Genomic-derived microsatellite markers for diversity analysis in Jatropha curcas

Abstract

New set of 1,122 novel genomic-derived microsatellite markers developed, validated and a set of 447 polymorphic SSR identified for Jatropha curcas. The AMOVA showed that 6 % of the total genetic variation exists among the population and 94 % within the populations. Jatropha curcas L., a non-edible, oil-rich crop has attracted global attention as a promising renewable resource for biodiesel production. Limited numbers of validated and characterized markers such as SSRs are available that could be utilized for molecular breeding in Jatropha. To enrich the marker resources, we have employed next-generation 454 sequencing to develop a large number of microsatellite markers from trinucleotide-enriched genomic libraries. A total of 124,279 raw reads were assembled into 2,845 contigs and 22,650 singletons. We designed 1,122 SSR flanking primer pairs and validated them with a panel of seven accessions of J. curcas and one J. integerrima to identify polymorphic SSRs. Out of these 1,122 SSRs, 447 (39.83 %) were found to be polymorphic among J. curcas accessions. A higher transferability of SSRs (76 %) to J. integerrima was noticed. A subset of randomly selected SSRs (41 SSRs) was amplified across 96 accessions of J. curcas, which detected a total of 152 alleles ranging from 2 to 9 with an average of 4.0 ± 1.9 alleles/SSR. The analysis of molecular variance (AMOVA) showed that 6 % of the total genetic variation exists among the population and 94 % within the populations indicated high genetic variation within population. The neighbor-joining (NJ) tree based on Jaccard’s coefficient grouped the 96 accessions into three major clusters. The non-toxic accessions form a separate cluster and rest of the accessions intermixed irrespective of geographical distribution. STRUCTURE-based clustering also resulted in a similar pattern of grouping.