Characterization of Selected Zambian Rice (Oryza sativa) Accessions using Simple Sequence Repeat (SSR) Markers

Abstract

Background: Rice (Oryza sativa L.) is grown in various parts of Zambia. Response of available varieties towards biotic (bacterial and fungal pathogens) and abiotic factors such as water stress remains unavailable. A systematic rice seed system or breeding program appears to be non-existent. This study was undertaken to assess the genetic diversity among some selected Zambian rice accessions using simple sequence repeat (SSR) molecular markers. Methods: Thirty accessions were selected for genetic diversity analysis using ten SSR markers (RM5, RM168, RM7, RM13, RM225, RM452, RM211, RM205, RM413 and RM46) selected from various chromosomal loci of the rice genome. Rice genomic DNA was amplified by the polymerase chain reaction and products were analyzed by 1% agarose gel electrophoresis. Most products appeared as single alleles in form of single bands averaging between 79-200 base pairs (bp). Significant relatedness within and among accessions was observed while most of the primers showed distinct polymorphism. Cluster analysis via a dendrogram revealed that most of the accessions were closely related and clustered into two major groups designated A and B. Result: Only one accession (ZM8321) appeared to be distinct and distantly related to all the other 29 accessions Cluster B contained the rest of the 29 accessions which were subdivided into 8 sub-clusters. Of the 29, accessions ZM8295 from Samfya District and ZM8313 from Kaputa district showed 100% similarity meaning that they are the same accession.