Explore the EST libraries for development microsatellite markers in halophyte grass Aeluropus littoralis

EST sequences recorded in the Gene bank database are an important source for microsatellite discovery in coding genome. These sequences give us the opportunity to discover new genes, as well as a resource for development of markers. Unlike genomic microsatellite markers (noncoding), EST-based microsatelite markers (EST-SSR) are effectively extracted from free publicly EST libraries with less time and expense and show the good performance. In this research using the halophyte grass, Aeluropus littoralis EST library and insilico analysis microsatelite motifs were identified and based on that 16 polymorphic markers (ALES), was developed for genomic studies. The results showed that in this plant (6.7%), such as rice (4.7%), there is a high rate of microsatellite in the coding regions. Also, tg, (gcg- gaa) and ttga motifs constitute the major variety of SSR motifs in a set of Aeluropus EST records. The polymorphism information content (PIC) values ranged from 0.27 to 0.37 with an average of 0.32 that higher values goes to ALES number 3,1,11,13 and 15. An average similarity coefficient (Jaccard) between samples was reached to 55%. These results suggest a great genetic variability in genomic coding regions of A. littoralis plant. Finally, cluster analysis grouped the A. littoralis ecotypes into six groups.