Developing EST-Derived Microsatellites in Sesame ( Sesamum indicum L.)

Abstract

To accelerate the application of molecular markers in sesame ( Sesamum indicum L.), expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using publicly available sesame EST data. A total of 1785 nonredundant EST sets were assembled among the 3328 identified sesame ESTs. One hundred and forty-eight microsatellite sequences containing 155 EST-SSRs were detected from these ESTs. The total length of the nonredundant EST sequences was 774.27 kb with an average of 4.99 kb. Among these EST-SSRs, dinucleotide AG/TC was the most abundant (occurring 58 times) with a frequency of 37.42%. Based on these EST sequences containing SSRs, 50 primer pairs were designed and tested with 36 sesame accessions, 2 cotton ( Gossypium barbadense L. and G. hirsutum L.) accessions, 2 soybean ( Glycine max Merr.) accessions, and 2 oil sunflower accessions ( Helianthus annuus L.) to detect their polymorphism and transferability. A few SSRs were able to be transferred to PCR markers, including 2 for cotton, to PCR markers, including 2 for cotton, 3for soybean, and 4 for oil sunflower. Using 44 EST-SSRs, 108 loci were successfully amplified in sesame with an average of 2.45 loci per primer pair. Twenty-seven out of the 44 primer pairs, 27 (61.4%) were polymorphic in the 36 sesame accessions. Their average polymorphism information content (PIC) was 0.390, ranging from 0.105 to 0.844. In the Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendrogram based on genetic similarity coefficient from 91 polymorphic loci, 36 accessions were classified into 4 groups. No geographic distribution was observed in these accessions. The EST-SSRs developed from sesame are valuable for genetic analysis, linkage mapping, and transferability study among oil plants.