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CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits
BACKGROUND: Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well unde...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171861/ https://www.ncbi.nlm.nih.gov/pubmed/32337028 http://dx.doi.org/10.1186/s40104-020-00442-5 |
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author | Zheng, Xianrui Zhao, Pengju Yang, Kaijie Ning, Chao Wang, Haifei Zhou, Lei Liu, Jianfeng |
author_facet | Zheng, Xianrui Zhao, Pengju Yang, Kaijie Ning, Chao Wang, Haifei Zhou, Lei Liu, Jianfeng |
author_sort | Zheng, Xianrui |
collection | PubMed |
description | BACKGROUND: Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood. RESULTS: In this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by next-generation sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight. CONCLUSIONS: The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs. |
format | Online Article Text |
id | pubmed-7171861 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-71718612020-04-24 CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits Zheng, Xianrui Zhao, Pengju Yang, Kaijie Ning, Chao Wang, Haifei Zhou, Lei Liu, Jianfeng J Anim Sci Biotechnol Research BACKGROUND: Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood. RESULTS: In this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by next-generation sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight. CONCLUSIONS: The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs. BioMed Central 2020-04-21 /pmc/articles/PMC7171861/ /pubmed/32337028 http://dx.doi.org/10.1186/s40104-020-00442-5 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Zheng, Xianrui Zhao, Pengju Yang, Kaijie Ning, Chao Wang, Haifei Zhou, Lei Liu, Jianfeng CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits |
title | CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits |
title_full | CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits |
title_fullStr | CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits |
title_full_unstemmed | CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits |
title_short | CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits |
title_sort | cnv analysis of meishan pig by next-generation sequencing and effects of ahr gene cnv on pig reproductive traits |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171861/ https://www.ncbi.nlm.nih.gov/pubmed/32337028 http://dx.doi.org/10.1186/s40104-020-00442-5 |
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