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

BMC Research Notes

Guohao He¹  Channapatna S Prakash¹  Yongli Zhao¹ 

[1] Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA

关键词: Cultivated peanut;    Polymorphism;    Motif;    SSR;   

Others  :  1166129
DOI  :  10.1186/1756-0500-5-362

 received in 2012-03-30, accepted in 2012-06-25,  发布年份 2012

【 摘 要 】

Background

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.

Conclusions

The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

【 授权许可】

   
2012 Zhao et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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