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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0026    [Accepted] Published online July 1, 2019.
Genome-wide scans for detecting the selection signature of the Jeju-island native pig (JNP) in Korea
Young-Sup Lee1  , Donghyun Shin1  , Kyeong-Hye Won1  , Dae Cheol Kim2  , Sang Cheol Lee3,*  , Ki-Duk Song1,4,* 
1Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea
2Livestock Promotion Institute, Jeju Special Self-governing Province, Jeju 63122, Korea
3Cronex Inc, Cheongju 28174, Korea
4The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju 54896, Korea
Correspondence:  Sang Cheol Lee, Tel: +82-043-716-2300, Fax: +82-063-270-2614, Email: dreamporc@cronex.co.kr
Ki-Duk Song,Email: kiduk.song@gmail.com
Received: 10 January 2019   • Revised: 3 May 2019   • Accepted: 11 June 2019
Abstract
Objective
s: The Jeju Native Pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs.
Methods
We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham’s Fst was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features.
Results
Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO.
Conclusion
The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP’s unique pork quality.
Keywords: Jeju-island Native Pig; Berkshire Pig; Linkage Disequilibrium; Population Differentiation Statistic; Selection Signatures; Yorkshire Pig


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