Characterization of ‘Suduru samba’ rice (Oryza sativa L.) Accessions using genome wide SSR polymorphism and seed morphology

Molecular characterization of genotypes gives precise information about the extent of genetic diversity. Correct identification of the traditional rice varieties is a timely requirement as there are a number of accessions per variety available at the PGRC. The main objective of this study was to select a set of representative accessions of 'Suduru samba' using molecular analysis inorder to solve variety identification problems while assessing the genetic diversity. A total of 13 accessions including eleven ‘Suduru samba’, and controls (Kaluheenati and Bg360) were evaluated using 31 SSR markers distributed widely over the rice genome. DNA was extracted from tender leaves of 14 days old seedlings using modified CTAB method and PCR ampilificons were separated using 8% polyacrylamide gel electrophoresis. Average linkage clustering, Principle component analysis (PCA) and Polymorphic information content (PIC) analysis were performed to assess the genetic diversity. A total of 184 alleles were detected by 31 markers, all of which were (100%) polymorphic. Allele richness ranged from 3 to 9 per locus. The first two principal components cumulatively explained about 39.89% of the total variation among the 13 accessions. Polymorphic information content values varied from 0.8758 to 0.4230. Seed morphology analysis was done using 7 seed characters to compare the results. The first three principal components cumulatively explained over 85% of the variation and first two principal components explained about 74.79% of the variations. Molecular and seed morphology clusters delineated the 11 accessions effectively and highly related accessions AC2202, AC3333, AC3594, AC5402 and AC3671 were selected as the representative set of Suduru samba. These results will the pave way for establishing a core collection and identification of ‘Suduru samba’ for evaluation of agronomic traits and seed paddy certification scheme to fulfill the current need.