Allelic tuning of PtoRLK609 kinase activity shapes adaptive xylem remodeling in Populus tomentosa

Climate change poses unprecedented challenges to perennial trees. However, the molecular mechanisms by which trees achieve long-term adaptive xylem remodeling remain poorly understood. Here, using transcriptomics and population genomics in 302 Populus tomentosa accessions sampled from three climatically distinct subpopulations, we identified receptor-like kinases (RLKs) associated with climate-related variation in xylem lignification. Among 49 candidates, the wall-associated kinase PtoRLK609 showed among the strongest signatures of population differentiation, a pattern consistent with climate-associated selection. Two major PtoRLK609 haplotypes, defined by four linked missense variants, showed marked geographic differentiation, with PtoRLK609Hap2 reaching fixation or near-fixation in northern populations that experience drier and cooler climates, and was associated with elevated lignin content. PtoRLK609 phosphorylates the transcription factor PtoERF105 at Ser171, which promotes its nuclear accumulation and enhances activation of the lignin biosynthesis genes PtoLAC4 and PtoCCoAOMT1, as well as the vessel development regulator PtoVND7. The PtoRLK609Hap2 protein variant showed higher kinase activity and more efficient phosphorylation of PtoERF105 than PtoRLK609Hap1, linking natural protein variation to differential transcriptional output. Consistent with this mechanism, gain- and loss-of-function analyses showed that PtoRLK609 promotes secondary cell wall lignification, elevates the syringyl-to-guaiacyl (S/G) ratio, increases vessel density, and is associated with better maintenance of stem water status under controlled water deficit. These findings characterize a PtoRLK609-PtoERF105 phosphorylation module associated with xylem remodeling and identify an RLK locus that is a strong candidate for contributing to climate-associated divergence in perennial trees.