SSR marker development in Abelmoschus esculentus (L.) Moench using transcriptome sequencing and genetic diversity studies

Abstract

Okra [Abelmoschus esculentus (L.) Moench] also known as bhindi or lady’s finger is an important vegetable crop in India, West Africa, South Africa, Brazil, USA and Turkey. It belongs to the family Malvaceae. Okra is mainly grown in tropics and subtropics of the world. The studies regarding the molecular marker development are very limited; still there is no SSR development from comprehensive transcriptome data in this crop. This study presents the first comprehensive transcriptome data, using RNA from different parts of okra such as root, stem, leaf, bud, flower, different stages of developing pod and from twenty days old plantlets of heat, drought and salt stressed. A total of 10,492 SSRs were identified in this study. Among these tri repeats (2112) were found to be predominant followed by di (1285), tetra (149), penta (24) and hexa. Thirty four SSRs were standardized for PCR and screened for 36 okra genotypes and accessions. Among these 18 SSR primers were found to be highly polymorphic with the PIC values more than 0.5. And the overall results of analysis showed that expected heterozygosity ranged from 0.000 to 0.971 with a mean of 0.593; the values for observed heterozygosity ranged from 0.000 to 0.794 with the mean of 0.254; the number of allele per locus ranged from 1 to 30 and the Polymorphic Information Content (PIC) ranged from 0.000 to 0.940 with the mean value of 0.5546. The genic SSR markers developed will help in germplasm characterization mapping, genetic diversity studies, molecular assisted breeding and also in gene discovery.

Keywords

• abelmoschus esculentus
• transcriptome
• rna sequencing
• microsatellite markers
• ngs
• next generation sequencing