Identification of SSR loci in Betula luminifera using birch EST data

Abstract

Expressed sequence tags (ESTs) are generated from single-pass sequencing of randomly picked cDNA clones and can be used for development of simple sequence repeat (SSR) markers or microsatellites. However, EST databases have been developed for only a small number of species. This paper provides a case study of the utility of freely available birch EST resources for the development of markers necessary for the genetic analysis of Betula luminifera. Based on birch EST data, primers for 80 EST-SSR candidate loci were developed and tested in birch. Of these, 59 EST-SSR loci yielded single, stable and clear PCR products. We then tested the utility of those 59 markers in B. luminifera. The results showed 28 (47.6%) yielded stable and clear PCR products for at least one B. luminifera genotype. In addition, this study describes a rapid and inexpensive alternative for the development of SSRs in species with scarce available sequence data.

Keywords

exploit / Betula luminifera / birch / EST database / EST-SSR

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