Data Mining for SSRs in ESTs and EST-SSR Marker Development in Chinese Cabbage

ACTA HORTICULTURAE SINICA ›› 2006, Vol. 33 ›› Issue (3): 549-554.

• 研究论文 • Previous Articles Next Articles

Data Mining for SSRs in ESTs and EST-SSR Marker Development in Chinese Cabbage

Xin Ya^{1, 3};Cui Hairui^1*;Lu Meizhen¹;Yao Yanling¹;Jin Jiqiang¹;Lim Yongpyo²;Choi Suryun²

(¹Institute of Nuclear and Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310029, China; ²Department of Horticulture, Chungnam National University, Taejeon 3052764, Korea; ³Biotechnology Research Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang 310024, China)

Received:2005-07-14 Revised:2005-11-14 Online:2006-06-25 Published:2006-06-25

Abstract

Abstract: Expressed sequence tags ( ESTs) , increased rapidly in number recently, are important resources for development of new SSR markers. In this study, 4 584 ESTs of Chinese cabbage were screened and 474 SSRs including 40 kinds of repeat motifs were mined out, accounting for 10.3% of ESTs. Dinucleotide
and trinucleotide repeats, with similar frequency and accounting for 83% together in all SSRs, were dominant, while the frequency for other repeat type is below 5% each. GA and GAA are the most frequentmotifs, accounting of 71.5% and 37.5% in dinucleotide and trinucleotide repeats respectively. 15 primer pairs for EST-SSRs were designed. Under a suitable PCR system, primers were screened against genomic DNA of inbred line A from which the cDNA library was constructed, and all the 15 primer pairs showed the amplification. Then all the primers available were subjected to PCR for DNAs from 28 Chinese cabbage varieties and 7 primer sets showed polymorphisms, accounting for 46.7% of total primers tested. Results indicate that it is a
simple and effective approach to develop SSR markers based on ESTs.

Key words: Chinese cabbage, EST, SSR information, Marker development

Xin Ya;;Cui Hairui;Lu Meizhen;Yao Yanling;Jin Jiqiang;Lim Yongpyo;Choi Suryun. Data Mining for SSRs in ESTs and EST-SSR Marker Development in Chinese Cabbage[J]. ACTA HORTICULTURAE SINICA, 2006, 33(3): 549-554.

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Data Mining for SSRs in ESTs and EST-SSR Marker Development in Chinese Cabbage

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