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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0888    [Accepted] Published online August 21, 2020.
Genetic characteristics of Korean Jeju Black cattle with high density SNP chips
Zahangir M. Alam1,2,a  , Yun-Mi Lee1,a  , Hyo-Jung Son1  , Lauren H. Hanna3  , David G. Riley4  , Hideyuki Mannen5  , Shinji Sasazaki5  , Se Pill Park6  , Jong-Joo Kim1,* 
1Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
2Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
3Department of Animal Sciences, North Dakota State University, Fargo, North Dakota, USA
4Department of Animal Sciences, Texas A&M University, College Station, Texas, USA
5Graduate School of Agricultural Science, Kobe University, Japan
6Faculty of Biotechnology, Jeju National University, Jeju, Korea
Correspondence:  Jong-Joo Kim, Tel: +82-53-810-3027, Fax: +82-53-801-3027, Email: kimjj@yumail.ac.kr
Received: 15 November 2019   • Revised: 3 January 2020   • Accepted: 29 June 2020
aThese authors contributed equally to this work.
Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula.
Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei’s genetic distance and Weir & Cockerham’s FST.
Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 ~ -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo.
This study indicates genetic uniqueness of Jeju Black Cattle. However, a small effective population size of Jeju Black cattle indicates the implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.
Keywords: Jeju Black Cattle; Hanwoo; Genetic Diversity; Population Structure; SNP Chip

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