Identification in silico of SSR markers for genotyping Hevea sp. clone gardens in Colombia

The rubber crops profitability depends largely on genotypes established in plantations, meaning that clone identity must be ascertained. This work was aimed at identifying commercial clones Hevea sp. by microsatellites. Primers were designed from sequences reported in Genbank using Primer3, PrimerQuest and OlgoPerfect software for PCR amplification of microsatellites. The primers so obtained were thermodynamically analysed by Oligo Analyzer 3.1 software and experimentally evaluated on 12 Hevea sp. clones. The 15 of the 561 microsatellite markers were selected; they had 2- and 3-bp repeat motifs and 11- to 23-bp repeat extension ranges. The most informative ones were microsatellites amplified with SSRH103, SSRH134, SSRH510 and SSRH516 primers with seven alleles and SSRH403 primers with eight alleles. Four microsatellite markers were sufficient for discriminating 10 of the 12 clones. Clustering analysis involved all the markers on the clones evaluated here, showing Brazilian clones’ narrow genetic base compared to Asiatic ones. The current work provides new markers and joins work published by other authors for identifying and diversity studies of natural rubber clone.