Development, characterization and application of novel expressed sequence tag- simple sequence repeat (EST-SSR) markers in radish (Raphanus sativus L.)

Abstract

In this study, 51,625 unique expressed sequence tag (ESTs) from a total of 289,621 radish ESTs in the National Center for Biotechnology Information (NCBI) database were used to search for simple sequence repeat (SSRs) by SSRLocate, and 2,917 SSRs in 2,891 ESTs were identified. The SSR marker motifs contained di-, tri-, tetra-, penta-, and hexa- nucleotide repeats, and the number was 945 (32.40%), 1,300 (44.57%), 179 (6.14%), 262 (8.98%) and 231 (7.92%), respectively. The motifs AG/CT (16.15%) and GA/TC (13.58%) were the most abundant type. Among 20 amino acids encoded by trinucleotide, Ser (16.17%) was the most common transcript, followed by Leu (13.00%) and Glu (9.90%). A total of 1,082 EST-SSR primers in Raphanus sativus were designed and synthesized, and 864 (79.85%) EST-SSRs were successfully amplified. Polymorphism of these loci was evaluated in a panel of 48 genotypes in Raphanus. The polymorphism information content (PIC) values of those primers varied from 0.33 to 0.84, with a mean value of 0.58. Moreover, it was found that 25 out of 53 EST-SSR primers could be successfully amplified in Brassica species. For its polymorphism, reproducibility and functionality, these novel EST-SSR markers could be used as a powerful tool for marker-assisted selection (MAS) and genetic mapping in radish.

Keywords: Raphanus sativus L., expressed sequence tag (EST), simple sequence repeat (SSR), genetic diversity, polymorphism information content

African Journal of Biotechnology Vol. 12(9), pp. 921-935