Simple Sequence Repeats (SSR) marker-based analysis on the genetic variation and population structure of local and exotic sorghum germplasm collection conserved ex-situ in Sri Lanka

Abstract

Sorghum (Sorghum bicolor (L.) Moench) is one of the most important cereal crops occupying the fifth position based on the cultivated extent among the cereal crops in the world. Characterization of genetic resources is a pre-requisite for utilization of conserved genetic resources in breeding programmes and cultivation. The present study was carried out to reveal the genetic variation and population structure of local and exotic sorghum germplasm collection conserved in ex-situ seed gene bank at the Plant Genetic Resources Centre, Sri Lanka. Total genomic DNA was extracted from 60 germplasm accessions using CTAB miniprep DNA extraction protocol. A two-step PCR amplification was performed at 16 Simple Sequence Repeat (SSR) loci. Four differentially labeled PCR products were multiplexed and size-fractioned using capillary electrophoresis. Data analyses were performed using GeneMapper 4.0, OSIRIS, PowerMarker 3.25, Structure 2.2 and STRUCTURE HARVESTER. The 16 SSR loci recorded polymorphism and the dendrogram revealed four distinct clusters. The optimum number of subpopulations was three in addition to two admixture subpopulations. The revealed population structure did not depict the geographical origin of the germplasm accessions. The present study confirmed that the majority of local sorghum germplasm accessions tested were genetically distinct. Varying degrees of outcrossing selfing in subsequent generations may have led to the creation of novel sorghum genotypes at global level.