Genetic diversity analysis of traditional and improved rice genotypes in Sri Lanka using SSR markers

Abstract

The objective of the present study was to find the genetic diversity of eight improved varieties and eighty-four traditional accessions of rice using nine polymorphic simple sequence repeat (SSR) markers. The SSR markers detected 32 alleles ranging from 2 to 5, with an average of 3.55 alleles per locus, indicating a high genetic diversity. The number of effective alleles (ne) ranged from 1.85 (RM208) to 3.84 (RM493), with an average of 2.64 alleles per locus, which reconfirms an existing broad genetic diversity. Nei’s genetic diversity index was very high (0.5955), indicating a high mean expected heterozygosity (HE). RM493 recorded the maximum polymorphism information content (PIC) value (0.8814). The mean PIC value was 0.5955 for the used SSR markers. Out of nine SSR markers, seven scored more than 0.5 PIC values, proving their potential to be used as genetic markers. Shannon’s information index (I) ranged from 0.65 (RM208) to 1.36 (RM493), with a mean value of 1.00. All genetic diversity indicators, na, ne, HE, PIC and I reflect the high genetic differentiation in representative sample of rice genotypes. According to the unweighted pair group method with arithmetic mean dendrogram and Nei’s genetic distance, the ninety-two rice genotypes were classified into seven groups at an ~85 level of similarity with additional sub-clusters within each group. Rice genotypes with significant genetic divergence can be chosen for upcoming breeding programmes by assessing their positions within the dendrogram. In the dendrogram, genotypes sharing the same name were not clustered together, indicating their distinct genetic backgrounds despite them sharing the same name. The traditional rice accessions clustered together in the dendrogram can be further analysed using more polymorphic SSR markers.