Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia

Abstract

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.

Multiple domestication of swamp buffalo in China and South East Asia

“…And such phylogeographic differentiation pattern also was observed in sheep (Zhao, Yu, Zhang, Kong, & Zhao, 2013), horse (Yue et al, 2012) and pig (Huo et al, 2016). It had been known that several species (cattle, goats, sheep and pig) showed a multiple domestication pattern in different regions (Beja-Pereira et al, 2006;Chen et al, 2018;Larson et al, 2005;Luikart et al, 2001;Pedrosa et al, 2005). Phylogenetic analysis reveals abundant genetic diversity and several haplogroups.…”

PRLH and SOD1 gene variations associated with heat tolerance in Chinese cattle

“…; Chen et al . a, b). In addition, to improve economic performance, exotic commercial breeds have been introduced into southern China since the 1970s to upgrade native breeds (Qiu et al .…”

Genetic diversity of Chinese cattle revealed by Y‐SNP and Y‐STR markers

“…Considering that several of the breeds analyzed in this study were also used by Chen et al . (), we infer that Y2‐102/104‐158 and Y2‐106/108/110/112‐158 belong to sub‐haplogroups Y2a and Y2b respectively. A previous study showed that Y2‐90‐158 was the most frequent haplotype in African N'Dama taurine cattle (Edwards et al .…”

“…In a recent whole‐genome resequencing study, Chen et al . () identified two distinct sub‐haplogroups in each of the Y2 (Y2a/b) and Y3 (Y3a/b) haplogroups.…”

“…Chen et al . () suggested that the Y2a sub‐haplogroup dominated cattle in south‐central Europe and northwestern China, whereas the sub‐haplogroup Y2b was distributed mainly in the Tibetan Plateau, north central China and northeastern Asia. Considering that several of the breeds analyzed in this study were also used by Chen et al .…”