Evaluation of the genetic architecture utilizing simple sequence repeat (SSR) markers in deep water rice (Oryza sativa L.) landraces of Assam, India

Deep water rice (DWR) is an essential agricultural practice in flood-prone regions, supporting millions of farmers in Asia and Africa. However, its cultivation is under threat from changing climates, modern agricultural practices and socio-economic shifts. Although the state has quite a large collection of deep water rice (Oryza sativa L.), there is less exploration on the nature and extent of genetic diversity. Therefore, the present study was conducted to investigate the genetic diversity in a set of 92 deep water rice landraces by evaluating genetic polymorphism using 56 polymorphic SSR markers. A total of 139 alleles were detected, showing high polymorphism among all these diverse landraces. The major allele frequency of SSR loci comes in the range of 0.299 to 0.88. Expected heterozygosity varied from 0.21 and 0.74, whereas the observed heterozygosity ranged from 0.00 to 0.73. The PIC value ranged from 0.18 to 0.69 and the RM 206 marker was found to be most appropriate to discriminate among these landraces, owing to the highest polymorphic information content value of 0.69. AMOVA revealed that the principal molecular variance existed within populations (96%) rather than among populations (4%). The phylogenetic analysis clustered these accessions into 7 clusters, in which cluster II had a maximum of 27 genotypes, followed by cluster III and cluster I. Similarly, structure analysis based on Bayesian clustering grouped these diverse accessions into 7 sub-populations and also observed admixture in the accessions. The information accrued from the current study offers valuable insights for effective use in improving DWR varieties.