Screening for salinity tolerance in rice (Oryza sativa L.) germplasm at reproductive and assessment of genetic diversity using SNPs

Genetic diversity is a valuable asset for agricultural development. Many important traits of economically important crop species are neglected and the alleles may eventually vanish from the gene pool. A total of 50 rice genotypes with diverse genetic background were screened for salinity tolerance at the reproductive stage using four different screening methods namely controlled mini-field, field gravel and soil. Different morpho-agronomic and physiological markers were used to classify tolerant and susceptible genotypes. On the other hand, tolerance indices were used to determine the efficiency of each screening method to distinguish tolerant and sensitive genotypes. The results showed high genetic variability in the response of rice genotypes to salinity. In general, the significant effect (P=0.01) of salinity include: increased Na+ sequestration and unfilled grains (except for the field method) and reduced pollen fertility, total yield, panicle length and average number filled grains/panicle. Plant height (except for the soil method) and K+ ion concentration were not significantly affected by salinity (P0.05). The percent reduction relative to non-stress condition is more pronounced in sensitive genotypes e.g. IR 29 than tolerant genotypes e.g. Pokkali. This study proved that controlled mini-field method is the most advantageous among the screening methods used and the GMPS, STI and YI are the tolerance indices that can be classified as better predictors of salinity tolerance considering the yield potentials of the genotypes. The grouping of genotypes at a particular cluster using SNP data also showed that their genetic make-up somehow do not necessarily indicate their over-all tolerance or susceptibility to salinity. Cluster analysis further supports the non-correspondence in clustering among rice genotypes using SNP and yield data. Genetic diversity analysis also indicates that germplasm evaluated exhibits moderate diversity (PIC x-bar = 0.2085). The notable genotypes that can be used for breeding in the future include Nona bokra and Mushkan 41 through low Na+:K+ ratio, and Damodar and Bhura Rata 4-10 for breeding salt tolerant activars with higher yield potentials. The use of controlled concrete minifield method is recommended for the future screening efforts.