Phenomics-derived temporal maize health and environmental index enhance physiology-informed genomic prediction of yield across environments

Integrating multi-omics data, including phenomic, genomic, and environmental inputs, offers a powerful approach for enhancing maize performance and predicting grain yield. In this study, crop health was quantified using temporal NGRDI (Normalized Green Red Difference Index) trajectories collected from 16 unoccupied (unmanned) aerial vehicle or system (UAV or UAS, drones and sensors) flights (from 19 to 117 d after planting) in maize trials conducted in Texas. Crop health indices (CHIs) were calculated through area under the curve (CHI_AUC) and functional principal component analysis (CHI_FPCA), capturing dynamic plant health responses throughout the growing season. Heritability estimates of NGRDI fluctuated between 0.3 and 0.7, averaging 0.51 ± 0.02, reflecting consistent genetic contributions to growth dynamics. CHIs derived from a favorable (irrigated) trial in Texas effectively separated high- and low-yielding hybrids across 41 environment-tester combinations, achieving significant differentiation in 27 (CHI_AUC) and 28 (CHI_FPCA1) environments. In comparison, only 21 environments were differentiated when using grain yield alone. Genomic mapping of temporal NGRDI revealed key quantitative trait loci (QTLs) linked to maize growth, containing candidate genes including br2, phyC1, wus1, mads69, cct1, rap2, miR172, and gl15, associated with canopy development, flowering regulation, and drought adaptation. Integrating multi-omics data into phenomic- and environment-informed genomic prediction models improved yield prediction accuracy by approximately 18.5%, particularly for untested genotypes in both tested and untested environments. These findings demonstrate that multi-omics integration provides a scalable framework for enhancing maize performance and advancing grain yield prediction across diverse agricultural systems.