Efficiently developing a large set of polymorphic EST-SSR markers for Xanthoceras sorbifolium by mining raw reads from high-throughput sequencing

Abstract

Yellow-horn (Xanthoceras sorbifolium Bunge) is an economically and ecologically important tree in northern China that is facing severe stress from human activity and the changing climate. Transcriptome-wide or genome-wide genetic markers are required for functional studies and development of conservation strategies based on genetic variation within the species. In this report, using an in silico microsatellite detection and primer design strategy implemented in the computer program QDD, we detected and designed primers for 477 candidate polymorphic EST-SSR (simple sequences repeat in expressed sequence tags) loci by mining raw reads from high-throughput transcriptome sequencing of pooled samples. A total of 48 primer loci were selected randomly and evaluated, of which 29 (60.42 %) were polymorphic in eight individuals. Based on these results, this development strategy can be used for the development of EST-SSR markers. This large set of marker resources can be used for mining, performing functional studies, and developing conservation strategies for this endangered species.