Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.

Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals fro...

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Autores principales:	Jiying Wang, Jicai Jiang, Haifei Wang, Huimin Kang, Qin Zhang, Jian-Feng Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/53a3a572928d41c8b6b99652fff5e128
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spelling	oai:doaj.org-article:53a3a572928d41c8b6b99652fff5e1282021-11-18T08:35:30ZEnhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.1932-620310.1371/journal.pone.0087571https://doaj.org/article/53a3a572928d41c8b6b99652fff5e1282014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475311/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.Jiying WangJicai JiangHaifei WangHuimin KangQin ZhangJian-Feng LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e87571 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jiying Wang Jicai Jiang Haifei Wang Huimin Kang Qin Zhang Jian-Feng Liu Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.
description	Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.
format	article
author	Jiying Wang Jicai Jiang Haifei Wang Huimin Kang Qin Zhang Jian-Feng Liu
author_facet	Jiying Wang Jicai Jiang Haifei Wang Huimin Kang Qin Zhang Jian-Feng Liu
author_sort	Jiying Wang
title	Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.
title_short	Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.
title_full	Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.
title_fullStr	Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.
title_full_unstemmed	Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.
title_sort	enhancing genome-wide copy number variation identification by high density array cgh using diverse resources of pig breeds.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/53a3a572928d41c8b6b99652fff5e128
work_keys_str_mv	AT jiyingwang enhancinggenomewidecopynumbervariationidentificationbyhighdensityarraycghusingdiverseresourcesofpigbreeds AT jicaijiang enhancinggenomewidecopynumbervariationidentificationbyhighdensityarraycghusingdiverseresourcesofpigbreeds AT haifeiwang enhancinggenomewidecopynumbervariationidentificationbyhighdensityarraycghusingdiverseresourcesofpigbreeds AT huiminkang enhancinggenomewidecopynumbervariationidentificationbyhighdensityarraycghusingdiverseresourcesofpigbreeds AT qinzhang enhancinggenomewidecopynumbervariationidentificationbyhighdensityarraycghusingdiverseresourcesofpigbreeds AT jianfengliu enhancinggenomewidecopynumbervariationidentificationbyhighdensityarraycghusingdiverseresourcesofpigbreeds
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Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.

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