Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry

Pongsakorn Wangkumhang; Alisa Wilantho; Philip J Shaw; Laurence Flori; Katayoun Moazami-Goudarzi; Mathieu Gautier; Monchai Duangjinda; Anunchai Assawamakin; Sissades Tongsima

doi:10.7717/peerj.1318

Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry

PeerJ. 2015 Oct 27:3:e1318. doi: 10.7717/peerj.1318. eCollection 2015.

Authors

Pongsakorn Wangkumhang¹, Alisa Wilantho¹, Philip J Shaw², Laurence Flori³, Katayoun Moazami-Goudarzi⁴, Mathieu Gautier⁵, Monchai Duangjinda⁶, Anunchai Assawamakin⁷, Sissades Tongsima¹

Affiliations

¹ Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology , Pathum Thani , Thailand.
² Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology , Pathum Thani , Thailand.
³ UMR INTERTRYP, CIRAD , Montpellier , France ; UMR 1313 GABI, INRA , Jouy-en-Josas , France.
⁴ UMR 1313 GABI, INRA , Jouy-en-Josas , France.
⁵ UMR CBGP (INRA/CIRAD/IRD/Supagro), INRA , Montferrier-sur-Lez , France.
⁶ Department of Animal Science, Faculty of Agriculture, Khon Kaen University , Khon Kaen , Thailand.
⁷ Department of Pharmacology, Faculty of Pharmacy, Mahidol University , Bangkok , Thailand.

Abstract

Cattle commonly raised in Thailand have characteristics of Bos indicus (zebu). We do not know when or how cattle domestication in Thailand occurred, and so questions remain regarding their origins and relationships to other breeds. We obtained genome-wide SNP genotypic data of 28 bovine individuals sampled from four regions: North (Kho-Khaolampoon), Northeast (Kho-Isaan), Central (Kho-Lan) and South (Kho-Chon) Thailand. These regional varieties have distinctive traits suggestive of breed-like genetic variations. From these data, we confirmed that all four Thai varieties are Bos indicus and that they are distinct from other indicine breeds. Among these Thai cattle, a distinctive ancestry pattern is apparent, which is the purest within Kho-Chon individuals. This ancestral component is only present outside of Thailand among other indicine breeds in Southeast Asia. From this pattern, we conclude that a unique Bos indicus ancestor originated in Southeast Asia, and native Kho-Chon Thai cattle retain the signal of this ancestry with limited admixture of other bovine ancestors.

Keywords: Admixture; Kho-Chon; Kho-Isaan; Kho-Khaolampoon; Kho-Lan; Population genetics; Population structure; ipPCA.

Grants and funding

ST is supported in part by the Thailand Research Fund (TRF grant number RSA5880061) and the National Science and Technology Development Agency, 2011 Research Chair Grant. PJS is supported by The Thailand Research Fund (TRF grant number RSA5780007). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.