Genetic Interaction Effects of Heading Date Genes Hd1 and Ghd7 on Photosynthetic Traits at the Heading Stage in Rice

In this study, we dissect the genetic effects of two major rice heading date genes, <i>Heading date 1</i> (<i>Hd1</i>) and <i>Grain number, plant height, and heading date 7</i> (<i>Ghd7</i>), in the regulation of six photosynthesis-related traits: the chlorophyll <i>a</i>/<i>b</i> contents, net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), and transpiration rate (Tr). Using two sets of near-isogenic lines (Z43 and Z44) derived from a Zhenshan97/Milyang46 cross, functional <i>Hd1</i> increased the chlorophyll contents but decreased the photosynthesis-related parameters; however, functional <i>Ghd7</i> consistently inhibited all six traits. More importantly, there is a significant epistatic interaction between them: <i>Hd1</i> only enhances the photosynthetic capacity under the non-functional background of <i>ghd7</i> but intensifies its photosynthesis inhibition under the functional background of <i>Ghd7</i>. Transcriptome analysis showed that functional <i>Ghd7</i> mainly down-regulated the expression of genes related to photosynthesis and chloroplast development, and the inhibitory effect was significantly enhanced in the presence of functional <i>Hd1</i>. GO enrichment analysis further confirmed that the chlorophyll synthesis, photosystem assembly, and electron transfer pathways were downregulated in the bifunctional allele combination. Although <i>Hd1</i> promotes chlorophyll accumulation, it reduces the actual photosynthetic efficiency, indicating that it has different regulatory paths for chlorophyll synthesis and photosynthetic function. Both physiological and molecular evidence showed that the <i>Hd1</i>-<i>Ghd7</i> module coordinated the regulation of the heading date and photosynthetic capacity, forming a trade-off relationship between "early heading-high photosynthesis" and "late heading-low photosynthesis". This study reveals the pleiotropy of genes at the heading stage and provides a theoretical basis for the optimization of the source-sink balance in high-yield rice breeding.