title: 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.
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
authors.forename: Riku
authors.initials: R
authors.lastname: Yonesaka
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
authors.forename: Shinji
authors.initials: S
authors.lastname: Sasazaki
authors.affiliation: Tsukuba GeneTechnology Laboratories, Tsukuba, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yasue
authors.affiliation: Kurabo Industries Ltd, Neyagawa, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Niwata
authors.affiliation: Yamaguchi Prefectural Agriculture & Forestry General Technology Center, Yamaguchi, Japan.
authors.forename: Yousuke
authors.initials: Y
authors.lastname: Inayoshi
authors.affiliation: Wagyu Registry Association, Kyoto, Japan.
authors.forename: Fumio
authors.initials: F
authors.lastname: Mukai
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Mannen
mesh_terms: D000818:Animals; D001208:Asia; D002417:Cattle / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D005060:Europe; D040342:Genetic Structures / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D060005:Genotyping Techniques / Q000379:methods* / Q000662:veterinary*; D020641:Polymorphism, Single Nucleotide
keywords: Asia; DigiTag2 assay; SNP; cattle; genetic structure