The Plant Journal最新文献

The wound healing process in postharvest citrus fruit represents a crucial physiological mechanism that effectively resists external stress and minimizes quality deterioration. Nevertheless, the molecular mechanisms involved in wound healing by GATA transcription factors in citrus remain largely unexplored. In this research, CsGATA5 was characterized as a newly identified transcriptional activator promoting wound healing in citrus fruit. Transient overexpression of CsGATA5 in tobacco also confirmed its role in promoting suberin accumulation. Gene expression and metabolite profiling analyses following CsGATA5 overexpression revealed that CsGATA5 activated pathways associated with amino acid metabolism during wound healing. DLR, EMSA, ChIP-qPCR, and Y1H assays demonstrated that CsGATA5 bound to the promoter regions of target genes in tryptophan metabolism (CsTRYS and CsTDC2), thereby activating their expression. Notably, the activation of CsTRYS and CsTDC2 genes during citrus wound healing contributed to the subsequent induction of downstream suberin biosynthesis. Moreover, the exogenous treatment of key metabolites of the amino acid pathway, including tryptophan, 5-hydroxytryptamine, and phenylalanine, significantly promoted wound healing and further supported a potential regulatory cascade of tryptophan metabolism– tricarboxylic acid cycle– suberin biosynthesis. This study sheds light on the molecular regulatory network by which GATA transcription factors modulate wound healing in fruit.

Perennial plants rely on two key ecological strategies to supply nitrogen (N) for photosynthetic tissue construction: root N remobilization (internal cycling) and soil N uptake. How plants trade-off these strategies determines the economy of N use and is likely context-dependent. Yet, it is rarely quantified in situ across growth stages and under varying management, limiting the mechanistic understanding of how plants rebalance N-use trade-offs to adapt to grazing disturbance. To address this gap, we conducted an in situ experiment using ¹⁵N isotope labelling techniques in a semiarid grassland to quantify the contributions of these two strategies at two plant growth stages under nil, summer or autumn grazing. We found that the plant relied more on soil N uptake (58%) during the regreen stage, but more on N remobilization (57%) during the rapid-growth stage. Grazing, especially in autumn, significantly leaned N use trade-off toward conservative N remobilization. The shift in plant N use strategies was driven primarily by plant growth demand and soil N supply, but not root N stock. Plant N use trade-off leaned toward internal cycling when source traits were below or sink traits were above the thresholds, for example, soil N availability <9.0 mg kg⁻¹ or shoot carbon content >41.88%. Our study highlights the importance of the N resource-sink relations in mediating the trade-off in plant N use strategies, buffering grazing stress to grassland plants. These findings provide a mechanistic basis for improving ecosystem N cycling modeling and adaptive grazing management.

Population genetic theory predicts that species with narrow geographic distributions experience stronger genetic drift, higher inbreeding, and greater mutational burden than their widespread relatives, yet how demographic history shapes the genomic basis of adaptation remains poorly understood. We hypothesized that (i) restricted-range species exhibit reduced genetic diversity, elevated inbreeding, and greater mutation load owing to smaller long-term effective population sizes; (ii) despite these demographic constraints, shared environmental pressures can still drive repeated adaptation; (iii) repeated adaptation may arise through ancestral standing genetic variation, adaptive introgression, or independent de novo mutations. We tested these hypotheses using two kiwifruit species, Actinidia hemsleyana (narrow-ranged) and Actinidia eriantha (widespread), which differ markedly in demographic history and range size but occupy overlapping environments in subtropical China. We show that demographic contraction and inbreeding have eroded genome-wide diversity in the range-restricted species, accompanied by a substantially higher load of deleterious mutations. Despite these contrasting demographic legacies, both species exhibit repeated genomic responses to shared climatic gradients, with adaptation targeting similar genes. Such repeated adaptation was driven primarily by ancestral standing variation, with smaller contributions from adaptive introgression and only limited evidence for independent de novo mutations. These results reveal that demographic constraints shape genome-wide diversity and mutation load but do not preclude repeated adaptation when shared genetic variation remains available.

Land plant mitochondria and plastids are endosymbiotic organelles that possess their own, reduced genomes. Gene expression is largely regulated at the transcript level, predominantly by nuclear-encoded proteins. Notably, up to thousands of cytidines in organellar RNAs are specifically edited to uridines, mostly restoring conserved genetic information. Key players in this process are nuclear-encoded pentatricopeptide repeat (PPR) proteins, which bind target RNAs in a one-PPR:one-nucleotide manner, following a two-amino-acid-based code. Cytidine deamination is catalyzed by intrinsic or trans-acting DYW domains. The modularity and programmability of PPR-RNA interactions make PPR editing factors attractive candidates for the development of biotechnological tools. However, RNA target selection is not determined by the ‘PPR code’ alone, hampering the generation of highly effective and specific editors. Refining such tools requires efficient assays to dissect the determinants of editor-RNA interaction. Here, we introduce a rapid assay to assess PPR editor specificity through transient expression in the cytosol of Nicotiana benthamiana, which offers a large and diverse transcriptome that enables extensive off-target editing. Profiling of these off-targets provides comprehensive information on an editor's target selectivity. Compared with a previous setup in the model moss Physcomitrium patens, which relies on stable transformation, the required experimental time is reduced from months to days. We demonstrate the power of the system by characterizing the off-targets of the moss editor PpPPR56. The new assay allows rapid functional assessment of editing factor variants and removes a bottleneck in understanding editor-RNA interactions, which is a prerequisite for the rational improvement of PPR-based RNA editing tools.

The ability of plants to reprogram their metabolism in response to fluctuating environments, referred to as metabolic plasticity, is a key feature that enables sessile organisms to maintain growth, survival, and reproduction under changing conditions. As a mechanistic component of phenotypic plasticity, metabolic plasticity can buffer environmental perturbations and confer adaptive advantages. However, despite growing evidence for extensive metabolic remodeling under stress, the genetic and regulatory basis of this plasticity remains incompletely understood. Here, we review metabolic plasticity across major metabolic domains in plants, with emphasis on carbon, nitrogen, photorespiratory, and lipid metabolism, emphasizing how environmental cues and genetic regulation jointly shape metabolic responses. We conclude that, although metabolic plasticity is widespread in plants, its mechanistic and genetic basis remains incompletely understood; population-scale studies and mathematical modeling offer promising avenues to resolve this gap and extend current insights from model systems to crops.

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8) is a plant-specific transcription factor essential for anther development, but its regulatory partners and downstream mechanisms remain largely unknown. We identified 26 SPL8-interacting transcription factors by yeast two-hybrid screening and bimolecular fluorescence complementation (BiFC) assays, with YABBY (YAB) and TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) family emerging as the predominant interactors. Among these, YAB3 and TCP19 were selected for detailed characterization. Their interactions with SPL8, as well as with each other, were confirmed in plant nuclei by fluorescence resonance energy transfer–fluorescence lifetime imaging microscopy (FRET-FLIM). Chromatin immunoprecipitation sequencing (ChIP-seq), ChIP-qPCR, yeast one-hybrid, and dual-luciferase assays demonstrated that SPL8 directly binds the regulatory regions of YAB3 and TCP19 and activates their transcription. Dexamethasone-inducible expression assays further showed that this induction occurs independently of de novo protein synthesis. Expression analyses revealed overlapping spatial and temporal patterns of SPL8, YAB3, and TCP19 during early anther development, particularly in tapetal cells, microspore mother cells, and vascular tissues. Genetic and cellular analyses of promoter-driven SRDX repression lines showed that SPL8, YAB3, and TCP19 regulate anther morphogenesis, tapetal differentiation, meiotic progression, and microspore development. Although individual family members exhibited functional redundancy, their repression caused severe developmental defects and male sterility. Together, these findings establish the SPL8–YAB3/TCP19 module as a multilayered regulatory system in which SPL8 controls anther development through both transcriptional activation of YAB3 and TCP19 and physical interaction with these proteins, expanding the regulatory framework of SPL-mediated reproductive development.

Meiotic recombination is not only a key mechanism for sexual adaptation in eukaryotes but crucial for the accumulation of beneficial alleles in breeding populations. The effective manipulation of recombination requires, however, a better understanding of the mechanisms regulating the rate and distribution of recombination events in genomes. Here, we identified the genomic features that best explain the recombination variation among a diverse set of segregating populations of barley at a resolution of 1 Mbp and investigated how methylation and structural variants (SVs) determine crossover (CO) hotspots and coldspots at a high resolution of 10 kb. Hotspots were found to be in proximity to genes, and the genetic effects not assigned to methylation were found to be the most important factor explaining differences in recombination rates among populations, along with the methylation and the parental sequence divergence. Interestingly, coldspots were associated with the inheritance of a highly methylated genomic fragment from one parent only, but hotspots were identified at genomic segments where both parents were equally low methylated. The parental sequence divergence was shown to have a sigmoidal correlation with recombination, indicating an upper limit of mismatch among homologous chromosomes for CO formation. SVs were shown to be correlated with CO suppression, and their type and size were not found to influence that effect. The joint act of methylation and SVs was associated with the location of coldspots in barley, and the weight of their relative effect depends on the genomic region. Our findings suggest that recombination in barley is highly predictable, occurring mostly in multiple short sections located in proximity to genes and being modulated by local levels of methylation and SV load.

Most extant plant lineages show evidence of past polyploidisation events in their genomes. Allopolyploids arise from hybridisation, resulting in polyploid genomes comprising subgenomes from different ancestors. Adaptation to their environment, pre- and post-hybridisation and selection for specific traits has led to several allopolyploids exhibiting an unequal contribution from their subgenomes to phenotypic traits. Associated regulatory changes may have given rise to cultivar-specific subgenome dominance that contributes to the diversity of phenotypes. Likewise, different tissues and developmental stages have distinct expression profiles that may exhibit higher contributions from one subgenome relative to the other. Here, we investigate different metrics for quantifying the contribution of each subgenome to expression in cultivars of Brassica napus, in space (tissue) and time (development). Brassica napus inherited two subgenomes, A and C, from its ancestors Brassica rapa (A) and Brassica oleracea (C). We find that the C subgenome has a larger contribution to transcript abundance than the A subgenome, whereas the mean abundance per expressed gene is higher for the A subgenome. Direct comparison of homoeologous pairs reveals higher expression of genes on the C subgenome. We find that the degree and direction of expression bias can change substantially within a homoeologous pair between cultivars, tissues and across development, suggesting that subgenome dominance is highly dynamic. The quantification of expression bias reveals a strong dependence on the metric and on classification thresholds. These findings help explain contradictory reports on expression bias and subgenome dominance.

Grain weight is a key determinant of wheat yield, yet the developmental mechanisms that define this trait remain poorly understood. Here, we identify TaPGW1-A1, a wheat-specific proline-rich gene that regulates grain weight. TaPGW1-A1 is a recently evolved gene found only in wheat. It is highly expressed in early developing grains, and its overexpression delays endosperm cellularization and prolongs the syncytial phase, resulting in an 8% increase in field-based grain weight. TaPGW1-A1 protein directly interacts with the ubiquitin receptor TaDSK2a (Dominant Suppressor of KAR2 homolog) via its N-terminal signal peptide, and the protein–protein complex localizes to the cell periphery. Biochemical assays show that TaDSK2a binds both K48- and K63-linked polyubiquitin chains. Loss-of-function of TaDSK2a leads to reduced grain size, confirming its essential role in grain development. The E3 ligase TaRGLG2 inhibits the binding of TaPGW1-A1 to TaDSK2a. Together, these findings define a TaPGW1-A1–TaDSK2a–TaRGLG2 regulatory module that links developmental timing with ubiquitin-mediated protein turnover, revealing a previously unrecognized mechanism controlling endosperm cellularization and grain yield in wheat.