Temporal dynamics of genetic architecture governing leaf development in Populus

Summary Leaf development is a multifaceted and dynamic process orchestrated by a myriad of genes to shape the proper size and morphology. The dynamic genetic network underlying leaf development remains largely unknown. Utilizing a synergistic genetic approach encompassing dynamic genome‐wide association study (GWAS), time‐ordered gene co‐expression network (TO‐GCN) analyses and gene manipulation, we explored the temporal genetic architecture and regulatory network governing leaf development in Populus . We identified 42 time‐specific and 18 consecutive genes that displayed different patterns of expression at various time points. We then constructed eight TO‐GCNs that covered the cell proliferation, transition, and cell expansion stages of leaf development. Integrating GWAS and TO‐GCN, we postulated the functions of 27 causative genes for GWAS and identified PtoGRF9 as a key player in leaf development. Genetic manipulation via overexpression and suppression of PtoGRF9 revealed its primary influence on leaf development by modulating cell proliferation. Furthermore, we elucidated that PtoGRF9 governs leaf development by activating PtoHB21 during the cell proliferation stage and attenuating PtoLD during the transition stage. Our study provides insights into the dynamic genetic underpinnings of leaf development and understanding the regulatory mechanism of PtoGRF9 in this dynamic process.