Microsatellite variability and its use in the characterization of cultivated clones of Hevea brasiliensis

Abstract

Microsatellite markers were developed and evaluated in Hevea brasiliensis, an important crop species producing natural rubber of commercial utility. Of eight microsatellite markers, four were found to be highly informative, amplifying a total of 19 alleles when evaluated against 27 cultivated Hevea clones/genotypes. Power of discrimination of the microsatellite loci was in the range of 0.62-0.89, with a mean of 0.76 indicating these microsatellites could be valuable genetic markers for diversity characterization. A combination of four microsatellite markers was successfully used to discriminate uniquely all the 27 Hevea clones and some clone-specific allelic profiles were generated. Crossspecies amplification of the markers developed in H. brasiliensis had also been demonstrated with two other Hevea species, H. benthamiana and H. spruceana, indicating a high degree of sequence homology at the flanking regions. Sequence analysis of the repeat region at the 3¢-UTR of the hydroxymethylglutaryl-coenzyme A reductase gene, containing clusters of AG repeats in 15 clones, revealed the existence of two alleles based on the repeat length polymorphisms. Homozygosity as well as heterozygosity for both the alleles had also been detected among the clones. Frequency of homozygotes for the smaller allele (allele-1) was found to be lower than the larger allele (allele-2) among the primary clones of H. brasiliensis.

Genomic validation of PB 260 clone of rubber (Hevea brasiliensis) at Cikumpay Plantation by SSR marker

“…For primer hmac5, the DNA profiles showed size among 200-300 bp with single band for each samples. They have same bands from 10 samples and same size with experiment reported by [15]. Primer hmct1 showed that DNA band from 10 sample of PB 260 clone have the same size and single band.…”

“…DNA profile from 10 rubber trees from PB 260 clone had been amplified with 4 SSR primers from [15]. The result showed that all of samples have the same bands when amplified with each primer.…”

“…Primers used for this research were 4 primers based on GenBank with accession numbers are: AY135656, AY135657, AY135651 and AY135653 for the loci i.e. hmac4, hmac5, hmct1, hmct1, and hmct5 [15] as seen at Table 2.…”

“…The result showed that all of samples have the same bands when amplified with each primer. Primer hmac4 has 1 single DNA band for each sample with size among 100-200 bp, this DNA bands different size with [15] that reported among 216-272 bp. For primer hmac5, the DNA profiles showed size among 200-300 bp with single band for each samples.…”

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

“…Several genetic analysis has been done using SSR markers, such as in coconut (Larekeng, Maskromo, Purwito, Matjik, & Sudarsono, 2015; and oil palm (Tinche, Asmono, Dinarti, & Sudarsono, 2014). Scientists have also done the evaluation of rubber tree genetic diversity analysis using RAPD or SSR markers (Besse et al, 1994;Saha, Roy, & Nazeer, 2005;Lam, Thanh, Chi, & Tuy, 2009;Gouvêa, Rubiano, Chioratto, Zucchi, & de Souza Gonçalves, 2010). Diversity analysis using SSR markers is more beneficial than using other dominant markers since SSR markers can differentiate the homozygous and the heterozygous individuals and exhibit high polymorphism.…”