The Plant Journal最新文献

Allopolyploid Spartina anglica C.E. Hubbard (2n = 120-124) has become recognized as a model system of recent allopolyploid speciation. It arose by interspecific hybridization between S. alterniflora (2n = 62) introduced from North America and the native European S. maritima (2n = 60) about 150 years ago. In addition, sterile first-generation homoploid hybrids S. × townsendii and S. × neyrautii (both 2n = 62) are still extant. In this study, we carried out a population-level study of epigenetic silencing of 35S rDNA loci, also known as nucleolar dominance. Using molecular, genomic, and cytogenetic methods, we analyzed 75 individuals of S. anglica (collected from 11 French populations and 5 UK populations), 34 individuals of S. × townsendii (3 populations, all from the UK), and 2 individuals of S. × neyrautii from the south of France. We observed strong transcriptional dominance of S. alterniflora-inherited rDNA in all hybrid and allopolyploid individuals. The dominant rDNA units were nearly devoid of methylation at CWG sites, in contrast to those of the silenced S. maritima-inherited rDNA (M-loci), which exhibited hypermethylation. At the DNA level, few (2%) S. anglica individuals have completely lost M-loci, indicating that rDNA diploidization proceeds extremely fast in Spartina, and such a process may be influenced by preceding epigenetic processes. We conclude that nucleolar dominance is already present in extant homoploid hybrid lineages and is largely maintained in S. anglica, with occasional partial relaxation.

The angiosperm calyces display considerable diversity and have adaptive functions. However, the evolutionary trajectories and underlying mechanisms of calyx morphological diversity remain unclear. In this study, ancestral state reconstruction revealed that the abscised calyx was ancestral; however, most extant angiosperms exhibited persistent calyces showing notable variation in size. Remarkably, the Solanaceae family may represent a miniature reflecting the calyx diversity of angiosperms. Distinct from Solanum and Capsicum, Physalis fruits featured a morphological novelty known as inflated calyx syndrome (ICS). To reveal the molecular repatterning events underlying ICS formation, we conducted time-course transcriptomic comparisons on developing calyces of ICS species (Physalis floridana) and non-ICS species (Capsicum annuum and two Solanum species), and detected that variations in heterometric expression and alternative splicing were predominant across these species. Moreover, two Physalis-calyx highly expressed genes respectively encoding PHYSALIS ORGAN SIZE 4 (POS4) and POS5 were knocked down and out using virus-induced gene silencing and CRISPR/Cas9 technologies, and the resulting genetically modified P. floridana plant lines displayed a significant reduction in ICS size. Furthermore, when compared with Solanum and Capsicum, heterotopically expressed genes in Physalis calyx relative to berry were mainly enriched for functions in photosynthesis and responses to stimuli, thereby supporting the hypothesis that the inflated fruiting calyx may have partitioned and exapted functions originally associated with berry. This work elucidates the calyx evolutionary pattern of angiosperms as well as transcriptomic repatterning mechanisms that may govern both developmental and functional evolution of fruiting calyx inflation within Solanaceae, thereby providing insights into plant morphological evolution.

Plant structural biology is entering a new era. Advances in cryo-electron microscopy, tomography, and AI-based prediction are making it possible to study plant macromolecular machines at near-atomic resolution, including complexes that long resisted analysis by traditional approaches. Yet, despite these developments, plant proteins remain underrepresented in structural databases, reflecting persistent challenges in sample preparation, in situ imaging, and capturing dynamics. At the same time, plants present unique opportunities for structural biology, from the photosynthetic apparatus and cellulose synthase rosettes to receptor-like kinases, resistosomes, and plastid protein import machinery. Understanding these systems requires not only technical innovation but also conceptual shifts toward structural landscapes that capture molecular heterogeneity across time, space, and environmental conditions. Here, we outline the main frontiers for the field: improving sample preparation pipelines, advancing in situ and time-resolved methods, integrating structural biology with omics, and harnessing computational modeling. We highlight biological questions where structural insights are most urgently needed, including photosynthesis, hormone signaling, cell wall synthesis, organelle biology, and immunity. We argue that investment in infrastructure, training, and collaborative networks is essential if plant structural biology is to realize its potential. By revealing the molecular logic of the green world, the field can contribute solutions to urgent challenges in agriculture, sustainability, and climate resilience.

Plants exhibit dynamic physiological and biochemical responses to herbivory that often involve extensive metabolic reprogramming. Withania somnifera (Ashwagandha), a globally important medicinal plant, is susceptible to herbivory by the pest Henosepilachna vigintioctopunctata, resulting in significant yield losses. Understanding herbivory-induced metabolic responses is essential for elucidating plant-insect interactions and identifying potential defense-associated metabolites. In this study, we investigated the metabolic responses of W. somnifera leaves to H. vigintioctopunctata infestation using a comprehensive metabolomics approach combining liquid chromatography-high-resolution accurate mass spectrometry and gas chromatography-mass spectrometry. Our findings revealed that the herbivore triggers a significant metabolic shift by upregulating secondary metabolites, withanosides and phenylpropanoids. Furthermore, primary metabolites from carbohydrate metabolism were significantly affected. In addition, elemental analysis using ICP-OES revealed the accumulation of micronutrients due to pest infestation in W. somnifera. Notably, we also found plant defense metabolites, specifically withanolides and withanosides, within the herbivore pests themselves. The accumulation of withanosides in response to pest infestation was further confirmed through gene expression analysis. Additionally, feeding on Withania leaf extract containing withanolides adversely affected beetle physiology and survival. Collectively, our findings demonstrate that herbivory induces substantial metabolic plasticity in W. somnifera, particularly involving withanolide glycosylation and phenylpropanoid metabolism. This study provides a valuable framework for understanding herbivory-associated metabolic responses and identifies candidate pathways for future functional and comparative studies.

An important source of nutrients and raw materials for humans, seed oils also provide energy for the post-germination growth of seeds. Hence, enhancing seed oil content is crucial to improve overall oil yield. Unsaturated fatty acids and rare neuronic acids are abundant in Yellowhorn (Xanthoceras sorbifolium Bunge) seed oil, which is used as a cooking oil or as a raw material to make biodiesel. Nevertheless, nothing is known about the genetic controls pertaining to Yellowhorn seed oil. Here, we identified 490 single-nucleotide polymorphism loci associated with Yellowhorn seeds. Furthermore, we identified two genes, XsLACS8 and XsMYB58, related to seed oil, where XsMYB58 directly activated XsLACS8 to promote oil content accumulation. When transgenic soybean lines with ectopic overexpression of XsMYB58 and XsLACS8 were compared with wild-type plants, improvements were observed in three key yield parameters: siliques per plant, seed size, and seeds per silique. In addition, transient suppression of XsMYB58 expression negatively impacted the transcription of genes linked to oil accumulation. This research sheds new light on regulatory mechanisms underlying seed oil biosynthesis. Regulating XsMYB58 activity may lead to increased oil yields in Yellowhorn and other oil-bearing plants.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

Understanding the early specification of tendrils versus inflorescences in grapevine is key for developmental biology and agricultural applications. Here, we performed a comparative anatomical and cyto-histological analysis of lateral buds from the tendril-prone cultivar "Pinot Noir" ("PN") and the inflorescence-prone cultivar "Einset Seedless" ("EinS"). Our results show that cytological differences between tendril and inflorescence primordia emerge early during floral initiation, prior to any visible structural divergence. In particular, rib zone (RZ) cells in the uncommitted lateral meristem (UM) of "PN" differentiated into vacuolated pith cells more rapidly than those in "EinS." We subsequently applied single-nucleus RNA sequencing (snRNA-seq) to 50 052 nuclei from lateral buds of both cultivars, generating a cell type-resolved transcriptional atlas. Reconstruction of shoot apical meristem (SAM) and UM developmental trajectories revealed accelerated SAM differentiation in "PN." Together with cyto-histological observations of a less abundant UM mantle zone and lower cell cycle gene activity in UM cells, these findings indicate that both accelerated SAM differentiation and reduced UM proliferative activity restrict complete inflorescence formation in "PN," which is consistent with the anatomical differences observed. Analyzing UM and inflorescence meristem differentiation trajectories distinguished inflorescences- and tendril-specific differentiation trajectories, and revealed the involvement of the autophagy and hormone signal transduction pathway in early tendril versus inflorescence determination. Furthermore, transcription factors from the GRF, B3, S1Fa-like, WRKY, GATA, and C2H2 families showed expression patterns correlated with tendril specification. These results provide key insights into the differentiation of homologous reproductive structures in grapevine, thereby advancing the theoretical framework for early tendril versus inflorescence specification and supporting future applied research.

Breeding new elite variegated cultivars of Phalaenopsis equestris remains a significant challenge due to the scarcity of variegated germplasm resources, despite their high ornamental and commercial value. Here, we investigate the roles of PeFtsH1 and PeFtsH2 in chloroplast development and leaf variegation formation in Phalaenopsis equestris. Phylogenetic analysis showed that thylakoid membrane-localized PeFtsH protease is composed of PeFtsH1 and PeFtsH2 subunits, which are homologs of Arabidopsis VAR1/FtsH5 (type A) and VAR2/FtsH2 (type B), respectively. Genetic complementation assays showed that both PeFtsH1 and PeFtsH2 can rescue the leaf variegation phenotype of var1 and var2 mutants, respectively. Consistently, reduced expression of PeFtsH1 or PeFtsH2 via virus-induced gene silencing (VIGS) resulted in variegated leaves, reduced photosynthetic efficiency, and defective thylakoid development. Furthermore, we found that PeFtsH1 and PeFtsH2 form a heteromeric hexamer with a subunit stoichiometry of approximately 2:1. These findings suggest an evolutionary adaptation of P. equestris to low-light and high-humidity environments. Taken together, our findings reveal a conserved role of PeFtsH1 and PeFtsH2 in chloroplast development through the formation of a 2:1 heterohexameric complex, providing key molecular insights into the mechanism of chloroplast development and leaf variegation in Phalaenopsis equestris. These insights open an avenue for improving ornamental traits in orchids through targeted breeding.

Low temperature stress during the reproductive phase of wheat (Triticum aestivum L.) is a major constraint on yield. The anther connective stage, which governs spikelet differentiation, is particularly susceptible to low-temperature injury. However, the mechanisms by which low temperature at this stage impairs spike development and reduces yield are poorly understood. In this study, we found that low temperature stress during the anther connective stage significantly reduced yield, primarily by increasing spikelet abortion at both the basal and apical regions of the spike. Metabolomic profiling revealed that low temperature stress reprogrammed linoleic acid metabolism, α-linolenic acid metabolism, the citrate cycle, and the pentose phosphate pathway across different wheat organs. Spatial metabolomic profiling further showed a more pronounced activation of linoleic acid and α-linolenic acid metabolism, along with weaker carbohydrate metabolism, in basal spikelets compared with central spikelets. Transcriptomic analysis indicated that genes including LOX1.1, OPR11, PFK3, TKL-2, and G6PDH were upregulated under low temperature conditions. Notably, basal spikelets exhibited higher expression of LOX1.1 than central spikelets, whereas the upregulation of TKL-2 and G6PDH was comparatively weaker. Functionally, exogenous application of methyl jasmonate alleviated yield reduction by balancing carbohydrate distribution, whereas inhibition of the pentose phosphate pathway exacerbated assimilate imbalance. In conclusion, the modulation of linoleic acid and α-linolenic acid metabolism, along with the activation of the pentose phosphate pathway, mitigated wheat yield reduction under low temperature stress by optimizing assimilate allocation within the spike.