Illuminating the phenotype–genotype black box under complex traits is an ambitious goal for researchers. The generation of temporally or spatially phenotypic data today has far outpaced its interpretation, due to their highly dynamic nature depending on the environment and developmental stages. Here, we propose an integrated enviro-pheno-geno functional approach to pinpoint the major challenges of decomposing physiological traits. The strategy first features high-throughput functional physiological phenotyping (FPP) to efficiently acquire phenotypic and environmental data. It then features functional mapping (FM) and the extended systems mapping (SM) to tackle trait dynamics. FM, by modeling traits as continuous functions, can increase the power and efficiency in dissecting the spatiotemporal effects of QTLs. SM could enable reconstruction of a genotype–phenotype map from developmental pathways. We present a recent case study that combines FPP and SM to dissect complex physiological traits. This integrated approach will be an important engine to drive the translation of phenomic big data into genetic gain.

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