Assessment of genetic diversity in Bangladeshi rice (Oryza sativa L.) varieties utilizing SSR markers

Abstract

One of the most fundamental staple foods for the vast majority of people on earth is rice. Farmer-grown traditional rice types which are well-adapted to a wide range of agro-ecological environments provide rich genetic resources for future rice enhancement. The quantity of allelic and genetic variety available in germplasm is a precondition for crop development and conservation techniques under severe climate conditions. However, adoption of high-yielding cultivars has led to their fast loss. Thus, the study's objective was to use marker-assisted selection (MAS) to examine the molecular diversity of rice genotypes using Simple Sequence Repeat (SSR) markers. Eighteen elite rice (Oryza sativa L.) germplasms from Bangladesh were chosen for genetic diversity analysis by SSR marker analysis. PCR amplification of the alleles was carried out and Visualized by Polyacrylamide Gel Electrophoresis (PAGE) system. Four primer pairs that were dispersed across eighteen rice chromosomes were used to detect polymorphisms initially. One representative from each chromosome made up the microsatellite marker panel that was selected, which included RM60, RM163, RM259, and RM278. With an average of 4.75 alleles per locus, a total of 19 alleles were found. Among the four loci spanning eighteen rice accessions, there was a moderate degree of genetic diversity; the average value of these loci is 0.67, ranging from 0.59 to 0.77. With an average of 0.7166, the polymorphism information content (PIC) represents the allele diversity frequency among the varieties, ranging from 0.6481 to 0.8025. Based on PIC values, RM 60 was determined to be the most effective marker for genotype identification. Six clusters were found with a similarity coefficient of 48 % using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and the broad range of dissimilarity values (0.25–0.1), indicating a high level of cultivar diversity. Using a molecular breeding program, the results of the genetic diversity will help to select parents for rice varieties that can withstand different biotic and abiotic stresses.