Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

Abstract Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we...

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Autores principales:	Congcong Liu, Yan Liu, Xinyi Zhang, Xuewen Xu, Shuhong Zhao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/40e08c3febdc48228cac1f275a1377ee
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spelling	oai:doaj.org-article:40e08c3febdc48228cac1f275a1377ee2021-12-02T12:30:52ZCharacterization of porcine simple sequence repeat variation on a population scale with genome resequencing data10.1038/s41598-017-02600-82045-2322https://doaj.org/article/40e08c3febdc48228cac1f275a1377ee2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02600-8https://doaj.org/toc/2045-2322Abstract Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we identified ~0.63 million polymorphic SSR loci from more than 100 individuals. Through intensive analysis of this dataset, we found that the SSR motif composition, motif length, total length of alleles and distribution of alleles all contribute to SSR variability. Furthermore, we found that CG-containing SSRs displayed significantly lower polymorphism and higher cross-species conservation. With a rigorous filter procedure, we provided a catalogue of 16,527 high-quality polymorphic SSRs, which displayed reliable results for the analysis of phylogenetic relationships and provided valuable summary statistics for 30 individuals equally selected from eight local Chinese pig breeds, six commercial lean pig breeds and Chinese wild boars. In addition, from the high-quality polymorphic SSR catalogue, we identified four loci with potential loss-of-function alleles. Overall, these analyses provide a valuable catalogue of polymorphic SSRs to the existing pig genetic variation database, and we believe this catalogue could be used for future genome-wide genetic analysis.Congcong LiuYan LiuXinyi ZhangXuewen XuShuhong ZhaoNature 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 Congcong Liu Yan Liu Xinyi Zhang Xuewen Xu Shuhong Zhao Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
description	Abstract Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we identified ~0.63 million polymorphic SSR loci from more than 100 individuals. Through intensive analysis of this dataset, we found that the SSR motif composition, motif length, total length of alleles and distribution of alleles all contribute to SSR variability. Furthermore, we found that CG-containing SSRs displayed significantly lower polymorphism and higher cross-species conservation. With a rigorous filter procedure, we provided a catalogue of 16,527 high-quality polymorphic SSRs, which displayed reliable results for the analysis of phylogenetic relationships and provided valuable summary statistics for 30 individuals equally selected from eight local Chinese pig breeds, six commercial lean pig breeds and Chinese wild boars. In addition, from the high-quality polymorphic SSR catalogue, we identified four loci with potential loss-of-function alleles. Overall, these analyses provide a valuable catalogue of polymorphic SSRs to the existing pig genetic variation database, and we believe this catalogue could be used for future genome-wide genetic analysis.
format	article
author	Congcong Liu Yan Liu Xinyi Zhang Xuewen Xu Shuhong Zhao
author_facet	Congcong Liu Yan Liu Xinyi Zhang Xuewen Xu Shuhong Zhao
author_sort	Congcong Liu
title	Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
title_short	Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
title_full	Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
title_fullStr	Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
title_full_unstemmed	Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
title_sort	characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/40e08c3febdc48228cac1f275a1377ee
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_version_	1718394273147125760

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

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