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Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs
Laiwu pigs are a Chinese indigenous breed that is renowned for its exceptionally high intramuscular fat content (average greater than 6%), providing an excellent genetic resource for the genetic improvement of meat quality of modern commercial pigs. To uncover genetic diversity, population structure...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7896721/ https://www.ncbi.nlm.nih.gov/pubmed/33664783 http://dx.doi.org/10.1111/eva.13124 |
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author | Wang, Xiaopeng Zhang, Hui Huang, Min Tang, Jianhong Yang, Lijuan Yu, Zhiqiang Li, Desen Li, Guixin Jiang, Yongchuang Sun, Yanxiao Wei, Shudong Xu, Pan Ren, Jun |
author_facet | Wang, Xiaopeng Zhang, Hui Huang, Min Tang, Jianhong Yang, Lijuan Yu, Zhiqiang Li, Desen Li, Guixin Jiang, Yongchuang Sun, Yanxiao Wei, Shudong Xu, Pan Ren, Jun |
author_sort | Wang, Xiaopeng |
collection | PubMed |
description | Laiwu pigs are a Chinese indigenous breed that is renowned for its exceptionally high intramuscular fat content (average greater than 6%), providing an excellent genetic resource for the genetic improvement of meat quality of modern commercial pigs. To uncover genetic diversity, population structure, signature of selection, and potential exotic introgression in this breed, we sampled 238 Laiwu pigs from a state‐supported conservation population and genotyped these individuals using GeneSeek 80K SNP BeadChip. We then conducted in‐depth population genetics analyses for the Laiwu pig in a context of 1,116 pigs from 42 Eurasian diverse breeds. First, we show that the current Laiwu population has more abundant genetic diversity than the population of 18 years ago likely due to gene flow from European commercial breeds. Both neighbor‐joining (NJ) and principal component analyses indicate the introgression of European haplotypes into Laiwu pigs. The admixture analysis reveals that an average 26.66% of Laiwu genetic components are of European origin. Then, we assigned the tested individuals to different families according to their clustering patterns in the NJ tree and proposed a family‐based conservation strategy to reduce the risk of inbreeding depression in Laiwu pigs. Next, we explored three statistics (ROH and iHS and EigenGWAS) to identify a list of candidate genes for fat deposition, reproduction, and growth in Laiwu pigs. Last, we detected a strong signature of introgression from European pigs into Laiwu pigs at the GPC6 locus that regulates the growth of developing long bones. Further association analyses indicate that the introgressed GPC6 haplotype likely contributed to the improvement of growth performance in Laiwu pigs. Altogether, this study not only benefits the better conservation of the Laiwu pig, but also advances our knowledge of the poorly understood effect of human‐mediated introgression on phenotypic traits in Chinese indigenous pigs. |
format | Online Article Text |
id | pubmed-7896721 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-78967212021-03-03 Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs Wang, Xiaopeng Zhang, Hui Huang, Min Tang, Jianhong Yang, Lijuan Yu, Zhiqiang Li, Desen Li, Guixin Jiang, Yongchuang Sun, Yanxiao Wei, Shudong Xu, Pan Ren, Jun Evol Appl Original Articles Laiwu pigs are a Chinese indigenous breed that is renowned for its exceptionally high intramuscular fat content (average greater than 6%), providing an excellent genetic resource for the genetic improvement of meat quality of modern commercial pigs. To uncover genetic diversity, population structure, signature of selection, and potential exotic introgression in this breed, we sampled 238 Laiwu pigs from a state‐supported conservation population and genotyped these individuals using GeneSeek 80K SNP BeadChip. We then conducted in‐depth population genetics analyses for the Laiwu pig in a context of 1,116 pigs from 42 Eurasian diverse breeds. First, we show that the current Laiwu population has more abundant genetic diversity than the population of 18 years ago likely due to gene flow from European commercial breeds. Both neighbor‐joining (NJ) and principal component analyses indicate the introgression of European haplotypes into Laiwu pigs. The admixture analysis reveals that an average 26.66% of Laiwu genetic components are of European origin. Then, we assigned the tested individuals to different families according to their clustering patterns in the NJ tree and proposed a family‐based conservation strategy to reduce the risk of inbreeding depression in Laiwu pigs. Next, we explored three statistics (ROH and iHS and EigenGWAS) to identify a list of candidate genes for fat deposition, reproduction, and growth in Laiwu pigs. Last, we detected a strong signature of introgression from European pigs into Laiwu pigs at the GPC6 locus that regulates the growth of developing long bones. Further association analyses indicate that the introgressed GPC6 haplotype likely contributed to the improvement of growth performance in Laiwu pigs. Altogether, this study not only benefits the better conservation of the Laiwu pig, but also advances our knowledge of the poorly understood effect of human‐mediated introgression on phenotypic traits in Chinese indigenous pigs. John Wiley and Sons Inc. 2020-09-16 /pmc/articles/PMC7896721/ /pubmed/33664783 http://dx.doi.org/10.1111/eva.13124 Text en © 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Articles Wang, Xiaopeng Zhang, Hui Huang, Min Tang, Jianhong Yang, Lijuan Yu, Zhiqiang Li, Desen Li, Guixin Jiang, Yongchuang Sun, Yanxiao Wei, Shudong Xu, Pan Ren, Jun Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs |
title | Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs |
title_full | Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs |
title_fullStr | Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs |
title_full_unstemmed | Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs |
title_short | Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs |
title_sort | whole‐genome snp markers reveal conservation status, signatures of selection, and introgression in chinese laiwu pigs |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7896721/ https://www.ncbi.nlm.nih.gov/pubmed/33664783 http://dx.doi.org/10.1111/eva.13124 |
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