Natural variants of <i>AGL80.5</i> and <i>FPA.3</i> contribute to bud break timing in poplar by controlling auxin biosynthesis

The molecular mechanisms governing phenological characteristics and local adaptation in woody perennials remain largely unexplored. Here, we identified that <i>AGAMOUS-LIKE 80</i> (<i>PtoAGL80.5</i>) and <i>FLOWERING TIME CONTROL PROTEIN FPA</i> (<i>PtoFPA.3</i>) were simultaneously associated with photoperiod factors and bud break (BB) timing in <i>Populus tomentosa</i>. Transgenic experiments in growth chamber and two latitudinal field trials confirmed their positive roles in promoting BB. Both are activated by the canonical phenological regulator <i>SUPPRESSOR OF OVEREXPRESSION OF CO 1</i>, which, in turn, up-regulates the auxin biosynthesis gene <i>TRYPTOPHAN AMINOTRANSFERASE-RELATED</i> (<i>PtoTAR2.1</i>), accelerating BB via auxin pathway. As superior haplotypes, PtoFPA.3^HAP1 binds <i>PtoAGL80.5</i>^HAP1 messenger RNA to elevate protein, up-regulating <i>PtoTAR2.1</i> and increasing indole-3-acetic acid accumulation. Under future climate scenarios, frequencies of <i>PtoFPA.3</i>^HAP1 and <i>PtoAGL80.5</i>^HAP1 are predicted to decline, narrowing BB variance across populations. This genetic regulatory network governing BB timing via the auxin pathway in perennial plants provides insights for molecular design breeding and ecological conservation amid climate change.