Development of EST-SSR markers using transcriptome data in okra (Abelmoschus esculentus L.): a genetically orphan crop

Okra is an important vegetable crop with few genomic resources and only limited simple sequence repeat (SSR) markers. In the present investigation, we have performed RNA sequencing (RNA-Seq) from leaf samples of okra varieties Pusa Sawani and Pusa Bhindi-5. Out of the 106224 EST-SSRs identified, mononucleotide repeats were dominant with a frequency of 72.20% (71699) followed by trinucleotide 15% (14897) and dinucleotide 10.68% (10604) repeats. In total, 183 best primer pairs (156 di and 27 trinucleotides) were selected for validation in 12 okra accessions comprising wild and cultivated Abelmoschus species. Overall, 163 primer pairs produced expected PCR amplicons with an amplification efficiency of 89%. A total of 23 primer pairs showed a 14.1% polymorphism percentage with an average value of 0.32 polymorphic information content (PIC) and these polymorphic markers were used further for diversity analysis. The UPGMA dendrogram analysis separated the okra accessions into two main clusters. This study provided insight into the distribution and frequency of EST-SSRs in the okra transcriptome. The EST-SSR markers developed here will be a robust molecular tool for germplasm identification, genetic diversity analysis, and comparative mapping in okra and related species due to their high polymorphism and cross-transferability.