Molecular characterization and genetic diversity of potential drought-tolerant F ₃ progenies from Salumpikit × IR20 cross

Climate change poses a significant challenge to rice production, underscoring the need to develop drought-tolerant varieties. Marker-assisted selection (MAS) provides an efficient tool to accelerate this selection process. This study evaluated the genetic diversity of an F3 rice population derived from Salumpikit × IR20, and identified potential drought tolerance genotypes using SSR markers. A total of 120 F3 progenies, along with seven check varieties, were evaluated with ten SSR markers. Five markers (RM316, RM228, RM454, RM6703, and RM11943) detected Salumpikit-derived alleles and showed moderate to high polymorphism (PIC = 0.46–0.59). Allelic richness ranged from 12.40 (RM228) to 21.50 (RM454), with an average 17.40. AMOVA revealed 94% of the genetic variation occurred within the population. UPGMA grouped genotypes into two clusters at a similarity of 0.25, whereas STRUCTURE and PCoA divided them into four subgroups. Salumpikit and IRAT112 formed distinct groups, suggesting diverse drought adaptation mechanisms. Interestingly, INPARI39, a moderately drought-tolerant check, clustered with susceptible varieties, indicating limitations in marker-based classification. In total, Sixty F3 genotypes grouped with drought-tolerant checks, representing potential candidates for selection. These findings support the utility of SSR markers for assessing diversity and selecting potential drought-tolerant rice genotypes for future breeding programs.