Abstract
BACKGROUND: Climate changes pose challenges to crop production. However, the causes of phenotypic differences across environments remain unclear. RESULTS: Here, heading date (HD), flowering date (FD), and plant height (PH) were measured along with four environmental factors (day length (DL), growing degree days (GDD), precipitation (PRCP), and photothermal ratio (PTR)) to investigate the genetic basis of phenotypic plasticity of these traits in 616 wheat accessions using genome-wide association studies. Regarding quantitative trait locus-by-environment interactions (QEIs), five known and three candidate genes for HD, six known and seven candidate genes for FD, and four known and eighteen candidate genes for PH were identified. For the genes associated with phenotypic plasticity, 10 genes exhibited responsiveness to alterations in diverse environmental conditions according to transcriptome data; haplotype effects of 33 genes were identified as significantly correlated with the changes in environmental factors; six candidate genes were identified as hub genes in the gene network, possibly influencing other genes and causing the phenotypic plasticity. And over-dominant effects can explain over 50% the genetic variance of phenotypic plasticity. More importantly, one FD/HD candidate gene (TraesCS4A01G180700) and two PH candidate genes (TraesCS5B01G054800 and TraesCS2A01G539400) partly explain the phenotypic plasticity for the FD/HD and PH traits, respectively. In addition, the potential utilization of these genes in wheat breeding was discussed. CONCLUSIONS: This study elucidated the genetic basis of phenotypic differences caused by environments and provided a foundation for addressing the impact of climate change on crop production.