Molecular screening of rice (Oryza sativa L.) genotypes for biotic and abiotic stress using trait-specific SSR markers

Abstract

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 primers amplified polymorphic bands (101-750 bp), yielding 46 alleles (average 2.88 per locus) with an average PIC of 0.567 (range: 0.321-0.879), indicating moderate to high informativeness. Drought-linked alleles were 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 divided genotypes into two major clusters with sub-clusters, revealing substantial genetic divergence. Conclusion: The identified multi-stress-tolerant genotypes, such as RTN 17-1817-1-2-1-2-1-2-2 (drought, blast, bacterial blight, BPH), serve as valuable donors for developing resilient cultivars via marker-assisted selection. SSR markers proved effective for rapid, precise stress screening and diversity assessment, supporting climate-adaptive rice breeding.