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Identification of Copy Number Variations in Xiang and Kele Pigs

Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic...

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Autores principales: Xie, Jian, Li, Rongrong, Li, Sheng, Ran, Xueqin, Wang, Jiafu, Jiang, Jicai, Zhao, Pengju
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740446/
https://www.ncbi.nlm.nih.gov/pubmed/26840413
http://dx.doi.org/10.1371/journal.pone.0148565
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author Xie, Jian
Li, Rongrong
Li, Sheng
Ran, Xueqin
Wang, Jiafu
Jiang, Jicai
Zhao, Pengju
author_facet Xie, Jian
Li, Rongrong
Li, Sheng
Ran, Xueqin
Wang, Jiafu
Jiang, Jicai
Zhao, Pengju
author_sort Xie, Jian
collection PubMed
description Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.
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spelling pubmed-47404462016-02-11 Identification of Copy Number Variations in Xiang and Kele Pigs Xie, Jian Li, Rongrong Li, Sheng Ran, Xueqin Wang, Jiafu Jiang, Jicai Zhao, Pengju PLoS One Research Article Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds. Public Library of Science 2016-02-03 /pmc/articles/PMC4740446/ /pubmed/26840413 http://dx.doi.org/10.1371/journal.pone.0148565 Text en © 2016 Xie et al http://creativecommons.org/licenses/by/4.0/ 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 author and source are credited.
spellingShingle Research Article
Xie, Jian
Li, Rongrong
Li, Sheng
Ran, Xueqin
Wang, Jiafu
Jiang, Jicai
Zhao, Pengju
Identification of Copy Number Variations in Xiang and Kele Pigs
title Identification of Copy Number Variations in Xiang and Kele Pigs
title_full Identification of Copy Number Variations in Xiang and Kele Pigs
title_fullStr Identification of Copy Number Variations in Xiang and Kele Pigs
title_full_unstemmed Identification of Copy Number Variations in Xiang and Kele Pigs
title_short Identification of Copy Number Variations in Xiang and Kele Pigs
title_sort identification of copy number variations in xiang and kele pigs
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740446/
https://www.ncbi.nlm.nih.gov/pubmed/26840413
http://dx.doi.org/10.1371/journal.pone.0148565
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