Genomic and environmental determinants and their interplay underlying phenotypic plasticity

Significance Integrated analysis of genotype by environment can reveal the pattern and mechanistic interplay underlying the observed phenotype dynamics. A critical question needs to be answered to enhance our ability to conduct genomic and environmental analysis of varied phenotypic plasticity observed in natural field conditions: How to uncover patterns at different levels to facilitate complex trait dissection and performance prediction. In this study, we first uncovered the pattern of genotype response to different environments. We then uncovered the pattern generated by the combination of environmental factors and the pattern of genetic effects at the individual gene level across environments. Finally, we demonstrated that trait dissection to individual genes and genome-wide performance prediction can be conducted through a joint genomic regression analysis framework.