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.

Effect of two non-synonymous ecto-5′-nucleotidase variants on the genetic architecture of inosine 5′-monophosphate (IMP) and its degradation products in Japanese Black beef

“…We obtained blood samples from Japanese Black cattle ( n = 542), Japanese Shorthorn cattle ( n = 109), Japanese Brown cattle ( n = 106), Angus cattle ( n = 118), and Holstein cattle ( n = 204) raised at Tokachi, Ohu, Iwate, Tottori, Miyazaki, and Kumamoto stations of NLBC, respectively, in order to screen for the two non-synonymous SNPs. Japanese Black cattle, Japanese Shorthorn cattle, and Japanese Brown cattle are beef cattle called “Wagyu” [ 44 ], with different genetic background [ 45 ]. For Japanese Black cattle and Holstein cattle, the samples were selected using the criteria of at most 5 progenies in each sire, and these animals were low relatives with the progeny of 164 sires and 110 sires, respectively.…”

New hematological key for bovine leukemia virus-infected Japanese Black cattle

“…Therefore, we strongly suspected that these BLV-infected JB cattle might have significantly increased number of lymphocytes but was hardly detected. Because JB and Holstein (Hol) cattle are genetically distinct species, the disease susceptibility or hematological characteristics after BLV infection might differ [ 17 , 22 ]. The purpose of this study was to evaluate the expansion of lymphocytes in BLV-infected JB cattle and to modify the EC Key for JB cattle.…”

Genetic characterization of Indonesian Pesisir cattle using mitochondrial DNA and Y-chromosomal haplotypes and loci associated with economical traits and coat color

“…However distribution of these polymorphisms in the zebu cattle remains unclear. Since remarkable differences in allelic frequencies of various genes between taurine and zebu cattle populations have been reported Kaneda et al 2011;Yonesaka et al 2016, Okuda et al 2017), whether or not these polymorphisms observed in populations of taurine cattle are also observed in populations of zebu cattle is of particular interest. In the present study, we found that the polymorphisms of EDG1, NCAPG, and MC1R genes reported in taurine cattle were also observed in the population of Pesisir cattle.…”