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Predicting polymorphic EST ‐ SSR s in silico

2013; Wiley; Volume: 13; Issue: 3 Linguagem: Inglês

10.1111/1755-0998.12078

1755-0998

Chris Duran, Richa Singhania, Harsh Raman, Jacqueline Batley, David Edwards,

Genomics and Phylogenetic Studies

Abstract The public availability of large quantities of gene sequence data provides a valuable resource of the mining of Simple Sequence Repeat ( SSR ) molecular genetic markers for genetic analysis. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated genes. This study presents the characterization of barley EST ‐ SSR s and the identification of putative polymorphic SSR s from EST data. Polymorphic SSR s are distinguished from monomorphic SSR s by the representation of varying motif lengths within an alignment of sequence reads. Two measures of confidence are calculated, redundancy of a polymorphism and co‐segregation with accessions. The utility of this method is demonstrated through the discovery of 597 candidate polymorphic SSR s, from a total of 452 642 consensus expressed sequences. PCR amplification primers were designed for the identified SSR s. Ten primer pairs were validated for polymorphism in barley and for transferability across species. Analysis of the polymorphisms in relation to SSR motif, length, position and annotation is discussed.