DNA fingerprinting of microsatellite loci in sesame (Sesamum indicum L.): Opportunities and Challenges

Abstract

Sesame is an ancient and multi-utility oilseed crop but has stagnated seed yield levels for quite a long-time and thereby constraining sesame-farming communities in realizing significant profit per unit land area. To circumvent the situation, an increasing number of varieties are being released every year. In this context, establishing a molecular evidence-based technology for ascertaining the distinctiveness of each variety from other is a pertinent yet a challenging task. In the present work, 30 sesame varieties were assessed for DNA fingerprinting of 50 microsatellite loci to establish their genomic distinctiveness. Sesame varieties were raised in pots and genomic DNA was isolated using CTAB method with minor modifications. PCR was carried out using template DNA of 30 genotypes across 50 microsatellite marker loci, validated and optimized in our laboratory, followed by agarose (3%) gel electrophoresis and allele determination. A panel of 50 SSR markers discriminated 30 sesame varieties, either singly or in combination. The resulting marker-variety matrix was obtained, and it is useful as a starting guide for selecting SSR markers for DNA fingerprinting of new varieties developed. Further, the matrix can be augmented as and when new varieties and their parents are analysed using the studied or new marker(s). Enrichment of markers with large number of SNPs and indels require genotyping by sequencing of all the released varieties and their parents to develop a fool-proof DNA-fingerprinting methodology for each variety.