Study On The Paternal Genetic Diversity And Origin Of The Yak(Bos Grunniens)

Yak?Bos grunniens?is a bovine species that distributed on the Qinghai-Tibetan Plateau and its adjacent high mountains and sub-alpine regions.The genetic diversity and origin of yak is one of the hot issues of yak research in recent years.Currently,studies on the genetic diversity and origin of yak mostly came from the variation analysis of mitochondrial DNA and autosomes,while the research based on Y chromosome sequence variation?i.e.,paternal genetic information?is relatively few.In this study,Y-SNP and Y-STR markers in yak were screened by direct sequencing and microsatellite?STR?genotyping techniques.The polymorphic Y-SNP and Y-STR markers were combined to determine the yak Y-chromosome haplotypes.A total of 682 male domestic yaks from 11 indigenous breeds?i.e.,Jiulong,Maiwa,Niangya,Sibu,Pali,Gaoyuan,Huanhu,Gannan,Bazhou,Zhongdian and Tianzhu yak breeds?,one improved breed?i.e.,Datong yak breed?and three populations?i.e.,Taxian,Xueduo and Leiwuqi yak populations?,and eight male wild yaks were analyzed.The Y chromosome variations,paternal genetic diversity,phylogeographic structure,genetic differentiation,clustering relationship,molecular variance and phylogenetic relationship of yak were studied.The results showed that:1)Based on the new sequencing data of previously analyzed five yak Y chromosome markers?i.e.,SRY4,USP9Y,UTY19,AMELY3 and OFD1Y10?,four new Y-SNPs in OFD1Y10 marker?i.e.,g.569A>C,g.578A>C,g.608G>T and g.653G>C?were identified for the first time on the basis of confirming six previously reported Y-SNPs.Meanwhile,the male specificity and polymorphism of 40 cattle Y-STR markers were detected in yak,it was found that 13 markers were Y chromosome non-specific markers,five markers were not amplified products,13 markers were Y chromosome-specific markers with lower amplification efficiency and nine markers were Y chromosome-specific markers with higher amplification efficiency.However,only INRA189 was polymorphic in above nine yak Y chromosome-specific markers with higher amplification efficiency and owned six alleles of139,149,155,157,159 and 161 bp.The results indicated that the six markers?i.e.,SRY4,USP9Y,UTY19,AMELY3,OFD1Y10 and INRA189?have the male specificity and abundant polymorphism in yak,which can be used for yak paternal genetic analysis.Overall,14Y-haplotypes?i.e.,H1Y1^H10Y1 and H11Y2^H14Y2?were identified by combining 10Y-SNPs with the six alleles from INRA189 marker.2)There is no obvious phylogeographic structure among domestic yak breeds/populations.The frequencies and distributions of 14 haplotypes were different among yak breeds/populations.Two kinds of haplogroups or lineages?i.e.,Y1 and Y2?identified by14 haplotypes had not correlation with each yak breed/population,nor with the geographical distributions of each breed/population.Except that Zhongdian yak breed belongs to Y1lineage,the remaining breeds/populations all contain Y1 and Y2 lineages.3)The paternal genetic diversity of domestic and wild yaks was relatively rich and the total haplotype diversity?Hd?was 0.6964±0.0141.The paternal genetic diversity of wild yaks?Hd=0.8214±0.1007?was higher than that of domestic yaks?Hd=0.6946±0.0143?.Among domestic yak breeds/populations analyzed,the paternal genetic diversity of Bazhou breed was the highest?Hd=0.7273±0.0667?,and that of Pali breed was the lowest?Hd=0.1174±0.0732?.From the provincial/regional distribution of domestic yaks in China,Qinghai,Gansu,Sichuan,Tibet,Xinjiang and Yunnan each have 12,6,6,5,7 and 2 Y chromosome haplotypes,and their paternal genetic diversity is in turn Xinjiang,Gansu,Sichuan,Tibet,Qinghai and Yunnan.A total of six private haplotypes were detected in some domestic yak breeds including two private haplotypes?i.e.,H4Y1 and H5Y1?in Gaoyuan breed,two?i.e.,H8Y1 and H14Y2?in Datong breed in Qinghai Province,one?i.e.,H13Y2?in Tianzhu breed in Gansu Province and one?i.e.,H7Y1?in Maiwa breed in Sichuan Province.According to the numbers of total haplotypes and private haplotypes,combined with archaeological,geological and mitochondrial DNA studies on yaks,it is speculated that Qinghai Province may be the origin and/or domestication locale for the yak.4)The average fixation indices(F_ST)among domestic yak breeds/populations was0.216±0.039,indicating that the degree of differentiation between domestic yak breeds/populations was higher.Most of yak breeds/populations reached the level of moderate and above differentiation with other breeds/populations,while only a few breeds/populations had a weak differentiation with other breeds/populations.Among domestic yak breeds/populations,only Pali breed and Taxian population had significant differentiation with other yak breeds/populations?P<0.05?.The average F_ST value between wild yak and domestic yak was 0.178±0.051,indicating that the differentiation degree between wild yak and domestic yak was also higher.5)79.67%of the total variation in domestic yak came from within breeds/populations,15.26%from between breeds/populations within geographical Province/region and only5.07%of the total variation components were from provincial/regional difference.This indicated that the difference between geographical provinces/regions was not the main reason for the differentiation of domestic yak breeds/populations,but the main reason for differentiation were from within breeds/populations and between breeds/populations.6)Multidimensional scale?MDS?analysis showed that 16 Chinese yak breeds/populations could obviously be clustered into five groups,of which Pali breed and Taxian population clearly separated from other yak breeds/populations and classified into two groups;Niangya,Sibu,Tianzhu breeds and wild yak clustered into one group;Zhongdian and Gannan breeds clustered into one group;and the remaining yak breeds/populations including Maiwa,Jiulong,Bazhou,Leiwuqi,Gaoyuan,Huanhu,Datong and Xueduo clustered into another group.7)14 yak Y-haplotypes could be divided into two distinct haplogroups/lineages?i.e.,Y1and Y2?,suggesting that the yak had two paternal lineages with two paternal origins.H1Y1and H11Y2,may be the original haplotypes in the two lineages,were in the central position of the two lineages with other haplotypes around them in the network analysis.Four haplotypes?i.e.,H1Y1,H6Y1,H9Y1 and H11Y2?,which fell into two Y chromosome lineages,were shared by wild yak and domestic yak.The result indicated that the appearance of two paternal lineages should occur before the domestication of domestic yak.These studies are the first reports in yak research,which will provide genetic evidence for comprehensively understanding the paternal genetic diversity,population structure,differentiation,origin,classification and phylogenetics of yak.At the same time,it has important theoretical and practical significance for early identification,introduction and allocation of yak bulls and the breeding of new yak breed.