Genetic Diversity And Origin Based On Y Chromosome Microsatellite And SNPS In Chinese Cattle

Cattle refer to all domestic cattle except for the buffalo and yak. In China, cattle are called yellow cattle, including Bos taurus and Bos indicus, whose ancestor is Bos primigenius. Animal geneticists are interested in the genetic diversity and origin and evolution of Chinese cattle. So far, the publications on genetic diversity and origin and evolution of Chinese cattle mainly based on on mitochondrial and autosomal DNA variations. Previous studies of Y-chromosomal variation only indentified Bos taurus and Bos indicus origins from Chinese cattle using Y-chromosome specific microsatellite markers. No paper was published based on Y-SNPs markers. The aim of our research was to investigate the Y-chromosome haplogroup patterns, frequencies, migration routes and paternal origin in Chinese 16 local cattle breeds, including HSK (Hazakh), ZS (Zaosheng), AX (Anxi), MG (Mongolian), JN (Jinnan), LX (Luxi), QC (Qinchuan), JX (Jiaxian Red), NY (Nanyang), XH (Xuanhan), JA (Ji'an), HN (Hainan), WN (Wannan), LZ (Leizhou), BH (Bohai) and ES (Enshi) with 284 male samples and 4 Burma male samples as control based on two bovine Y-STRs(INRA18 and BM861), four Y-SNPs markers (DDX3Y-7, ZFY-9, UTY-19 and ZFY-10), PCR-SSCP and sequencing methods. The results are as follows:1. Two bovine Y-STRs can be used to study the genetic diversity and paternal origin in Chinese cattleWe investigated the genetie diversity in 284 bulls of 16 Chinese local breeds using two special Y-STRs markers (INRA18 and BM861). INRA189 and BM861 markers were polymorphic with three alleles respectively. The allele size of INRA189 marker in Chinese cattle is 166 bp, 156 bp and 144 bp. Of which, the allele sizes of INRA189 marker in Bos indicus and Bos taurus of Chinese cattle are 156/144 bp and 166/156 bp, respectively. The allele size of BM861 marker is 187 bp, 169 bp and 167 bp. Of which, the allele sizes of INRA861 marker in Bos indicus and Bos taurus of Chinese cattle are 187/167 bp and 187/169 bp, respectively. These results showed that the two Y-STR markers can distinguish two distinct paternal origins of Bos taurus and Bos indicus in Chinese cattle breeds.2. Four bovine Y-SNPs can be used to study the genetic diversity and paternal origin of Chinese cattleThree (DDX3Y-7, ZFY-9 and ZFY-10) out of four Y-SNPs marker(sDDX3Y-7, ZFY-9, ZFY-10 and UTY-19)can distinguish Bos taurus and Bos indicus from Chinese cattle. UTY-19 marker can distinguish Bos taurus Y1 from Bos taurus Y2 haplotypes in Chinese cattle. However, only Y2 (Bos taurus) and Y3 (Bos indicus) haplogroups were detected in Chinese cattle. Interestingly, the Y1 haplogroup was not found in Chinese native cattle. These results showed that Chinese cattle originated from Y2 (Bos taurus) and Y3 (Bos indicus) paternal origins and not from Y1 (Bos taurus) paternal origin. The haplotype diversity varied among cattle breeds in China from 0 (Hazakh, Mongolian, Luxi, Xuanhan, Wannan and Hainan) to 0.473±0.003 in Qinchuan breed.3. There were two paternal origins with Y2 (Bos taurus) and Y3 (Bos indicus) in Chinese cattleChinese cattle had two distinct paternal origins with Y2 (Bos taurus) and Y3 (Bos indicus) based on Y-STR, Y-SNP and sequencing methods.Among the 284 Chinese bulls analyzed, the haplotype frequency of Bos taurus origin being 57% (162/284), was higher than that of Bos indicus origin being 43% (126/284). In Chinese northern cattle group, the haplotype frequency of Bos taurus origin was predominant with 98.3%, however, In Chinese southern cattle group, the haplotype frequency of Bos indicus origin was predominant with 76.1%. Cattle breeds from the central Chinese group were admixed from Bos taurus and Bos indicus, of which, the haplotype frequency of Bos taurus origin being 63.8%, was higher than that of Bos indicus origin being 36.2%.Chinese northern cattle group is almost the taurine (Y2) origin, whilst Chinese southern cattle group is mainly the indicine origin (Y3). The Y2 haplotype frequency of Chinese cattle decreased from North to South, and Y3 haplotype frequency increased from North to South, so the Central China became a hybrid zone of taurine (Y2) and indicine (Y3) cattle.