Machine Learning-Driven Identification of Key Environmental Factors Influencing Fiber Yield and Quality Traits in Upland Cotton.

Abstract

Understanding the influence of environmental factors on cotton performance is crucial for enhancing yield and fiber quality in the context of climate change. This study investigates genotype-by-environment (G×E) interactions in cotton, using data from 250 recombinant inbred lines (CCRI70 RILs) cultivated across 14 diverse environments in China's major cotton cultivation areas. Our findings reveal that environmental effects predominantly influenced yield-related traits (boll weight, lint percentage, and the seed index), contributing to 34.7% to 55.7% of their variance. In contrast fiber quality traits showed lower environmental sensitivity (12.3-27.0%), with notable phenotypic plasticity observed in the boll weight, lint percentage, and fiber micronaire. Employing six machine learning models, Random Forest demonstrated superior predictive ability (R² = 0.40-0.72; predictive Pearson correlation = 0.63-0.86). Through SHAP-based interpretation and sliding-window regression, we identified key environmental drivers primarily active during mid-to-late growth stages. This approach effectively reduced the number of influential input variables to just 0.1-2.4% of the original dataset, spanning 2-9 critical time windows per trait. Incorporating these identified drivers significantly improved cross-environment predictions, enhancing Random Forest accuracy by 0.02-0.15. These results underscore the strong potential of machine learning to uncover critical temporal environmental factors underlying G×E interactions and to substantially improve predictive modeling in cotton breeding programs, ultimately contributing to more resilient and productive cotton cultivation.