Research Article Identification and Characterization of Microsatellites in Expressed Sequence Tags and Their Cross Transferability in Different Plants

Copyright © 2014 Shamshad ul Haq et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Expressed sequence tags (EST) are potential source for the development of genicmicrosatellitemarkers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4 % frequency). Analysis revealed that trinucleotide repeats (47.52%)weremost abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84 % to 98.06 % in different plants, with an average of 67.86%.Thus, the validation study of annotated 35 EST-SSRmarkers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants. 1