Plant flavor diversity arises from genomic variation across species and cultivars, yet the mechanisms linking natural genomic variation to flavor‐related phenotypes remain insufficiently integrated. Here, we systematically review how diverse forms of genomic variation reshape the biosynthesis, transport, and accumulation of flavor‐related metabolites, thereby driving diversification in sweetness, acidity, bitterness, piquancy, astringency, and aroma. We further integrate evidence from genomics, transcriptomics, metabolomics, and functional validation to outline a mechanistic framework linking genomic variation to the molecular and metabolic basis of flavor phenotypes. We then examine how artificial intelligence‐assisted breeding and precision gene editing can accelerate the identification of causal variants and enable targeted improvement of flavor‐related traits. This framework establishes plant flavor as a mechanism‐based target for plant improvement, with broad implications for quality, nutrition, and sustainability.

Identifying male-sterile genes and developing biotechnology-based male-sterility systems are crucial for advancing hybrid maize breeding. However, this progress is hampered by the limited number of characterized key regulators and their incomplete mechanistic understanding in male sterility, as well as fertility instability of male-sterile lines and a lack of efficient maintainer lines in maize. Here, we elucidate the multifaceted roles of ZmMS1, an LBD transcription repressor. ZmMS1 coordinates timely tapetal PCD by repressing ROS- scavenging genes to regulate anther ROS homeostasis, while its DNA-binding activity is redox- sensitive, suggesting a potential redox-dependent feedback mechanism. In addition, ZmMS1 balances lipid allocation between anther cuticle and pollen exine by directly repressing sporopollenin biosynthesis and indirectly promoting cutin/wax formation. Constitutive overexpression of ZmMs1 induces dwarfism associated with GA and ABA homeostasis, and produces ~50% sterile and small pollen grains in maize and rice, offering a potential route for dwarf and male-sterile breeding. Leveraging the findings that loss and precocious expression of ZmMs1 cause recessive and dominant sterility, respectively, we develop a non-transgenic multi-control sterility system and a dominant genic male-sterility system, both showing stable and complete sterility across diverse backgrounds without yield penalty, thereby providing flexible options for hybrid maize breeding. Our findings reveal that ZmMS1, as a redox-sensitive transcription factor, regulates male fertility with previously unrevealed mechanisms, and provide practical tools for efficient hybrid maize breeding.

Peanut (Arachis hypogaea) is an allotetraploid legume crop of agricultural and economic importance worldwide. Despite advances in peanut genomics, the integration of genetic diversity with multi-omics landscapes remains limited, and a comprehensive understanding of subgenome asymmetry is still lacking. Here, we present a high-quality genome assembly of an elite peanut cultivar Zhonghua 5 (ZH05; 2,622.85 Mb with 73,718 predicted genes) and construct a species-specific pan-genome based on 1,286 accessions, uncovering 849.82 Mb of non-reference sequences and 18,484 novel genes. Over 23 million genetic variants and extensive gene PAVs substantially expand the landscape of genetic diversity in peanut. Integrative multi-omics (transcriptome, DNA methylation, chromatin accessibility, and three-dimensional genome architecture), combined with population genomics analyses, reveal pronounced and multi-layered subgenome asymmetry. Specifically, SubA shows higher chromatin accessibility and overall gene expression, whereas SubB displays more transposable elements, elevated DNA methylation, more genes under selection during domestication, and stronger three-dimensional chromatin interactions with more stable topologically associating domains. Furthermore, genetic dissection using a recombinant inbred line population identified several major stable QTLs for seed size, whose pyramiding contributes to ZH05's superior yield performance. Collectively, this study establishes an integrated genomic framework for peanut, illuminates asymmetric subgenome evolution across sequence, epigenetic, and chromatin architecture, and provides valuable resources for accelerating molecular breeding and crop improvement.

Auxin, primarily indole-3-acetic acid (IAA), is a central regulator of growth and development in land plants, but its physiological role in chlorophyte algae remains unclear. Here, we show that exogenous IAA modulates growth in Chlorella sorokiniana, Chlorella variabilis, and Chlamydomonas reinhardtii in a concentration-dependent manner. Low IAA concentrations promoted growth by accelerating the onset of cell division without affecting cell size, whereas higher concentrations inhibited proliferation. Radiotracer assays showed that all three species take up and release IAA across the plasma membrane through a combination of passive diffusion and energy-dependent, saturable processes. Competition by excess unlabeled natural and synthetic auxins further supported the presence of carrier-mediated transport with broad substrate recognition. Phylogenetic analyses identified potential PIN-like auxin exporters in chlorophytes and other non-plant eukaryotes, and structural modeling supported conservation of the overall PIN fold and predicted auxin-binding residues. However, functional assays in Xenopus laevis oocytes, tobacco BY-2 cultured cells, and Arabidopsis thaliana did not support a role for these proteins in directional auxin export. Instead, non-plant PIN homologs localized predominantly to the endoplasmic reticulum and showed limited or no transport activity in heterologous systems. Together, these findings indicate that auxin responsiveness and basic cellular auxin transport predate canonical PIN-mediated directional auxin export, which appears to be a later innovation of the streptophyte lineage.

Meiotic crossover (CO) exchanges genetic information between homologs, thereby promoting genetic diversity among offspring. COs are non- randomly distributed across chromosomes, tending to occur in euchromatin, but rarely in heterochromatin. In plants, H3 lysine 27 monomethylation (H3K27me1) is crucial for maintaining heterochromatin condensation and genome stability in somatic cells; however, its role in germline cells remains to be determined. Here, we demonstrate that the plant-specific H3K27 mono-methyltransferases ATXR5/6 (ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5/6) play an important role in inhibiting CO formation in meiotic heterochromatin. In atxr5 atxr6, both ZMM-dependent Type I COs and ZMM-independent Type II COs are significantly increased. We further observed decondensation, decreased H3K27me1 signals, and specifically compromised non-CG methylation in atxr5 atxr6 meiotic heterochromatin. Unexpectedly, in contrast to their roles in somatic cells, where ATXR5/6 primarily regulate heterochromatin condensation and gene silencing without influencing DNA methylation, in meiocytes, ATXR5/6 mainly function in suppressing recombination and preserving heterochromatic DNA methylation without directly regulating gene expression. Moreover, loss of Type II CO regulator MMS AND UV SENSITIVE 81 (MUS81) leads to pericentromeric fragmentation and polyad formation during meiosis in the absence of ATXR5/6, indicating that MUS81 is critical for resolving atypical recombination intermediates in pericentromeric heterochromatin. Taken together, our results provide insights into the roles of ATXR5/6 in repressing meiotic recombination within heterochromatin by regulating chromosome compaction and modifications.

Vitamin B6 (VB6) is an essential nutrient that must be obtained from the diet by humans and livestock, and plays an important role in response to various biotic and abiotic stresses in plants. Although the VB6 biosynthesis pathway has been uncovered in higher plants, understanding of its genetic control remains limited, and the role of VB6 in responding to cold stress is largely unknown. Here, we showed that variation in VB6 levels in rice is attributable to differential transcription of OsPDX1.2, a pyridoxal phosphate synthase, due to polymorphisms in its promoter. Natural variations in the OsPDX1.2 promoter affect the binding affinity of OsbZIP18, a transcriptional factor repressing OsPDX1.2 transcription. Loss of function in OsPDX1.2 or overexpression of OsbZIP18 significantly reduces cold tolerance in rice. Further investigation revealed that both genes affect cold tolerance by regulating VB6 and abscisic acid (ABA) biosynthesis. Moreover, the frequency of the cold‐tolerant pOsPDX1.2^Hap2 increases at higher latitudes, whereas the cold-sensitive pOsPDX1.2^Hap1 increases at lower latitudes, indicating that natural variation in OsPDX1.2 contributes to differential cold adaptation in rice. Overall, our results reveal a regulatory pathway controlling rice VB6 accumulation and cold tolerance via the OsbZIP18–OsPDX1.2 module, providing a potential target for improving rice quality and stress tolerance.

Thermogenesis represents one of the oldest pollination traits; yet, the ecological function of the microclimates that it creates remains poorly understood. Here, we elucidate how the spatiotemporally dynamic microclimate of Alocasia odora orchestrates pollinator movement within its inflorescence. Upregulation of alternative oxidase (AOX) in the upper spadix generates a steep, diurnally fluctuating thermal gradient against the non-thermogenic lower chamber, forming a “thermal map”. We demonstrate that this thermal push–pull mechanism, interacting synergistically with the insects' innate requirements, drives the cyclical vertical movements of its specialized Colocasiomyia pollinators. While strict feeding requirements establish a baseline preference for the lower sterile zone, species‐specific oviposition preferences dictate their distinct movement trajectories. Specifically, C. xenalocasiae primarily drives pollen importation, whereas C. alocasiae acts as the dominant contributor to pollen exportation. In contrast, floral scent primarily functions in long-distance pollinator attraction, while light plays only a minor modulatory role in this fine‐scale within-inflorescence navigation. Our comparative analysis reveals a prevalent spatiotemporal separation of sexual organs across thermogenic flowers globally. We therefore propose that microclimate‐guided pollinator movement—where thermal gradients overcome structural constraints to ensure reproductive success—constitutes a widespread, yet underappreciated evolutionary strategy.

Phytophthora infestans, the causal agent of late blight in potato and tomato, is a historically devastating pathogen that continues to pose a major threat to global food security. Although conventional fungicides remain a cornerstone of crop protection, growing concerns over their environmental impact and long-term sustainability have driven the search for safer and more selective alternatives. In this context, next-generation fungicides with high specificity and minimal ecological footprint are urgently needed. This study introduces CP32, a small cyclic peptide, identified via yeast two-hybrid screening of a genetically encoded combinatorial peptide library, based on its specific interaction with the catalytic domain of the P. infestans enzyme Cellulose Synthase 2. CP32 exhibits anti-oomycete activity, effectively inhibits sporangial growth at low micromolar concentrations, and significantly reduces late blight symptoms on tomato leaves and entire plants. In silico docking analyses, supported by molecular and biochemical evidence, confirm that CP32 compromises cell-wall integrity by interfering with cellulose deposition and altering glucan composition. Furthermore, CP32 readily permeates the Phytophthora membrane and displays oomycete-static properties, while showing no detectable toxicity toward non-target organisms, such as bacteria, yeast, or plants. Collectively, these findings identify CP32 as a promising, targeted anti-oomycete agent with a unique mode of action, targeting the P. infestans cell wall, representing a valuable contribution to the development of sustainable strategies for the control of late blight.

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.