Climate change poses an increasing threat to global biodiversity and food security. As a wild relative of cultivated apples, Malus baccata exhibits broad environmental adaptability and robust stress tolerance. However, its effective utilization in breeding is constrained by the absence of a complete reference genome and insufficient population-level genomic characterization. In this study, we assembled a haplotype-resolved, telomere-to-telomere genome for M. baccata, providing unprecedented resolution for a wild apple reference genome. Population genomic analyses revealed four distinct genetic clusters. Among these, the Hebei Group 2 harbors the highest genetic diversity and heterozygosity, alongside the lowest runs of homozygosity, suggesting a complex history of genetic admixture in this population. By integrating population genomics with genotype-environment association analyses, we identified a series of climate-associated single-nucleotide polymorphisms and structural variants. A substantial proportion of these adaptive variants is localized within the coding and regulatory regions of candidate genes, providing a genomic basis for their roles in environmental adaptation. Notably, DREB1A/D and NAC6 are associated with temperature seasonality and annual precipitation, respectively. Furthermore, future climate projections indicate that the Northeastern (NE) clusters face the highest risk of maladaptation, especially under high-emission scenarios. Collectively, these findings provide critical insights into the genetic basis of climatic adaptation in wild apples, establishing a solid foundation for the conservation of crop wild relatives and the breeding of climate-resilient cultivars.

Under anthropogenic global change, mountain plants are among the most threatened flora, making it essential to address conservation gaps to achieve the “30×30” target outlined in the Convention on Biological Diversity. Focusing on Rhododendron, the emblematic genus of montane ecosystems in Asia, we compiled an updated checklist of 603 Rhododendron species in China and integrated high-resolution distribution, phylogenetic, functional trait, and environmental data to examine spatial diversity patterns, driving factors, and priority conservation areas. Our results indicated that the taxonomic, phylogenetic, and functional dimensions of Rhododendron diversity were highly consistent. The Three-Parallel-Rivers-Region in the Hengduan Mountains emerged as the overarching hotspot for richness, endemism, and uniqueness. These diversity patterns were collectively influenced by temperature seasonality and elevation range, with temperature-related energy factors further contributing to the overall phylogenetic and functional structures. The mechanisms underlying uniqueness exhibited regional divergence: In southwestern China, high uniqueness was attributed to the accumulation of intermediate-aged and younger distinctive lineages, coupled with rapid community differentiation; in southern China, it was mainly associated with strong spatial compositional differentiation among communities; whereas in northeastern China, it largely resulted from the preservation of relict lineages. Under the 10% conservation target, we delineated nine priority conservation units across the southwestern, southern, and northeastern mountainous regions of China. However, when the conservation target was increased to 30%, these priority areas expanded to encompass broader mountain regions, highlighting a greater conservation gap. This study provides innovative insights for incorporating multidimensional diversity into effective conservation efforts for Rhododendron species in China.

Phosphate starvation response (PHR) transcription factors are master regulators of the plant phosphate (Pi) starvation response (PSR), yet the mechanisms governing the dynamic control of their transcriptional activity remain elusive. Here, we report a dual regulatory module comprising the coactivator SlMED25 and the corepressor SlSPX2 that fine-tunes SlPHR3 activity in Solanum lycopersicum (tomato). Genetic and biochemical evidence collectively confirmed that SlPHR3 acts as the central regulator orchestrating tomato PSR. Specifically, the mediator subunit SlMED25 interacts with the N-terminal domain (NTD) of SlPHR3 to recruit RNA polymerase II (Pol II) to SlPHR3 target promoters in a SlPHR3-dependent fashion, whereas SlSPX2 binds to the same NTD of SlPHR3 to robustly suppress its transcriptional activity. Biochemical assays further demonstrated that SlSPX2 and SlMED25 compete for binding to SlPHR3, with SlSPX2 exhibiting higher binding affinity. This competitive binding module functions as a key molecular switch that mediates dynamic PSR modulation in tomato, thus yielding distinct functional outputs in response to varying intracellular Pi levels. Our findings uncover a previously uncharacterized regulatory layer in the PSR network, wherein a Mediator subunit and a Pi-sensing protein modulate PHR activity via competitive binding, thereby enhancing the mechanistic insight into Pi homeostasis regulation in plants.

Plant Cullin RING Ubiquitin E3 ligases (CRLs) play a critical role in targeted protein degradation, essential for physiological development and stress adaptation. The deneddylase activity of the COP9 signalosome (CSN) tightly regulates the cellular balance of neddylated cullins, which is crucial for maintaining the full spectrum of CRL functions. Although selective inositol polyphosphates (InsPs) act as cofactors in plant responses that involve ubiquitylation of negative regulators, their connection to CSN–CRL activities has remained unclear. In this study, we reveal that the two Arabidopsis thaliana InsP-kinases, IPK1 and ITPK1, physically interact and orchestrate the metabolic regulation of the CSN holo-complex activity. Notably, ITPK1 deficiency lowers Nedd8 processing rates, elevates the cellular ratios of neddylated cullins, and disturbs the dissociation equilibrium of CSN5 and CUL1 from the holo-complex. These findings uncover a novel autoregulatory switch in CSN functions, governed by deneddylation activity. Furthermore, we demonstrate that the phosphate starvation response (PSR), induced in phosphate-limited wild-type plants and constitutively active in the InsP-kinase mutants, is partly regulated by reduced deneddylation rates, which affect the stability of SPX4, a key negative regulator of PSR. Pharmacological inhibition of cullin neddylation stabilizes SPX4 and impairs PSR, thereby linking CSN–CRL dynamics to phosphate sensing. Conversely, pharmacologically inhibiting CSN5 deneddylase activity causes wild-type plants to exhibit PSR phenotypes similar to those of the InsP-kinase mutants. Collectively, these results reveal that specific InsP-kinases are partly involved in modulating plant PSR by fine-tuning the coordination between CRL and CSN activities.

In contrast to animals, plants possess a remarkable regenerative capacity and are capable of forming new organs or even entire organisms from a limited number of cells present in adult tissues, in response to injury or environmental changes. In this study, we describe the isolation and characterization of the more adventitious roots1-1 (mars1-1) mutant, which exhibits enhanced regenerative potential upon wounding in tomato hypocotyl explants. Additionally, the mars1-1 fruits exhibited a rough surface because of ectopic subepidermal cell proliferation, resulting in the formation of callus-like structures on their cuticle. The MARS1/ROUGH gene encodes a conserved lysine-specific histone demethylase, SlLDL1, which regulates processes such as cell proliferation, stem cell pluripotency, and embryogenesis in metazoans. Two CRISPR/Cas9 null alleles, mars1-2 and mars1-3, were generated, and their pleiotropic phenotypes were characterized. ChIP-seq analysis revealed elevated levels of methylated lysine 4 in histone 3 within specific regions of the mars1/rough genome. To determine the impact of altered epigenetic marks on gene expression regulation in mars1/rough mutants, we analyzed the transcriptome of tomato hypocotyls during adventitious root formation. Using specific bioinformatic workflows and the resolution of the directional RNA-seq data, we identified several dozen distinct genomic regions with de novo expression in the mars1/rough mutants. One such region includes a novel B-type cyclin gene that is upregulated in mars1/rough mutants and may account for adventitious root and fruit skin phenotypes. Our findings indicate that SlLDL1 plays a role in maintaining silencing in specific genomic regions that are essential for tissue-specific reprogramming.

Flooding is one of the most devastating abiotic stresses in agriculture, and enhancing flood tolerance is critical for sustainable crop production. Soybean (Glycine max) is highly susceptible to flooding stress. However, the molecular mechanism underlying soybean response to flooding stress remains largely unknown, and the genes available for improving soybean flood tolerance are relatively limited. In this study, we characterized the function of the predicted cytochrome P450 gene, GmSUR2a, in regulating submergence tolerance in both soybean and Arabidopsis. The Arabidopsis SUR2 gene played a positive role in regulating submergence tolerance. The GmSUR2a, which localizes to a previously identified quantitative trait locus (QTL) for waterlogging tolerance on soybean chromosome 03, shared conserved functions with AtSUR2 in regulating submergence tolerance. Transgenic soybean plants overexpressing GmSUR2a displayed enhanced submergence tolerance accompanied by reduced auxin levels. Further experiments revealed that auxin negatively regulates submergence tolerance: Exogenous auxin application decreased survival rates, and auxin signaling mutants exhibited improved tolerance. We also identified that GmAGL15 transcription factor directly repressed GmSUR2^a expression. Importantly, field trials confirmed that GmSUR2^a overexpression not only improved submergence tolerance but also increased the yield of transgenic soybean plants. Our findings provide new insights into the molecular mechanisms of submergence tolerance and establish GmSUR2^a as a promising target for breeding flood-resistant soybean varieties.