Unravelling population structure and marker trait association using SSR markers among the identified drought tolerant rice landraces (Oryza sativa L.)

With climate change, plants face numerous stresses, notably drought for rice cultivation. Improving rice drought tolerance isvital for sustainable production inwater-scarce regions. Identification ofdrought tolerant genotypes atthe seedling stage ofthe crop contributes tobuild aclimate resilient genotype during the period ofwater scarcity and under challenging environmental conditions. Hence, polyethylene glycol-6000 (PEG-6000) induced drought conditions could beused for testing the drought tolerance inrice atan earlier stage ofthe crop. Optimization of PEG-6000 concentration for screening index at-6 bar was done using three drought-tolerant and two drought-susceptible check varieties based onprobit analysis. Subsequently, 100 rice landraces underwent PEG-6000 induced drought screening at–6 bar and atotal of32 genotypes were selected astolerant. After 14 days oftreatment, the nine observations viz. germination %, root length (cm), shoot length (cm), number ofsecondary roots, fresh weight (g), dry weight(g), shoot/root ratio, root/shoot ratio and vigour index were recorded. Variance analysis, revealing significant genetic variation among genotypes for all studied traits, indicating genetic variability. Post hoc analysis confirmed notable variation among treatments. Principal component analysis revealed three components, with the first three accounting for 88.89% oftotal variability. With respect tothe biplot, the ten genotypes viz., IRGC109, IRGC403, IRGC448, IRGC461, IRGC466, IRGC486, IRGC508, IRGC518, IRGC527 and IRGC535 are the seedling stage drought tolerant genotypes based onshoot length, number ofsecondary roots and vigour index. Population structure classified the accessions into two subpopulations, reflecting diversity. The allele frequency divergence is0.095 which isameasure offixation index revealing that the moderate divergence isnot extremely pronounced. Genetic diversity, assessed through 26 SSR markers selected from drought tolerant QTLs and markers related tovigour index, exhibited 100% polymorphism with 115 alleles and anaverage PIC value of0.61 per primer. Shannon index varied between 0.34 (RM212) and 1.96 (RM252), averaging 1.18. Six SSR markers viz., RM246, RM302, RM252, RM219, RM251, and RM486 were associated with the six key traits viz., shoot length, root length, number of secondary roots, dry weight, shoot/root ratio, and root/shoot ratio respectively offering valuable resources for selecting drought-tolerant accessions as it provides the first step in the selection of genotypes based on the key traits.