Genetic Diversity, Molecular Phylogeny, and Selection Evidence of Jinchuan Yak Revealed by Whole-Genome Resequencing

Abstract

Jinchuan yak, a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics, such as high meat production, milk yield, and reproductive performance. However, there is limited information about its overall genetic structure, relationship with yaks in other areas, and possible origins and evolutionary processes. In this study, 7,693,689 high-quality single-nucleotide polymorphisms were identified by resequencing the genome of Jinchuan yak. Principal component and population genetic structure analyses showed that Jinchuan yak could be distinguished as an independent population among the domestic yak population. Linkage disequilibrium analysis showed that the decay rate of Jinchuan yak was the lowest of the domestic yak breeds, indicating that the degree of domestication and selection intensity of Jinchuan yak were higher than those of other yak breeds. Combined with archaeological data, we speculated that the origin of domestication of Jinchuan yak was ∼6000 yr ago (4000-10,000 yr ago). The quantitative dynamics of population growth history in Jinchuan yak was similar to that of other breeds of domestic and wild yaks, but was closer to that of the wild yak. No significant gene exchange between Jinchuan and other domestic yaks occurred. Compared with other domestic yaks, Jinchuan yak possessed 339 significantly and positively selected genes, several of which relate to physiological rhythm, histones, and the breed's excellent production characteristics. Our results provide a basis for the discovery of the evolution, molecular origin, and unique traits of Jinchuan yak.

Keywords: Jinchuan yak; genetic diversity; genome; molecular phylogeny; selection evidence.

Figure 1

Graphical representation of Jinchuan yaks. (A) Image. (B) Skeleton. Arrows indicate excess ribs.

Figure 2

Geographical distribution of the selected yaks in this study. The blue star indicates the location of Jinchuan yaks, triangles correspond to locations of other domestic yaks, and the circle shows the location of wild yaks.

Figure 3

Population genetic polymorphism and LD decay analysis of Jinchuan yak. (A) Phylogenetic tree analysis. Jinchuan yaks are indicated in red, other domesticated yak groups are denoted in green, and wild yaks are shown in yellow. (B) PCA. (C) Population genetic structure analysis. (D) LD decay analysis.

Figure 4

Gene flow analysis of Jinchuan yak. (A) Maximum likelihood tree with two migration events. The arrows (migration events) are colored according to their weight. The horizontal branch length is proportional to the degree of genetic drift in the branch. The scale bar on the left shows 10 times the average SE of the entries in the sample covariance matrix. (B) Residual fit from the maximum likelihood tree in (A).

Figure 5

Differentiation time and demographic history of Jinchuan yak. (A) Differentiation time analysis. (B) Demographic history inferred by PSMC for different populations. Changes in the effective population size of the ancestral population of three yak populations, namely Jinchuan, other domesticated yaks, and wild yaks. Time is plotted along the x-axis, and the effective population size is represented along the y-axis. Colored lines indicate various populations. XG (Xixiabangma Glaciation; 1170–800 thousand years ago, kya), NG (Naynayxungla Glaciation; 780–500 kya), and LGM (last glacial maximum; ∼20 kya) are shaded in gray.

Figure 6

Genome-wide selective sweep analysis of Jinchuan yak. Distribution of θπ ratio (θπ, other domesticated yaks/θπ, Jinchuan yak) and FST values calculated in 500 kb windows sliding in 10 kb steps. Data points in red are regions under selection in Jinchuan yaks.