Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database

Zhao, Y. and Prakash, C. S. and He, G. (2012) Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database. BMC Research Notes, 5 (362). 15 p..

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Abstract

There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L.) genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5%) within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5%) was the most abundant followed by AAG (12.1%), AAT (10.9%), and AT (10.3%).The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased.

Item Type: Article
Additional Information: We greatly appreciate the help of Dr. David Bertioli in the University of Brasilia, Brazil and Dr. Santie de Villiers in ICRISAT-Nairobi, Kenya for their suggestions and critical reading of the manuscript. This work was partially supported by grants from the USAID-Zambia groundnut project and the George Washington Carver Agricultural Experiment Station of Tuskegee University.
Uncontrolled Keywords: SSR, motif, polymorphism, cultivated peanut.
Author Affiliation: Agricultural Biotechnology, Tuskegee University, Alabama, US
Subjects: Crop Improvement
Divisions: Groundnut
Depositing User: Mr Siva Shankar
Date Deposited: 25 Jul 2012 08:27
Last Modified: 25 Jul 2012 08:28
Official URL: http://dx.doi.org/10.1186/1756-0500-5-362
URI: http://eprints.icrisat.ac.in/id/eprint/6984

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