Phenotype-driven screening and machine learning integration for developing high-performance Miscanthus genotypes for saline-alkaline soils

Cultivation of dedicated bioenergy crops on marginal lands is critical for sustainable development, yet breeding climate-resilient genotypes remains a major bottleneck. This study introduces a powerful, integrated framework for accelerating the selection of high-performance Miscanthus hybrids adapted to saline-alkaline soils. The framework uniquely combines phenotypic classification (scatter vs. cespitose plant types) with explainable machine learning (ML). An Extra Trees Regressor (ETR) model, optimized through hyperparameter tuning, achieved high predictive accuracy for biomass (R 2 = 0.916) in a diverse hybrid population. Crucially, SHapley Additive exPlanations (SHAP) analysis revealed two distinct, data-driven ideotypes: the optimal cespitose type maximizes tiller number, whereas the optimal scatter type prioritizes individual tiller biomass and stem diameter. SHAP also uncovered critical physiological trade-offs, identifying potential thresholds for key traits beyond which biomass gains diminish. Applying this framework, we screened 216 genotypes and identified five superior lines. Subsequent two-year field trials on both farmland and saline-alkaline soil validated our approach, with genotype S88 demonstrating superior yield and stability under stress. This study not only establishes a scalable strategy for industrial crop breeding but also offers novel insights into the architectural determinants of yield under marginal conditions. • Developed a phenotype-driven and machine learning integrated framework for Miscanthus breeding. • Established architecture-specific biomass prediction models for scatter and cespitose hybrids. • Identified trait thresholds via SHAP as testable targets for ideotype breeding. • Selected five elite genotypes with stable biomass and salt–alkali stress adaptability. • Provided a reproducible, scalable breeding approach for sustainable industrial crop cultivation on marginal lands.