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Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle

Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array...

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Autores principales: Yang, Liu, Xu, Lingyang, Zhu, Bo, Niu, Hong, Zhang, Wengang, Miao, Jian, Shi, Xinping, Zhang, Ming, Chen, Yan, Zhang, Lupei, Gao, Xue, Gao, Huijiang, Li, Li, Liu, George E., Li, Junya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662686/
https://www.ncbi.nlm.nih.gov/pubmed/29085051
http://dx.doi.org/10.1038/s41598-017-14768-0
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author Yang, Liu
Xu, Lingyang
Zhu, Bo
Niu, Hong
Zhang, Wengang
Miao, Jian
Shi, Xinping
Zhang, Ming
Chen, Yan
Zhang, Lupei
Gao, Xue
Gao, Huijiang
Li, Li
Liu, George E.
Li, Junya
author_facet Yang, Liu
Xu, Lingyang
Zhu, Bo
Niu, Hong
Zhang, Wengang
Miao, Jian
Shi, Xinping
Zhang, Ming
Chen, Yan
Zhang, Lupei
Gao, Xue
Gao, Huijiang
Li, Li
Liu, George E.
Li, Junya
author_sort Yang, Liu
collection PubMed
description Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V (i) statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V (ST). We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V (i) value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
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spelling pubmed-56626862017-11-08 Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle Yang, Liu Xu, Lingyang Zhu, Bo Niu, Hong Zhang, Wengang Miao, Jian Shi, Xinping Zhang, Ming Chen, Yan Zhang, Lupei Gao, Xue Gao, Huijiang Li, Li Liu, George E. Li, Junya Sci Rep Article Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V (i) statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V (ST). We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V (i) value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle. Nature Publishing Group UK 2017-10-30 /pmc/articles/PMC5662686/ /pubmed/29085051 http://dx.doi.org/10.1038/s41598-017-14768-0 Text en © The Author(s) 2017 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Yang, Liu
Xu, Lingyang
Zhu, Bo
Niu, Hong
Zhang, Wengang
Miao, Jian
Shi, Xinping
Zhang, Ming
Chen, Yan
Zhang, Lupei
Gao, Xue
Gao, Huijiang
Li, Li
Liu, George E.
Li, Junya
Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
title Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
title_full Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
title_fullStr Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
title_full_unstemmed Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
title_short Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
title_sort genome-wide analysis reveals differential selection involved with copy number variation in diverse chinese cattle
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662686/
https://www.ncbi.nlm.nih.gov/pubmed/29085051
http://dx.doi.org/10.1038/s41598-017-14768-0
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