Integrating Molecular Markers for Screening of Salinity Tolerance in Rice Genotypes

This study assessed the genetic diversity among fifteen rice germplasms, including selected landraces, wild species, released cultivars, improved lines and standard tolerant/susceptible check varieties, using the Saltol QTL and other salt stress-associated SSR markers. The analysis revealed a high level of polymorphism and genetic diversity, with an average of 6.19 alleles per locus and a mean gene diversity of 0.73. The polymorphism information content (PIC) values ranged from 0.53 to 0.78, averaging 0.70, indicating the SSR markers' effectiveness in distinguishing the genotypes. Notably, markers RM490, RM7158, RM562, RM3412, RM493, RM7075, RM8094, RM6811 and RM10825 out of total markers were particularly proficient in screening for salinity tolerance. The genetic relationships among the genotypes were visualized through a dendrogram, forming several distinct clusters. Cluster 1, containing Lalkada gold, Oryza nivara and Purna, showed strong genetic similarity despite varying salt tolerance levels. Other clusters also displayed genetic groupings with phenotypic variances, highlighting the complexity of salt tolerance as a trait. The discrepancies between phenotypic classifications and genetic clustering were attributed to factors such as genetic recombination, multiple mechanisms of salt tolerance, incomplete marker coverage, gene interactions and environmental influences. The dissimilarity matrix further underscored significant genetic relationships, with highly similar genotypes (e.g., GR 17 and IR 28) and completely dissimilar ones (e.g., GR 17 and IR55179-3B-11-3). These findings demonstrate the utility of SSR markers in genetic diversity assessment and marker-assisted selection. The study emphasizes the importance of considering genetic nuances in breeding programs to develop robust, salt-tolerant rice varieties.