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-SSRs and the identification of putative polymorphic SSRs from EST data. Polymorphic SSRs are distinguished from monomorphic SSRs 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 SSRs, from a total of 452 642 consensus expressed sequences. PCR amplification primers were designed for the identified SSRs. 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.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Duran C,Singhania R,Raman H,Batley J,Edwards Ddoi
10.1111/1755-0998.12078subject
Has Abstractpub_date
2013-05-01 00:00:00pages
538-45issue
3eissn
1755-098Xissn
1755-0998journal_volume
13pub_type
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journal_title:Molecular ecology resources
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