Genetic Diversity and Nutritional Composition of Cottonseed: A Multi-Trait Analysis

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, Pi = 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.