Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6–49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.

BackgroundChina exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K).ResultsIn principal component analysis (PCA) and neighbour-joining (NJ) tree analysis, samples of the same breeds were grouped together, leading to clear separation from other breeds. And Chinese indigenous cattle were clustered into two groups of southern and northern breeds, originated from Asian Bos indicus lineage and Eurasian Bos taurus lineage, respectively. In STRUCTURE K = 2, a clear transition occurred from the northern breeds to the southern breeds. Additionally, the northern breeds contained a smaller Eurasian taurine (62.5%) descent proportion than that reported previously (more than 90%). In STRUCTURE K = 3, a distinct descent was detected in the southern Chinese breeds, which could reflect a long-term selection history of Chinese indigenous cattle. The results from TreeMix and f3 statistic provided the evidence of an admixture history between southern breeds and northern breeds.ConclusionsConsistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0705-9) contains supplementary material, which is available to authorized users.

Background The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity is yet to be fully discovered. Results In this study, we describe the demographic events and selective pressures of buffalo by analyzing 121 whole genomes (98 newly reported) from 25 swamp and river buffalo breeds. Both uniparental and biparental markers were investigated to provide the final scenario. The ancestors of swamp and river buffalo diverged ∼0.23 million years ago and then experienced independent demographic histories. They were domesticated in different regions, the swamp buffalo at the border between southwest China and southeast Asia, while the river buffalo in south Asia. The domestic stocks migrated to other regions and further differentiated, as testified by (at least) 2 ancestral components identified in each subspecies. Different signals of selective pressures were also detected in these 2 types of buffalo. The swamp buffalo, historically used as a draft animal, shows selection signatures in genes associated with the nervous system, while in river dairy breeds, genes under selection are related to heat stress and immunity. Conclusions Our findings substantially expand the catalogue of genetic variants in buffalo and reveal new insights into the evolutionary history and distinct selective pressures in river and swamp buffalo.

Simple SummaryChinese indigenous cattle were clustered into two groups of southern and northern breeds. The populations distributed in the hot south are mainly dominated by Bos indicus, and the populations distributed in the cold north are mainly dominated by Bos taurus. Myosin-1a (MYO1A) gene is a candidate gene related to pigmentation, which may be closely related to the heat tolerance traits of cattle. Therefore, our study aimed to explore the relationship between MYO1A gene and heat tolerance in Chinese indigenous cattle. AbstractBased on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a (MYO1A) gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. In our study, four novel candidate SNPs highly conserved in B. indicus breeds but barely existed in B. taurus were identified in MYO1A gene according to Bovine Genome Variation Database and Selective Signatures (BGVD). PCR and DNA sequencing were used to genotype 1072 individuals including 34 Chinese indigenous cattle breeds as well as Angus and Indian zebu. Two synonymous mutations (rs208210464 and rs110123931), one missense mutation (rs209999142; Phe172Ser), and one intron mutation (rs135771836) were detected. The frequencies of mutant alleles of the four SNPs gradually increased from northern groups to southern groups of Chinese cattle, which was consistent with the distribution of various climatic conditions of China. Additionally, four SNPs were significantly associated with four climatic conditions including annual mean temperature (T), relative humidity (H), temperature-humidity index (THI), and average annual sunshine hours (100-cloudiness) (SR). Among these, rs209999142 and Hap 1/1 had better performance than others. Our results suggested that rs209999142 was associated with heat-tolerance trait and rs208210464, rs110123931, and rs135771836 showed high phenotypic effect on heat-tolerance trait because of the strong linkage with rs209999142. These SNPs could be used as candidates for marker-assisted selection (MAS) in cattle breeding.