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Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding
OBJECTIVE: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig bree...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST)
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206397/ https://www.ncbi.nlm.nih.gov/pubmed/31480149 http://dx.doi.org/10.5713/ajas.19.0289 |
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author | Zhang, Wei Yang, Min Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Yin, Zongjun |
author_facet | Zhang, Wei Yang, Min Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Yin, Zongjun |
author_sort | Zhang, Wei |
collection | PubMed |
description | OBJECTIVE: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. METHODS: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (F(ST)) and π ratios. RESULTS: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. CONCLUSION: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs. |
format | Online Article Text |
id | pubmed-7206397 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) |
record_format | MEDLINE/PubMed |
spelling | pubmed-72063972020-05-15 Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding Zhang, Wei Yang, Min Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Yin, Zongjun Asian-Australas J Anim Sci Article OBJECTIVE: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. METHODS: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (F(ST)) and π ratios. RESULTS: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. CONCLUSION: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs. Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) 2020-05 2019-08-23 /pmc/articles/PMC7206397/ /pubmed/31480149 http://dx.doi.org/10.5713/ajas.19.0289 Text en Copyright © 2020 by Asian-Australasian Journal of Animal Sciences This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Article Zhang, Wei Yang, Min Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Yin, Zongjun Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding |
title | Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding |
title_full | Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding |
title_fullStr | Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding |
title_full_unstemmed | Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding |
title_short | Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding |
title_sort | genomic analysis reveals selection signatures of the wannan black pig during domestication and breeding |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206397/ https://www.ncbi.nlm.nih.gov/pubmed/31480149 http://dx.doi.org/10.5713/ajas.19.0289 |
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