In this study, GH19 chitinase (Chi) gene family was systematically identified and characterized using genomic assemblies from four cotton species: Gossypium barbadense, G. hirsutum, G. arboreum, and G. raimondii. A suite of analyses was performed, including genome-wide gene identification, physicochemical property characterization of the encoded proteins, subcellular localization prediction, phylogenetic reconstruction, chromosomal mapping, promoter cis-element analysis, and comprehensive expression profiling using transcriptomic data and qRT-PCR (including tissue-specific expression, hormone treatments, and Fusarium oxysporum infection assays). A total of 107 GH19 genes were identified across the four species (35 in G. barbadense, 37 in G. hirsutum, 19 in G. arboreum, and 16 in G. raimondii). The molecular weights of GH19 proteins ranged from 9.9 to 97.3 kDa, and they were predominantly predicted to localize to the extracellular space. Phylogenetic analysis revealed three well-conserved clades within this family. In tetraploid cotton, GH19 genes were unevenly distributed across 12 chromosomes, often clustering in certain regions, whereas in diploid species, they were confined to five chromosomes. Promoter analysis indicated that GH19 gene promoters contain numerous stress- and hormone-responsive motifs, including those for abscisic acid (ABA), ethylene (ET), and gibberellin (GA), as well as abundant light-responsive elements. The expression patterns of GH19 genes were largely tissue-specific; for instance, GbChi23 was predominantly expressed in the calyx, whereas GbChi19/21/22 were primarily expressed in the roots and stems. Overall, this study provides the first comprehensive genomic and functional characterization of the GH19 family in G. barbadense, laying a foundation for understanding its role in disease resistance mechanisms and aiding in the identification of candidate genes to enhance plant defense against biotic stress.

Cotton is one of the most significant economic crops cultivated worldwide. Cottonseed is a strategic reservoir of high-quality plant protein and an underexploited resource for the food and feed industries. To quantify nutritional diversity and identify superior germplasm, we evaluated 312 upland cotton (Gossypium hirsutum L.) accessions over two consecutive growing seasons and characterized 30 agronomic and nutritional traits. Protein content varied widely (29.6–48.8%), with a coefficient of variation of 7.5–11.7% and a two-year mean of 37.0%. Glutamic acid (Glu; 154.0 mg/g) and aspartic acid (Asp; 90.7 mg/g) were the most abundant amino acids, and lysine and arginine were relatively high among essential amino acids. Correlation analysis based on genotype best linear unbiased estimates (BLUEs) showed that most nutritional traits were positively or neutrally associated with key yield-related traits, particularly lint percentage (LP) (e.g., protein vs. LP: r = 0.18, p < 0.01), indicating the feasibility of simultaneous improvement in seed nutritional quality and lint yield potential. Using 29 core traits with complete two-year data, we developed an integrated evaluation framework combining principal component analysis (PCA), grey relational analysis (GRA), TOPSIS, and the analytic hierarchy process (AHP) to rank accessions comprehensively. This framework identified 10 elite germplasm lines with high protein content and favorable yield potential, exemplified by “Xinluzhong 34” (Rank 1; phenotypic comprehensive value, P_i = 0.733). These results provide a quantitative foundation for value-added cottonseed utilization and support breeding strategies aimed at developing cultivars with both high yield and enhanced nutritional quality.