Development And Application Of New Markers Of Y Chromosome Haplogroupsin Cattle

Chinese cattle hasrich genetic resources,and it is one of the important components of the world cattle breeds.According to the results of chromosome karyotype,exterior appearance,D-loop region and Cytb gene of mitochondrial DNA and Y-SNPs and Y-STRs,Chinese cattle can be divided into two origins: Bos tuarusand Bos indicus.According to the published Y-SNPs markers,cattle can be divided into three haplogroups: Bostaurus Y1,Y2 and Bos indicus Y3.A total of 4male samples representing 4 geographically differentcattle breeds in China(Wandong cattle,Mongolian cattle,Wannan cattle,and Tibetan cattle)were selected for whole-genome resequencing in this study,and at the same time,6male whole-genome resequencing data including Angus,Holstein,Brahman,Simmental,Mishima from Japanand Gir breeds were downloaded from Gen Bank.In order to identify the specific markers on Y chromosome,the Xd-degenerate regions of the Btau＿5.0.1 Y chromosome reference sequence(GCF＿000003205.7)was selected.Meanwhile usingthe Y chromosome reference sequence of one male Brahman and one male Simmental Y chromosome genome as the standard of Bos indicus and Bos taurus.Based on the traditional Y-SNPs(ZFY10 and UTY19)markers,7new Y-SNPs markerswere used to analyzethe paternal origin and migration routesof Chinese31 indigenouscattle breeds and a specialized beef cattle breed-Xia’nan cattle.The new results were as follows:(1)745 bovine single-copy specific SNPs on the male specific region of the Y chromosome were found,which can be used to analyze the paternal origin of Chinese cattle.(2)Seven new Y-SNPs markers(42385076,3172750,2962837,3617274,2619981,3616035 and 3616189)were designed from 745 bovine Y-SNPs,which can be further devided the Y chromosome haplogroups into Y1(European taurine),Y2a(Eurasian taurine),Y2b(East Asian taurine),Y3a(Chinese indicine)and Y3b(Indian indicine)subhaplogroups.(3)Using these7 new markers to study the polymorphism of Chinese cattle,the results showed that amongall the 756 male samples,330 taurinesamples were found,of which,19 belonged to Europeantaurine(Y1)and accounted for 5.8%;174 belonged to Eurasian taurine(Y2a)and accounted for 52.7%;137 belonged to East Asian taurine(Y2b)and accounted for41.5%.(4)Amongall the 756 male samples,426 zebusamples were found,of which,69 belonged to Indian indicine(Y3b)and accounted for 16.2%;357 belonged to Chinese indicine(Y3a)and accounted for 83.8%.The results showed that the Indianindicine(Y3b)accounted for 26.1%of the Yunnan-Guizhou Plateau samples and 28.6% of the Shigatse Humped cattle,which suggested that Yunnan-Guizhou Plateauand Shigatse area mightbe the two important places where the Indian indicineinfiltratedinto the local Chinese cattle.