Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

Microsatellites, or simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated by 454 sequencing and representing 70,654 contigs and 52,082 singletons) from soybean globular stage embryos. A...

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Autores principales:	Li,Ai Qin, Zhao,Chuan Zhi, Wang,Xing Jun, Liu,Zhan Ji, Zhang,Li Feng, Song,Guo Qi, Yin,Juan, Li,Chang Sheng, Xia,Han, Bi,Yu Ping
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2010
Materias:	454 sequencing EST Glycine max polymorphism SSR
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582010000500006
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spelling	oai:scielo:S0717-345820100005000062011-05-24Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryosLi,Ai QinZhao,Chuan ZhiWang,Xing JunLiu,Zhan JiZhang,Li FengSong,Guo QiYin,JuanLi,Chang ShengXia,HanBi,Yu Ping 454 sequencing EST Glycine max polymorphism SSR Microsatellites, or simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated by 454 sequencing and representing 70,654 contigs and 52,082 singletons) from soybean globular stage embryos. Among 122,736 unique ESTs, 3,729 contained one or more SSRs. In total, 3,989 SSRs were identified including 304 mono, 1,374 di, 2,208 tri, 70 tetra, 13 penta and 20 hexanucleotide SSRs. Thirty three EST-SSRs were selected for primer design and polymorphism analysis using twenty soybean cultivars and one wild-type soybean. Successful amplification was obtained using 21 of these primer pairs, 11 of which detected polymorphisms in these soybean cultivars. These results demonstrated that 454 high throughput sequencing is a powerful tool for molecular marker development. From the 3,989 identified SSRs we expect to obtain a large number of makers with polymorphism among different soybean cultivars, which would be useful for analysis of genetic diversity and maker assisted selection in the soybean breeding programs.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.13 n.5 20102010-09-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582010000500006en
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	454 sequencing EST Glycine max polymorphism SSR
spellingShingle	454 sequencing EST Glycine max polymorphism SSR Li,Ai Qin Zhao,Chuan Zhi Wang,Xing Jun Liu,Zhan Ji Zhang,Li Feng Song,Guo Qi Yin,Juan Li,Chang Sheng Xia,Han Bi,Yu Ping Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos
description	Microsatellites, or simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated by 454 sequencing and representing 70,654 contigs and 52,082 singletons) from soybean globular stage embryos. Among 122,736 unique ESTs, 3,729 contained one or more SSRs. In total, 3,989 SSRs were identified including 304 mono, 1,374 di, 2,208 tri, 70 tetra, 13 penta and 20 hexanucleotide SSRs. Thirty three EST-SSRs were selected for primer design and polymorphism analysis using twenty soybean cultivars and one wild-type soybean. Successful amplification was obtained using 21 of these primer pairs, 11 of which detected polymorphisms in these soybean cultivars. These results demonstrated that 454 high throughput sequencing is a powerful tool for molecular marker development. From the 3,989 identified SSRs we expect to obtain a large number of makers with polymorphism among different soybean cultivars, which would be useful for analysis of genetic diversity and maker assisted selection in the soybean breeding programs.
author	Li,Ai Qin Zhao,Chuan Zhi Wang,Xing Jun Liu,Zhan Ji Zhang,Li Feng Song,Guo Qi Yin,Juan Li,Chang Sheng Xia,Han Bi,Yu Ping
author_facet	Li,Ai Qin Zhao,Chuan Zhi Wang,Xing Jun Liu,Zhan Ji Zhang,Li Feng Song,Guo Qi Yin,Juan Li,Chang Sheng Xia,Han Bi,Yu Ping
author_sort	Li,Ai Qin
title	Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos
title_short	Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos
title_full	Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos
title_fullStr	Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos
title_full_unstemmed	Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos
title_sort	identification of ssr markers using soybean (glycine max) ests from globular stage embryos
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2010
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582010000500006
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Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

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