Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array

Abstract Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 ...

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Autores principales:	Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7a7ff38e36024200b5c2b5730b6194ff
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spelling	oai:doaj.org-article:7a7ff38e36024200b5c2b5730b6194ff2021-12-02T15:06:17ZGenome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array10.1038/s41598-017-00847-92045-2322https://doaj.org/article/7a7ff38e36024200b5c2b5730b6194ff2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00847-9https://doaj.org/toc/2045-2322Abstract Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.Qing MaXuexue LiuJianfei PanLina MaYuehui MaXiaohong HeQianjun ZhaoYabin PuYingkang LiLin JiangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qing Ma Xuexue Liu Jianfei Pan Lina Ma Yuehui Ma Xiaohong He Qianjun Zhao Yabin Pu Yingkang Li Lin Jiang Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
description	Abstract Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.
format	article
author	Qing Ma Xuexue Liu Jianfei Pan Lina Ma Yuehui Ma Xiaohong He Qianjun Zhao Yabin Pu Yingkang Li Lin Jiang
author_facet	Qing Ma Xuexue Liu Jianfei Pan Lina Ma Yuehui Ma Xiaohong He Qianjun Zhao Yabin Pu Yingkang Li Lin Jiang
author_sort	Qing Ma
title	Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
title_short	Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
title_full	Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
title_fullStr	Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
title_full_unstemmed	Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
title_sort	genome-wide detection of copy number variation in chinese indigenous sheep using an ovine high-density 600 k snp array
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/7a7ff38e36024200b5c2b5730b6194ff
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Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array

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