Temporal and Canopy-Position Trade-Offs Between Cottonseed Nutritional Quality and Yield–Fiber Traits in Upland Cotton Under an Arid Oasis Production System

Elucidating the spatiotemporal interaction patterns among cotton yield, fiber quality, and seed nutritional traits is crucial for the efficient use of cotton as an oil, fiber, and feed crop and for advancing multi-objective breeding. A two-year field experiment (2023–2024) with eight upland cotton varieties was conducted to systematically analyze the dynamic evolution and association networks of multiple traits across flowering stages and canopy positions. Significant genotypic differences were observed: J206-5 (A8) showed a strong yield potential; Tada 1611 (A6) demonstrated an excellent and stable fiber quality; and Xinhuimian 230 (A4) and Shida K9 (A5) showed a consistently high oil and protein accumulation. Temporally, mid-July emerged as a critical window for the synergistic improvement of the fiber quality and protein, while late July favored the boll weight, lint percentage, and oil content. Spatially, the central fruit branches optimized the yield; the upper branches enhanced nutrient accumulation; and the lower branches showed a superior fiber quality. Correlation analysis revealed that fiber quality traits had a stable internal structure, but yield–quality associations were significantly reshaped by interannual environmental fluctuations. Notably, the oil content and protein content were positively correlated across years and positions, yet independently of fiber traits, suggesting that kernel nutrition and fiber development are governed by relatively independent pathways. A comprehensive evaluation classified the germplasm into three groups: integrated high-yield, high-quality, high-nutrition types; trait-specific types; and poor performers. This study provides systematic evidence for the phenotypic feasibility of synergistically improving cottonseed nutrition and fiber quality. It identifies July 17 as the critical flowering window and middle fruit branches as the core canopy position for multi-trait coordination, offering a theoretical basis and practical reference for oil–fiber–feed utilization and multi-objective breeding in southern Xinjiang cotton.