| The salt composition of natural saline-alkali soils is inherently complex, and single-salt stress treatments do not accurately reflect real-world conditions. This study aimed to screen and identify cotton genotypes with tolerance to composite salt-alkali stress from a panel of 166 genotypes, providing valuable genetic resources for cotton cultivation in saline-alkali soils and for further gene discovery. Cotton seeds were subjected to composite salt-alkali stress using 0.15 mol/L and 0.3 mol/L solutions during the germination and three-leaf stages. Based on a comprehensive evaluation of germination rate, fresh weight, and embryo root length, genotypes with better growth performance under 0.15 mol/L stress were initially selected. Principal component analysis and fuzzy membership function methods were then used to assess the salt-alkali tolerance of these genotypes under 0.3 mol/L stress, ultimately identifying those with stronger tolerance at the germination stage.The selected genotypes, along with control varieties Zhong 9807 (salt-tolerant) and Xinong 606 (salt-sensitive), were grown to the three-leaf stage and subjected to composite salt-alkali stress. Measurements of leaf morphology, relative chlorophyll content, gas exchange parameters, and chlorophyll fluorescence were conducted to further assess their tolerance at this stage. Results showed that seed germination and embryo root growth were significantly inhibited under 0.15 mol/L composite salt-alkali stress in most genotypes. Specifically, the germination vigor, germination rate, germination index, fresh weight, and embryo root length decreased by 72.558%, 63.542%, 74.737%, 52.790%, and 17.080%, respectively, compared with the control group treated with distilled water. However, 32 genotypes screened using germination traits showed relatively mild inhibition. At 0.3 mol/L concentration, the inhibitory effects were significantly greater than those observed at 0.15 mol/L, with five measured traits showing reductions of 96.247%, 90.909%, 95.389%, 98.097%, and 97.602%, respectively. Through comprehensive evaluation, two composite salt-alkali-tolerant genotypes, De 93-04 (ID: X170743) and 4SA-805 (ID: X170523), were ultimately identified. Three-leaf stage evaluations confirmed that these two genotypes maintained larger leaf areas and higher photosynthetic activity than the controls under high-concentration composite salt-alkali stress, indicating their strong tolerance at the seedling stage. |