Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

Abstract

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.