Characterization of novel developed expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers and their application in diversity analysis of eggplant

Abstract

A total of 101,270 eggplant expressed sequence tag (EST) sequences at public databases were used to search for simple sequence repeats (SSRs) and 405 potential SSR loci were identified from 388 sequences. The highest proportion (34.07%, 138) was represented by trinucleotide, followed by dinucleotide (19.51%, 79) and hexanucleotide (15.8%, 64). Among the dinucleotide repeats, AG/CT was the most common (55.69%), followed by AT/AT (31.64%) and AC/GT (12.66%). Further, 288 pairs of primers were developed from these sequences. A random set of 100 EST-SSR primers were amplified in 12 eggplant accessions and 88 successfully amplified expect PCR products. 32 markers revealed 83 polymorphic alleles among the 42 cultivated accessions and the number of allelles per locus varied between 2 and 6 (mean 2.6). Polymorphism information content (PIC) values among the 42 cultivated types were calculated and varied from 0.045 to 0.701 (mean 0.289). The markers showed low frequency transferability in Solanaceae. The 32 SSRs were used to evaluate genetic diversity. These SSRs will be valuable markers for future genetic study, such as genetic diversity estimation, linkage mapping, association mapping and molecular breeding.

Key words: Expressed sequence tags, transferability, diversity, dendrogram.