Vol. 9, Special Issue 11, Part C (2025)

Aim: This study aimed to molecularly screen 30 rice (Oryza sativa L.) genotypes for tolerance to biotic (blast, bacterial blight, brown planthopper) and abiotic (drought, salinity) stresses using trait-specific simple sequence repeat (SSR) markers, assess genetic diversity, and identify superior accessions as potential donors for marker-assisted breeding to enhance stress resilience and sustainable production.

Study Design: An experimental molecular genetics approach was employed, integrating SSR-based polymorphism analysis, allele scoring, and cluster-based diversity evaluation to profile stress-linked loci and relationships among genotypes.

Place and Duration of Study: The research was conducted at the Plant Biotechnology Centre, Dr. Balasaheb Sawant Konkan Krishi Vidyapeeth (DBSKKV), Dapoli, Maharashtra, India, from 2023 to 2025.

Methodology: Genomic DNA was extracted from young leaves of greenhouse-raised seedlings using a modified CTAB method, followed by RNase treatment and quantification. Sixteen SSR primers linked to key QTLs/genes (e.g., Saltol for salinity, Pi genes for blast, Xa genes for bacterial blight, Bph genes for brown planthopper, Dr genes for drought) were amplified via PCR with optimized annealing temperatures (52-67°C). Products were resolved on 2% agarose gels, scored as binary data, and analyzed for polymorphism percentage, polymorphic information content (PIC), and genetic similarity using Multivariate Statistical Package (MVSP) software. Dendrograms were constructed via the unweighted pair group method with arithmetic mean (UPGMA) based on Jaccard's coefficients.

Results: All 16 SSR markers exhibited 100% polymorphism, yielding 46 alleles (average 2.88 per locus) with an average PIC of 0.567 (range: 0.321–0.879). Drought tolerance was detected in genotypes like RTN 17-1814-2-2-1-1-1-1-2; salinity tolerance in nine accessions (e.g., RTN 18-1914-2-1-4-1-1-5); bacterial blight resistance (Xa5) in four; blast resistance (Pi-1, Pi-z) in four; and brown planthopper resistance (Bph25, Bph26) in two. UPGMA clustering revealed two major clusters with sub-clusters, indicating significant genetic divergence.

Conclusion: This study highlights the efficacy of SSR markers in identifying multi-stress-tolerant rice genotypes, including RTN 17-1814-2-2-1-1-1-1-2 (drought), RTN 18-1914-2-1-4-1-1-5 (salinity and blast), and RTN 18-IR-5-2 (blast and BPH), as valuable donors for MAS. These findings support the development of climate-resilient, high-yielding rice varieties, enhancing sustainable production.