Decoding living systems: Reassessing crop model frontiers via biological dynamics and optimized phenotype.

Modeling and optimizing phenotypic performance of biological systems demands understanding how physiological processes mediate genotype-by-environment interactions. While AI-driven approaches achieve predictive accuracy, they often function as black boxes that obscure biological causality. Process-based models address this limitation through explicit mechanistic representation, enabling both quantitative optimization and biological interpretation. This study contributes an inverse engineering framework with three integrated layers: sensitivity analysis validating biological coherence, genetic algorithm exploring virtual phenotypes to identify adaptive strategies, and similarity analysis quantifying routes from computational optima to field-validated cultivars. Sensitivity analysis identified eight genetic-based coefficients governing yield with robust rankings (95% CI width = 0.04). The genetic algorithm explored 5,364 virtual cultivars across 40 generations, revealing two strategies: extended growth (116 days) achieving 4,837 kg/ha under higher water availability (815 mm, field capacity 0.30), and shortened cycles (100-103 days) maintaining high efficiency (HI: 0.55-0.58) under water deficit (540 mm, field capacity 0.23)-covering 89% of the cultivation area. Similarity analysis against 21 field-validated cultivars identified WAB56-50 (70.7%) and DKAP2 (67.2%) as breeding candidates, quantifying a 22-30% genetic gap between current germplasm and computational optima. The framework, built upon 3 years of field characterization, compressed the evaluation and selection cycle, enabling adaptation across regional precipitation gradients identified through GMM-based classification. The principles demonstrated here extend across biological scales-from organismal phenotyping to cellular systems where biological dynamics can be modeled and traits measured.