Genetic structure and relationships of 16 Asian and European cattle populations using DigiTag2 assay

Abstract

In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3). In addition, Japanese Holstein exhibited an admixture pattern with Asian and European cattle (K=3-5). Mongolian (K=13-16) and Japanese Black (K=14-16) populations exhibited admixture patterns with different ancestries. Bos indicus populations exhibited a uniform genetic structure at K=2-11, thereby suggesting that there are close genetic relationships among Bos indicus populations. However, the Bhutan and Bangladesh populations formed a cluster distinct from the other Bos indicus populations at K=12-16. In conclusion, our study could sufficiently explain the genetic construction of Asian cattle populations, including: (i) the close genetic relationships among Bos indicus populations; (ii) the genetic influences of European breeds on Japanese breeds; (iii) the genetic admixture in Japanese Holstein, Mongolian and Japanese Black cattle; and (iv) the genetic subpopulations in Southeast Asia.

Keywords: Asia; DigiTag2 assay; SNP; cattle; genetic structure.

Figure 1

Phylogenetic constructions for 16 cattle populations. (A) neighbor‐joining tree, (B) unweighted pair group method with arithmetic mean tree. Population abbreviations are defined in Table 1. Bos taurus population indicated by blue and Bos indicus by green letters. Scale bar indicates the standard genetic distance of Nei (1972).

Figure 2

Principal component analysis (PCA) of 16 cattle populations. Population abbreviations are defined in Table 1. Bos taurus population indicated by blue and Bos indicus by green letters.

Figure 3

Genetic structure of 16 cattle populations based on 117 single nucleotide polymorphisms (SNPs) using STRUCTURE 2.3.4. Each individual is represented as a single vertical line and the proportion of the colored segment represents their estimated ancestry deriving from different populations. Population abbreviations are defined in Table 1.