Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species

Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and th...

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Main Authors:	Huang, Li, Wu, Bei, Zhao, Jiaojiao, Li, Haitao, Chen, Weigang, Zheng, Yanli, Ren, Xiaoping, Chen, Yuning, Zhou, Xiaojing, Lei, Yong, Liao, Boshou, Jiang, Huifang
Format:	Online
Language:	English
Published:	Public Library of Science 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887017/

id	pubmed-4887017
recordtype	oai_dc
spelling	pubmed-48870172016-06-10 Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species Huang, Li Wu, Bei Zhao, Jiaojiao Li, Haitao Chen, Weigang Zheng, Yanli Ren, Xiaoping Chen, Yuning Zhou, Xiaojing Lei, Yong Liao, Boshou Jiang, Huifang Research Article Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data. The GSS-SSRs had a density of 159.9–239.8 SSRs/Mb for wild Arachis and 1,015.8 SSR/Mb for cultivated Arachis, whereas the EST-SSRs had the density of 173.5–384.4 SSR/Mb and 250.9 SSRs/Mb for wild and cultivated Arachis, respectively. The trinucleotide SSRs were predominant across Arachis species, except that the dinucleotide accounted for most in A. hypogaea GSSs. From Arachis GSS-SSR and EST-SSR sequences, we developed 2,589 novel SSR markers that showed a high polymorphism in six diverse A. hypogaea accessions. A genetic linkage map that contained 540 novel SSR loci and 105 anchor SSR loci was constructed by case of a recombinant inbred lines F6 population. A subset of 82 randomly selected SSR markers were used to screen 39 wild and 22 cultivated Arachis accessions, which revealed a high transferability of the novel SSRs across Arachis species. Our results provided informative clues to investigate microsatellite patterns across A. hypogaea and its wild relative species and potentially facilitate the germplasm evaluation and gene mapping in Arachis species. Public Library of Science 2016-05-31 /pmc/articles/PMC4887017/ /pubmed/27243460 http://dx.doi.org/10.1371/journal.pone.0156633 Text en © 2016 Huang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Huang, Li Wu, Bei Zhao, Jiaojiao Li, Haitao Chen, Weigang Zheng, Yanli Ren, Xiaoping Chen, Yuning Zhou, Xiaojing Lei, Yong Liao, Boshou Jiang, Huifang
spellingShingle	Huang, Li Wu, Bei Zhao, Jiaojiao Li, Haitao Chen, Weigang Zheng, Yanli Ren, Xiaoping Chen, Yuning Zhou, Xiaojing Lei, Yong Liao, Boshou Jiang, Huifang Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species
author_facet	Huang, Li Wu, Bei Zhao, Jiaojiao Li, Haitao Chen, Weigang Zheng, Yanli Ren, Xiaoping Chen, Yuning Zhou, Xiaojing Lei, Yong Liao, Boshou Jiang, Huifang
author_sort	Huang, Li
title	Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species
title_short	Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species
title_full	Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species
title_fullStr	Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species
title_full_unstemmed	Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species
title_sort	characterization and transferable utility of microsatellite markers in the wild and cultivated arachis species
description	Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data. The GSS-SSRs had a density of 159.9–239.8 SSRs/Mb for wild Arachis and 1,015.8 SSR/Mb for cultivated Arachis, whereas the EST-SSRs had the density of 173.5–384.4 SSR/Mb and 250.9 SSRs/Mb for wild and cultivated Arachis, respectively. The trinucleotide SSRs were predominant across Arachis species, except that the dinucleotide accounted for most in A. hypogaea GSSs. From Arachis GSS-SSR and EST-SSR sequences, we developed 2,589 novel SSR markers that showed a high polymorphism in six diverse A. hypogaea accessions. A genetic linkage map that contained 540 novel SSR loci and 105 anchor SSR loci was constructed by case of a recombinant inbred lines F6 population. A subset of 82 randomly selected SSR markers were used to screen 39 wild and 22 cultivated Arachis accessions, which revealed a high transferability of the novel SSRs across Arachis species. Our results provided informative clues to investigate microsatellite patterns across A. hypogaea and its wild relative species and potentially facilitate the germplasm evaluation and gene mapping in Arachis species.
publisher	Public Library of Science
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887017/
_version_	1613586607257944064

Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species

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