Evaluation of Salt-Tolerant Germplasms and Identification of Salt Tolerance-Related Proteins in Upland Cotton at the Seedling Stage

Currently, developing cotton cultivation in saline-alkali soils is a vital focus for restructuring the cotton industry in China. The seedling stage, specifically the three-leaf stage, is a crucial period for assessing the salt tolerance of cotton. This research examined 430 natural populations of upland cotton, including 45 semi-wild germlines of Gossypium purpurascens. We measured the phenotypic responses of salt stress injury on seedlings as well as potassium (K), calcium (Ca), sodium (Na), and magnesium (Mg) concentrations in the roots, stems, and leaves following a 72 h exposure. The comprehensive salt tolerance index (CSTI) was determined using a membership function, principal component analysis, and cluster analysis based on 48 phenotypic traits related to salt tolerance. The results revealed significant variations in the phenotypic traits of the ion group under salt stress. Salt stress greatly affected the relative contents of Mg, K, and Ca ions in the aboveground parts of cotton, and correlations were observed among the 48 indices. The CSTI was calculated using seven principal component indexes, identifying 30 salt-tolerant, 114 weakly salt-tolerant, 39 salt-sensitive, and 4 highly sensitive materials based on cluster analysis. Among the 45 G. purpurascens cotton resources, 28 were weakly salt-tolerant, while 17 were salt-sensitive. Through TMT (Tandem Mass Tag)-based quantitative analysis, we identified 3107 unique peptides among 28,642 detected peptides, resulting in 203,869 secondary mass spectra, with 50,039 spectra successfully matched to peptides. Additionally, we identified several salt tolerance-related pathways (carbon metabolism; glutathione metabolism; the biosynthesis of amino acids, etc.) and proteins classified within the CAZy (Carbohydrate-Active EnZYme) family and expansin proteins. The results of this study concerning salt-tolerant materials provide a crucial theoretical foundation for the identification and evaluation of salt-tolerant breeding parents in cultivated cotton.