Identification of novel microsatellite markers in okra (Abelmoschus esculentus (L.) Moench) through next-generation sequencing and their utilization in analysis of genetic relatedness studies and cross-species transferability

Abstract

Abelmoschus esculentus L. (Malvaceae), populary known as okra, is one of the important pod vegetable crops in tropics and subtropics. To develop the microsatellite markers, we have partially sequenced genomicDNA using Roche 454 Titanium pyrosequencing technology. A total of 979,806 bp data from 61,722 reads were obtained. These reads were assembled into 3735 contigs of which 2708 had microsatellites. Primers were designed for 402 microsatellites, from which 50 randomly selected SSR primerswere standardized for amplification of okraDNA. Genetic analysis was done by employing 29 genotypes. Polymorphic information content (PIC) across all 50 loci ranged from 0.000 to 0.865 with a mean value of 0.519. The observed and expected heterozygosity ranged from 0.000 to 0.750 and 0.000 to 0.972, respectively. Alleles per locus ranged from 1 to 27. This is the first report on the development of genomic SSR markers in okra using next-generation sequencing technology. We have also assessed cross species transferability of microsatellite markers with related wild species A. tetraphyllus (84%), A. ficulneus (78%), A. moschatus (92%), A. angulosus grandiflorus (90%) and A. caillei (86%), and demonstrated their use in genetic relatedness study and molecular characterization