Paternal origins of Chinese cattle

Summary To determine the genetic diversity and paternal origin of Chinese cattle, 302 males from 16Chinese native cattle breeds as well as 30 Holstein males and four Burma males as controlswere analysed using four Y-SNPs and two Y-STRs. In Chinese bulls, the taurine Y1 and Y2haplogroups and indicine Y3 haplogroup were detected in seven, 172 and 123 individualsrespectively, and these frequencies varied among the Chinese cattle breeds examined. Y2dominates in northern China (91.4%), and Y3 dominates in southern China (90.8%).Central China is an admixture zone, although Y2 predominates overall (72.0%). Thegeographical distributions of the Y2 and Y3 haplogroup frequencies revealed a pattern ofmale indicine introgression from south to north China. The three Y haplogroups werefurther classified into one Y1 haplotype, five Y2 haplotypes and one Y3 haplotype inChinese native bulls. Due to the interplay between taurine and indicine types, Chinese cattlerepresent an extensive reservoir of genetic diversity. The Y haplotype distribution of Chinesecattle exhibited a clear geographical structure, which is consistent with mtDNA, historicaland geographical information.Keywords native breeds, Y-SNP, Y-STR, haplotype, genetic diversityChina has rich cattle genetic resources, including 28identified indigenous cattle breeds and populations (Qiuet al. 1988). These cattle breeds have been divided intothree major groups on the basis of their geographicaldistribution, morphological characteristics and sex chromo-some polymorphisms: the northern group in northernChina, the central group in the central and lower areas ofthe Yellow River and the Huaihe River and the southerngroup in southern China (Qiu et al. 1988; Chen & Qiu1993). Chinese farmers traditionally valued cattle fortraction, but increasing demands for meat have promotedthe need for higher beef production in recent decades.Although Chinese cattle are known for their good meatquality, their low growth rate makes them uncompetitivewith the exotic beef breeds in the market (Chen et al. 1990).Previous genetic analyses indicate that Chinese cattlebreeds belong to both taurine and indicine lineages (Laiet al. 2006; Lei et al. 2006; Cai et al. 2007). Y chromosomemorphology and low-resolution Y microsatellite (Y-STR)data showed that northern Chinese cattle are of the taurinetype, whereas southern Chinese cattle are of the indicinetype, with both taurine and indicine types contributing tothe gene pool of cattle in central China (Chen & Qiu 1993;Cai et al. 2006; Xin et al. 2010).Y chromosome haplotype analysis has provided power-ful information about the origins and genetic structure ofcattle worldwide. G€otherstr €om et al. (2005) defined threecattle Y haplogroups (Y1 and Y2 in B. taurus and Y3 inB. indicus) using Y chromosome single nucleotide poly-morphisms (Y-SNPs). Recent studies using Y-STRs haverefined the paternal lineages within these three majorhaplogroups, displaying diverse distributions of haplotypediversity in African (Li et al. 2007; Pa´rez-Pardal et al.2010), Eurasian (Kantanen et al. 2009) and Europeancattle breeds (Edwards et al. 2011). Here, we extendprevious research on Y chromosome haplotype structure,genetic diversity and paternal origins of worldwide cattlebreeds of China.