Development and application of EST-SSR markers in Hevea brasiliensis Muell. Arg

Abstract

Three thousand and ninety Unigenes were obtained from 10 778 Hevea brasiliensis ESTs. Four hundred and thirty SSRs were distributed in 353 Unigenes, which accounts for 11.42% of the total number of Unigenes. The frequency of SSRs was 1/3.93 kb. Dinucleotide and trinucleotide repeats were the dominant types among the obtained unigenes, accounting for 63.49% and 32.09%, respectively. TC/AG, CT/GA and CTT/GAA, AAG/TTC, and AGA/TCT were the most abundant motifs for dinucleotide and trinucleotide motifs. One hundred and forty-eight primer pairs were designed by PRIMER5.0 and 21 primer pairs were synthesized. Among them, 15 primer pairs can produce clear and stable bands, and the PCR products were screened in denaturing polyacrylamide gel following silver staining. Genetic diversity of 44 rubber clones were investigated with these primer pairs, and a dendrogram of 44 rubber clones was built. The results indicated that it is an effective and feasible way to develop EST-SSR markers from H. brasiliensis EST sequences, and the primers designed in this study can be used in genetic study of rubber tree.