Identification of Salt‐Tolerant Upland Cotton Genotypes at the Seedling Stage Using Multivariate Analysis and Composite Stress Tolerance Index

Upland cotton is a globally significant cash crop; however, its early growth, especially the seedling stage, is highly susceptible to salinity stress. Therefore, this study was conducted utilising multivariate approaches and stress indices of morphological, water relations, gaseous exchange, and ionic homeostasis to enhance the selection of tolerant genotypes under salt stress at the seedling stage. Salt stress significantly reduced shoot and root biomass, gaseous exchange, and water relations in sensitive genotypes as compared to tolerant genotypes. Tolerant genotypes exhibited better ionic homeostasis (K + /Na + ) in both roots and shoots under saline conditions. Principal component (PCA) and correlation analyses identified relative water content (RWC), photosynthesis (Pn), water‐use efficiency (WUE), root and shoot K + /Na + ratios, as well as biomass traits such as fresh shoot length (FSL) and dry shoot weight (DSW), as key indicators of salt tolerance. Further, heatmap clustered genotypes by tolerance level, while a composite stress tolerance index (CSTI) classified them into tolerant, moderately tolerant and susceptible groups. These combined approaches identified NIAB‐512‐68‐SB, FH‐326 and FH‐540 as the potential salt‐tolerant lines. These results show that combining multivariate analysis with the CSTI index improves early salinity screening and helps identify traits and genotypes useful for breeding salt‐tolerant cotton.