Developmental Genetic Analysis of Cotton Seed Protein Using the ADM Model

[Background] Cotton seed protein is an important seed quality trait with considerable utilization potential; however, the genetic mechanisms governing its developmental dynamics remain incompletely understood. [Methods] Field trials were conducted during the 2024 and 2025 growing seasons. Using 11 upland cotton parental lines and 36 F1 hybrid combinations obtained through Griffing-II double-cross hybridization, three planting configurations were evaluated (three-row (FR3), four-row (FR4), and six-row (FR6) film mulch configurations). Samples were harvested at eight developmental stages: 10, 15, 20, 25, 30, 40, 50, and 60 days after anthesis. Cotton seed protein content was determined using the Kjeldahl method, and protein accumulation parameters were estimated using a logistic growth model. Unconditional and conditional genetic analyses were conducted using a developmental ADM model that incorporated genotype–environment interactions. [Results] Cotton seed protein accumulation exhibited an S-shaped trend: it first increased, entered a plateau phase, then declined slightly, and rose gradually in the later developmental stage. Genotype, year, planting configuration, and their interactions significantly affected protein content and growth parameters but did not alter the underlying developmental trajectory. Among the planting configurations, FR4 exhibited the highest protein accumulation rate and maximum protein accumulation, with the lowest trait variation, and showed the most favorable overall performance under the conditions tested. Genetic analyses indicated that the dominance–environment and maternal–environment interactions were the principal components of protein accumulation, whereas additive, dominance, and maternal main effects were significant only at specific developmental stages. In terms of the genetics of cotton seed protein, the predicted genetic effects across different environments and developmental stages indicated that P6 exhibited the highest stability of genetic effects, P7 and P9 showed moderate stability, whereas P3 had relatively low stability of genetic effects. [Conclusions] The developmental pattern of cotton seed protein accumulation was largely governed by genetic effects and remained relatively stable, whereas environmental conditions mainly modified the magnitude of accumulation. For breeding aimed at improving cotton seed protein, the genetic backgrounds of parental lines should be considered together with environmental effects on cotton seed protein accumulation.