Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea
Objective 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 surv...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2020-04-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://ajas.info/upload/pdf/ajas-19-0026.pdf |
| _version_ | 1819017223333740544 |
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| author | Young-Sup Lee Donghyun Shin Kyeong-Hye Won Dae Cheol Kim Sang Chul Lee Ki-Duk Song |
| author_facet | Young-Sup Lee Donghyun Shin Kyeong-Hye Won Dae Cheol Kim Sang Chul Lee Ki-Duk Song |
| author_sort | Young-Sup Lee |
| collection | DOAJ |
| description | Objective 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. |
| first_indexed | 2024-12-21T03:00:06Z |
| format | Article |
| id | doaj.art-f9fd8fd9b48e476188771e096556d55c |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-21T03:00:06Z |
| publishDate | 2020-04-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-f9fd8fd9b48e476188771e096556d55c2022-12-21T19:18:12ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172020-04-0133453954610.5713/ajas.19.002624304Genome-wide scans for detecting the selection signature of the Jeju-island native pig in KoreaYoung-Sup Lee0Donghyun Shin1Kyeong-Hye Won2Dae Cheol Kim3Sang Chul Lee4Ki-Duk Song5 Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea Livestock Promotion Agency, Jeju Special Self-Governing Province, Jeju 63122, Korea Cronex Co., Cheongju 28174, Korea Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, KoreaObjective 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.http://ajas.info/upload/pdf/ajas-19-0026.pdfjeju island native pigberkshire piglinkage disequilibriumpopulation differentiation statisticselection signaturesyorkshire pig |
| spellingShingle | Young-Sup Lee Donghyun Shin Kyeong-Hye Won Dae Cheol Kim Sang Chul Lee Ki-Duk Song Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea Asian-Australasian Journal of Animal Sciences jeju island native pig berkshire pig linkage disequilibrium population differentiation statistic selection signatures yorkshire pig |
| title | Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea |
| title_full | Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea |
| title_fullStr | Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea |
| title_full_unstemmed | Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea |
| title_short | Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea |
| title_sort | genome wide scans for detecting the selection signature of the jeju island native pig in korea |
| topic | jeju island native pig berkshire pig linkage disequilibrium population differentiation statistic selection signatures yorkshire pig |
| url | http://ajas.info/upload/pdf/ajas-19-0026.pdf |
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