Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.

Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identifi...

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Autores principales:	Jiying Wang, Haifei Wang, Jicai Jiang, Huimin Kang, Xiaotian Feng, Qin Zhang, Jian-Feng Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/462ccbc0a6734e7db45869f9e6e3c3f1
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spelling	oai:doaj.org-article:462ccbc0a6734e7db45869f9e6e3c3f12021-11-18T09:03:23ZIdentification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.1932-620310.1371/journal.pone.0068683https://doaj.org/article/462ccbc0a6734e7db45869f9e6e3c3f12013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23935880/?tool=EBIhttps://doaj.org/toc/1932-6203Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.Jiying WangHaifei WangJicai JiangHuimin KangXiaotian FengQin ZhangJian-Feng LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68683 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jiying Wang Haifei Wang Jicai Jiang Huimin Kang Xiaotian Feng Qin Zhang Jian-Feng Liu Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
description	Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.
format	article
author	Jiying Wang Haifei Wang Jicai Jiang Huimin Kang Xiaotian Feng Qin Zhang Jian-Feng Liu
author_facet	Jiying Wang Haifei Wang Jicai Jiang Huimin Kang Xiaotian Feng Qin Zhang Jian-Feng Liu
author_sort	Jiying Wang
title	Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
title_short	Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
title_full	Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
title_fullStr	Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
title_full_unstemmed	Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.
title_sort	identification of genome-wide copy number variations among diverse pig breeds using snp genotyping arrays.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/462ccbc0a6734e7db45869f9e6e3c3f1
work_keys_str_mv	AT jiyingwang identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays AT haifeiwang identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays AT jicaijiang identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays AT huiminkang identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays AT xiaotianfeng identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays AT qinzhang identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays AT jianfengliu identificationofgenomewidecopynumbervariationsamongdiversepigbreedsusingsnpgenotypingarrays
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Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.

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