Multivariate screening of upland cotton genotypes reveals key traits for salt tolerance at the seedling stage

Soil salinity poses a serious threat to cotton production worldwide by impairing growth, yield, and fiber quality. Salt stress disrupts key morphological, physiological, and biochemical processes in cotton plants, leading to considerable reductions in productivity. Therefore, identifying salt-tolerant cotton genotypes is essential for improving crop performance in saline environments.

In this study, fifty-one cotton genotypes were evaluated for their response to salinity stress at the seedling stage. Plants were grown in hydroponic culture under controlled glasshouse conditions and subjected to 200 mM NaCl to simulate salt stress. The experiment followed a completely randomized design (CRD) with three replications, and data were analyzed using two-way analysis of variance (ANOVA) and multivariate approaches, including principal component analysis (PCA), heatmap analysis, and the multi-trait genotype-ideotype distance index (MGIDI).

ANOVA showed significant variation among genotypes for all traits. Salt stress caused significant reductions in growth traits, including shoot and root length, fresh and dry biomass, water relation traits, gaseous exchange traits and photosynthetic pigments. In contrast, excised leaf water loss (ELWL), sodium (Na⁺ )accumulation in roots and shoots, oxidative stress markers like hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), osmolytes including proline, glycine betaine (GB), and saponin, and antioxidant enzyme activities like superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) increased, while potassium contents (K⁺) and sodium to potassium ratio (K⁺/Na⁺) decreased. Under control conditions, PCA showed little variation, whereas under salt stress, it explained 64.8% of the variance and separated growth- from stress-related traits. Heatmap analysis confirmed these patterns and grouped genotypes into three clusters based on ion homeostasis and oxidative stress traits. MGIDI index integrated all traits into a single score and identified superior genotypes like G2 (NIAB-868), G22 (NIA-Noori), G32 (FH-530), G3 (NIAB-878-B), G49 (FH-911), G28 (FH-416), G33 (FH-534), and G39 (FH-546).

These findings suggest that multivariate and multi-trait screening at the seedling stage is a useful method for identifying cotton germplasm with salt tolerance, providing a foundation for breeding programs and further field evaluation that may contribute to stable yields under saline conditions.