A Modified Method for the Development of SSR Molecular Markers Based on Redundant EST Data and Its Application in Soybean

doi:10.1016/S1671-2927(00)8574

Journal of Integrative Agriculture ›› 2012, Vol. 12 ›› Issue (4): 545-555.DOI: 10.1016/S1671-2927(00)8574

A Modified Method for the Development of SSR Molecular Markers Based on Redundant EST Data and Its Application in Soybean

ZHAO Xue, CHANG Wei, HAN Ying-peng, TENG Wei-li , LI Wen-bin

1.Key Laboratory of Soybean Biology, Ministry of Education/Soybean Research Institute, Northeast Agricultural University, Harbin 150030,P.R.China

收稿日期:2011-01-18 出版日期:2012-04-01 发布日期:2012-04-11
通讯作者: Correspondence LI Wen-bin, Tel: +86-451-55190778, E-mail: wenbinli@neau.edu.cn
作者简介:ZHAO Xue, Tel: +86-451-55190401, Mobile: 13836142414, E-mail: zhaoxue8311@yahoo.com.cn; CHANG Wei, Tel: +86-451-55190401, E-mail: weichang0@tom. com;
基金资助:
This study was conducted in the Key Laboratory of Soybean Biology, Ministry of Education, China, and Soybean Development Centre, Ministry of Agriculture, China, financially supported by the National High-Tech R&D Program of China (2006AA10Z1F1), the National Core Soybean Genetic Engineering Project, China (2008ZX08004- 002, 2009ZX08004-002B, 2009ZX08009-089B), the National Natural Science Foundation of China (60932008, 30971810), the National Basic Research Program of China (2009CB118400), the Soybean Molecular Design Team of Education of Ministry, China, the Soybean Molecular Design Team of the Heilongjiang Provincial Education Department, China (11541025), and the Technology Project of Harbin, China (2009RFQXN085).

A Modified Method for the Development of SSR Molecular Markers Based on Redundant EST Data and Its Application in Soybean

ZHAO Xue, CHANG Wei, HAN Ying-peng, TENG Wei-li , LI Wen-bin

1.Key Laboratory of Soybean Biology, Ministry of Education/Soybean Research Institute, Northeast Agricultural University, Harbin 150030,P.R.China

Received:2011-01-18 Online:2012-04-01 Published:2012-04-11
Contact: Correspondence LI Wen-bin, Tel: +86-451-55190778, E-mail: wenbinli@neau.edu.cn
About author:ZHAO Xue, Tel: +86-451-55190401, Mobile: 13836142414, E-mail: zhaoxue8311@yahoo.com.cn; CHANG Wei, Tel: +86-451-55190401, E-mail: weichang0@tom. com;
Supported by:
This study was conducted in the Key Laboratory of Soybean Biology, Ministry of Education, China, and Soybean Development Centre, Ministry of Agriculture, China, financially supported by the National High-Tech R&D Program of China (2006AA10Z1F1), the National Core Soybean Genetic Engineering Project, China (2008ZX08004- 002, 2009ZX08004-002B, 2009ZX08009-089B), the National Natural Science Foundation of China (60932008, 30971810), the National Basic Research Program of China (2009CB118400), the Soybean Molecular Design Team of Education of Ministry, China, the Soybean Molecular Design Team of the Heilongjiang Provincial Education Department, China (11541025), and the Technology Project of Harbin, China (2009RFQXN085).

摘要/Abstract

摘要： EST-derived SSR marker has been developed in many species, but few methods of high efficiency have been reported for the exploitation of EST-SSR markers. Thus, a high efficiency method for mining millions of redundant EST data is needed. A modified method for the EST-SSR development with high efficiency was established based on the redundant EST data of soybean in this study. The method achieved its function through classifying ESTs according to the same SSR motif and detected candidate loci with redundant sequences. In this study, a total of 80 polymorphic EST-SSR markers of soybean were developed, 50 of them were exploited by this modified method which proved the higher speed and efficiency of this method. All the 80 polymorphic EST-SSRs were mapped on soybean physical map through in silico mapping and 15 markers were integrated on a genetic map constructed in previous study. A software named hpSSR (high polymorphic SSR) was programmed based on the concept of the up-built method for EST-SSR development. This method is not only pragmatic for EST-SSR exploitation in soybean, but also effective for the development of the marker in other species if the redundancy EST data is available.

关键词: EST-SSR, soybean, polymorphism, genetic mapping, in silico mapping

Abstract: EST-derived SSR marker has been developed in many species, but few methods of high efficiency have been reported for the exploitation of EST-SSR markers. Thus, a high efficiency method for mining millions of redundant EST data is needed. A modified method for the EST-SSR development with high efficiency was established based on the redundant EST data of soybean in this study. The method achieved its function through classifying ESTs according to the same SSR motif and detected candidate loci with redundant sequences. In this study, a total of 80 polymorphic EST-SSR markers of soybean were developed, 50 of them were exploited by this modified method which proved the higher speed and efficiency of this method. All the 80 polymorphic EST-SSRs were mapped on soybean physical map through in silico mapping and 15 markers were integrated on a genetic map constructed in previous study. A software named hpSSR (high polymorphic SSR) was programmed based on the concept of the up-built method for EST-SSR development. This method is not only pragmatic for EST-SSR exploitation in soybean, but also effective for the development of the marker in other species if the redundancy EST data is available.

Key words: EST-SSR, soybean, polymorphism, genetic mapping, in silico mapping

ZHAO Xue, CHANG Wei, HAN Ying-peng, TENG Wei-li , LI Wen-bin. A Modified Method for the Development of SSR Molecular Markers Based on Redundant EST Data and Its Application in Soybean[J]. Journal of Integrative Agriculture, 2012, 12(4): 545-555.

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A Modified Method for the Development of SSR Molecular Markers Based on Redundant EST Data and Its Application in Soybean

A Modified Method for the Development of SSR Molecular Markers Based on Redundant EST Data and Its Application in Soybean

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