo-Sang2, SILANG Wang-Mu2, LEI Chu-Zhao1, BASANG Zhu-Zha2,*, CHEN Ning-Bo1,*
1 College of Animal Science and Technology/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling 712100, China; 2 Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
Abstract：The Qinghai-Tibet plateau (QTP) cattle (Bos taurus) is a rare local genetic resource of cattle in China plateau region due to its unique geographical environment and numerous breeds. To analyze the paternal genetic diversity and phylogenetic relationship of QTP cattle, this study integrated the whole genome re-sequencing data of 77 male QTP cattle and scanned the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in the single-copy gene region of the X-degenerate region of the Y chromosome. A total of 2 672 Y-SNPs and 712 Y-INDELs were identified. Based on Y-SNPs, 30 Y-SNPs haplotypes of QTP cattle were defined in this study, among which hap10 was the dominant haplotype, accounting for 16.88%. It was found that QTP cattle belonged to 6 Y haplogroups/sub-haplogroups (Y1, Y2A, Y2B, Y3A2, Y3B1 and Y3B4), among which Y2B (59.74%) was the main haplogroup, individuals of QTP cattle were mainly concentrated in the Y2B haplogroup. The analysis based on Y-INDELs was also consistent with Y-SNPs. The haplotype diversity of Y-SNPs in the QTP cattle population was 0.973±0.006, and the nucleotide diversity was 0.237±0.046. This study confirmed that QTP cattle had 6 paternal origins, including 3 taurine cattle (B. taurus taurus) and 3 indicine cattle (B. taurus indicus) paternal origins, clarified the high paternal genetic diversity of QTP cattle. This study provides a theoretical basis for the protection, development and utilization of QTP cattle.
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