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Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig
Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic s...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527633/ https://www.ncbi.nlm.nih.gov/pubmed/33093844 http://dx.doi.org/10.3389/fgene.2020.566255 |
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author | Zhang, Wei Yang, Min Zhou, Mei Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Zhao, Guiying Yin, Zongjun Wang, Chonglong |
author_facet | Zhang, Wei Yang, Min Zhou, Mei Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Zhao, Guiying Yin, Zongjun Wang, Chonglong |
author_sort | Zhang, Wei |
collection | PubMed |
description | Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation (F(ST)) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color (MC1R), salivary secretion (STATH), reproduction (SPIRE2, OSBP2, LIMK2, FANCA, and CABS1), olfactory transduction (OR5K4), and growth (NPY1R, NPY5R, and SELENOM). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production. |
format | Online Article Text |
id | pubmed-7527633 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75276332020-10-21 Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig Zhang, Wei Yang, Min Zhou, Mei Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Zhao, Guiying Yin, Zongjun Wang, Chonglong Front Genet Genetics Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation (F(ST)) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color (MC1R), salivary secretion (STATH), reproduction (SPIRE2, OSBP2, LIMK2, FANCA, and CABS1), olfactory transduction (OR5K4), and growth (NPY1R, NPY5R, and SELENOM). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production. Frontiers Media S.A. 2020-09-17 /pmc/articles/PMC7527633/ /pubmed/33093844 http://dx.doi.org/10.3389/fgene.2020.566255 Text en Copyright © 2020 Zhang, Yang, Zhou, Wang, Wu, Zhang, Ding, Zhao, Yin and Wang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Zhang, Wei Yang, Min Zhou, Mei Wang, Yuanlang Wu, Xudong Zhang, Xiaodong Ding, Yueyun Zhao, Guiying Yin, Zongjun Wang, Chonglong Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig |
title | Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig |
title_full | Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig |
title_fullStr | Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig |
title_full_unstemmed | Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig |
title_short | Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig |
title_sort | identification of signatures of selection by whole-genome resequencing of a chinese native pig |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527633/ https://www.ncbi.nlm.nih.gov/pubmed/33093844 http://dx.doi.org/10.3389/fgene.2020.566255 |
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