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Complex of Proteins Associated with Set1 complexes and their increasing roles in crop improvement 与Set1复合物相关的蛋白质复合物及其在作物改良中的日益重要的作用。
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-12-01 Epub Date: 2025-09-17 DOI: 10.1016/j.pbi.2025.102788
Jun-Yu Chen , Pan-Yi Zhang , Cheng-Guo Duan
The Complex of Proteins Associated with Set1 (COMPASS) complexes represent a group of highly conserved, multi-subunit complexes that catalyze histone H3 lysine 4 methylation across eukaryotic species. In Drosophila and mammals, COMPASS complexes are classified into distinct subtypes with diverse functions determined by their subunit composition. Plants have evolved analogous COMPASS assemblies that similarly exhibit functional diversification, playing pleiotropic roles in regulating vegetative growth, flowering transition, and stress adaptation. Recent studies have significantly advanced our understanding of the composition, chromatin targeting, and biological functions of plant COMPASS. In this review, we summarize the conserved core components of COMPASS in several plant species, the chromatin targeting strategies, crosstalk with other epigenetic marks, and regulatory role of COMPASS in stress adaptation. We also talk about the researches that may provide clues for crop improvement.
与Set1相关的蛋白质复合物(COMPASS)复合物代表了一组高度保守的多亚基复合物,在真核生物物种中催化组蛋白H3赖氨酸4甲基化。在果蝇和哺乳动物中,COMPASS复合物被分为不同的亚型,其亚基组成决定了其不同的功能。植物也进化出类似的COMPASS组件,它们同样表现出功能多样化,在调节营养生长、开花转变和逆境适应方面发挥多效作用。近年来的研究极大地促进了我们对植物COMPASS的组成、染色质靶向和生物学功能的了解。本文综述了COMPASS在几种植物中保守的核心成分、染色质靶向策略、与其他表观遗传标记的串扰以及COMPASS在逆境适应中的调控作用。我们还讨论了可能为作物改良提供线索的研究。
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引用次数: 0
Meiotic recombination and advances in quantitative trait locus mapping 减数分裂重组与数量性状位点定位研究进展。
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-12-01 Epub Date: 2025-10-15 DOI: 10.1016/j.pbi.2025.102814
Dohwan Byun , Sang-jun Park , Kyuha Choi
In plants, meiotic crossovers preferentially occur near and within genes, reshuffling preexisting genetic variation from parental genomes and thereby generating diversity in offspring. However, crossovers are generally limited to one to three per chromosome pair, tend to be widely spaced, and are rare in heterochromatic pericentromeric regions. These constraints on crossover number and distribution limit the genetic variation available for crop improvement and hinder the fine mapping of quantitative trait loci (QTLs). Unleashing meiotic crossovers has, therefore, become a key objective in plant genetics and breeding. Here, we review recent findings on pro- and anti-crossover factors that regulate crossover numbers, along with epigenetic mechanisms that suppress pericentromeric crossover recombination. We then explore genetic strategies to manipulate these regulators to maximize crossovers in both chromosomal arms and pericentromeric regions. Finally, we consider the implications of substantially elevating crossover frequency for enhancing QTL mapping resolution and accelerating plant breeding.
在植物中,减数分裂杂交优先发生在基因附近和基因内部,从亲本基因组中重新洗牌先前存在的遗传变异,从而在后代中产生多样性。然而,交叉通常限于每对染色体一到三个,往往间隔很宽,并且在异色中心点周围区域很少见。这些交叉数量和分布的限制限制了作物改良的遗传变异,阻碍了数量性状位点的精细定位。因此,释放减数分裂杂交已成为植物遗传学和育种的关键目标。在此,我们回顾了调控交叉数量的亲交叉因子和反交叉因子的最新发现,以及抑制中心点周围交叉重组的表观遗传机制。然后,我们探索遗传策略来操纵这些调节因子,以最大化染色体臂和中心点周围区域的交叉。最后,我们考虑了大幅提高交叉频率对提高QTL定位分辨率和加速植物育种的意义。
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引用次数: 0
The versatile role of guard cell starch in speedy stomata: Beyond Arabidopsis 保卫细胞淀粉在快速气孔中的多功能作用:超越拟南芥
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-08-05 DOI: 10.1016/j.pbi.2025.102762
Hongyuan Zhang, Trang Dang, Lucia Piro, Diana Santelia
Engineering rapid stomatal responses to improve the coordination between stomatal conductance and carbon assimilation under fluctuating light conditions is crucial for enhancing crop productivity while conserving water. To identify promising engineering targets, we applied machine learning models to analyze published data from diverse plant lineages to reveal the primary factors driving the natural variation in the speed of stomatal opening. We highlight the versatile role of guard cell starch in integrating and modulating some of these factors and suggest starch as a previously overlooked target for optimizing stomatal function.
在波动光照条件下,设计快速的气孔响应来改善气孔导度与碳同化之间的协调,对于提高作物产量和节约水分至关重要。为了确定有希望的工程目标,我们应用机器学习模型来分析来自不同植物谱系的已发表数据,以揭示驱动气孔打开速度自然变化的主要因素。我们强调了保护细胞淀粉在整合和调节这些因素中的多种作用,并建议淀粉作为一个以前被忽视的优化气孔功能的目标。
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引用次数: 0
The multifaceted roles of autophagy in plant immunity 自噬在植物免疫中的多重作用
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-08-30 DOI: 10.1016/j.pbi.2025.102781
Hwi Seong Jeon , Eunjeong Jang , Ohkmae K. Park
Autophagy is a highly conserved trafficking pathway that mediates selective degradation of intracellular components via the vacuole or lysosome. Although its roles in cellular homeostasis and stress adaptation are well characterized, the specific functions of autophagy in plant immunity remain incompletely understood. Emerging evidence reveals that autophagy dynamically modulates plant immune responses, contributing to both resistance and susceptibility to a broad spectrum of pathogens. In this review, we explore recent advances in understanding the multifaceted roles of autophagy in plant immunity, with an emphasis on its mechanistic contributions to plant–microbe interactions.
自噬是一种高度保守的运输途径,通过液泡或溶酶体介导细胞内成分的选择性降解。虽然自噬在细胞稳态和逆境适应中的作用已经被很好地描述,但自噬在植物免疫中的具体功能仍然不完全清楚。新出现的证据表明,自噬动态调节植物的免疫反应,有助于对广泛的病原体的抗性和易感性。在这篇综述中,我们探讨了自噬在植物免疫中的多方面作用的最新进展,重点介绍了自噬在植物与微生物相互作用中的机制贡献。
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引用次数: 0
From genes to epidemics: Genomic insights into bacterial plant pathogen emergence. 从基因到流行病:对细菌植物病原体出现的基因组见解。
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-08-07 DOI: 10.1016/j.pbi.2025.102765
Daniel Maddock, Michelle T Hulin

Bacterial phytopathogens are major causal agents of newly emerging plant diseases. The roles of both agricultural practices and the alteration of bacterial genomic content are well understood in the evolution of novel pathogens. However, translating this knowledge into effective tools for the comparison, prediction and understanding of current outbreaks remains challenging. To be pathogenic bacteria must be able to avoid plant immune responses, colonize host tissue and cause disease. Recent advances in both sequencing technologies and imaging techniques have provided fascinating insights into how bacterial interactions with each other and mobile genetic elements play a role in virulence evolution. This review explores these interactions, with a focus on the role of mobile genetic elements in plant pathogen evolution. Special consideration is given to how recent technologies can be applied to allow the observation of these interactions in the field and the future directions required to integrate these tools in field-based monitoring to further understand and enhance early management practices.

细菌性植物病原菌是植物新发病害的主要致病因子。农业实践和细菌基因组内容的改变在新型病原体的进化中所起的作用已得到很好的理解。然而,将这些知识转化为对当前疫情进行比较、预测和了解的有效工具仍然具有挑战性。病原细菌必须能够避免植物的免疫反应,在宿主组织中定植并引起疾病。测序技术和成像技术的最新进展为细菌如何相互作用以及移动遗传元件在毒力进化中发挥作用提供了令人着迷的见解。这篇综述探讨了这些相互作用,重点是移动遗传元件在植物病原体进化中的作用。特别考虑了如何应用最新技术,以便在实地观察这些相互作用,以及将这些工具纳入实地监测以进一步了解和加强早期管理做法所需的未来方向。
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引用次数: 0
Genomic balance effects on gene expression and the organism 基因组平衡对基因表达和机体的影响
IF 8.3 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-07-22 DOI: 10.1016/j.pbi.2025.102761
James A. Birchler, Hua Yang
Changes in dosage of individual chromosomes have long been known to have detrimental effects on the phenotype. Molecular analyses have revealed that aneuploidy affects gene expression across the genome with the major effects being direct and inverse correlations with the varied dosage. The inverse effect is typically more prevalent especially in aneuploids with an increased chromosomal dosage. Small heterozygous deletions removing one of the two copies of a gene typically exhibit a gene dosage effect for the included genes, but larger aneuploids exhibit the global modulations. When the inverse effect also operates on the target genes being varied in an aneuploid, dosage compensation results with expression levels similar to the corresponding genomically balanced control. Most substantial aneuploids alter the total transcriptome size but with subsets of genes deviating from the general trend. The greatest reductions in transcriptome size are associated with the most detrimental phenotypic effects on the organism. Aneuploidy effects in the endosperm involve a maternal to zygotic balance or a cumulative effect typical of other tissues. Genomic balance analyses reveal the stoichiometric effects on gene regulation, the trajectory of duplicated genes in evolution, and the eventual consequences for the organism.
人们早就知道,单个染色体剂量的变化对表型有不利影响。分子分析表明,非整倍性影响整个基因组的基因表达,其主要影响与剂量的变化呈正相关和负相关。相反的效果通常更普遍,特别是在染色体剂量增加的非整倍体中。小的杂合缺失去除一个基因的两个拷贝中的一个通常表现出基因剂量效应,但较大的非整倍体表现出全局调节。当反向效应也作用于非整倍体中变化的靶基因时,剂量补偿结果的表达水平与相应的基因组平衡对照相似。大多数实质性的非整倍体改变总的转录组大小,但与亚群的基因偏离一般趋势。转录组大小的最大减少与生物体中最有害的表型效应有关。胚乳的非整倍体效应涉及母体与合子的平衡或其他组织的典型累积效应。基因组平衡分析揭示了化学计量学对基因调控的影响,在进化中复制基因的轨迹,以及对生物体的最终后果。
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引用次数: 0
Ethylene signal integration through epigenetic mechanisms in plants 植物表观遗传机制中的乙烯信号整合
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-08-25 DOI: 10.1016/j.pbi.2025.102780
Aida Maric , Advait Agashe , Johanna Söntgerath , Sjon Hartman
Ethylene is an essential phytohormone that controls a plethora of plant developmental and stress responses. Accordingly, ethylene signal generation and progression must be under tight spatiotemporal control. This review highlights the latest milestones in understanding how epigenetic mechanisms govern ethylene biosynthesis and signaling, and how ethylene-mediated recruitment of epigenetic modifiers in turn controls gene expression and biological processes. We discuss a central mechanism of how ethylene-controlled histone acetylation is essential for ethylene signal progression. In addition, we outline how a wide range of epigenetic mechanisms control ethylene-mediated developmental and stress responses, with a focus on fruit ripening. Finally, we propose future research directions and open questions of ethylene signal integration through epigenetic mechanisms in plants.
乙烯是一种重要的植物激素,控制着过多的植物发育和胁迫反应。因此,乙烯信号的产生和发展必须受到严格的时空控制。本文综述了在理解表观遗传机制如何控制乙烯生物合成和信号传导,以及乙烯介导的表观遗传修饰子如何反过来控制基因表达和生物过程方面的最新里程碑。我们讨论了乙烯控制的组蛋白乙酰化对乙烯信号进展至关重要的中心机制。此外,我们概述了广泛的表观遗传机制如何控制乙烯介导的发育和胁迫反应,重点是水果成熟。最后,提出了乙烯信号在植物表观遗传机制中的整合研究方向和有待解决的问题。
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引用次数: 0
The histone crosstalk code in plants: Deciphering epigenetic complexity 植物组蛋白串扰密码:解读表观遗传复杂性
IF 8.3 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-07-26 DOI: 10.1016/j.pbi.2025.102763
Koki Nakamura, Nobutoshi Yamaguchi , Toshiro Ito
Histone modifications are essential regulators of chromatin architecture and gene expression in plants. Traditionally, each modification was viewed as an independent signal marking specific chromatin states. However, recent advances in epigenome profiling, genome editing, and proteomics have revealed that histone marks often function in combination, engaging in hierarchical, cooperative, and antagonistic relationships. In particular, studies in Arabidopsis thaliana have uncovered dynamic interactions between activating and repressive modifications, as well as their coordination with DNA methylation, histone variants, and RNA modifications. Among these, H3K4 and H3K36 methylation have emerged as key regulatory hubs that integrate developmental and environmental signals into context-dependent transcriptional responses. This growing body of evidence suggests that chromatin regulation involves not isolated modifications but rather a complex network of interdependent marks. In this review, we discuss recent examples of crosstalk between histone modifications and other regulatory layers to highlight how combinatorial chromatin regulation and its underlying molecular mechanisms contribute to transcriptional control and epigenetic responsiveness in plants. Such key insights expand our understanding of the diverse and context-dependent roles of histone modifications in plant biology.
组蛋白修饰是植物染色质结构和基因表达的重要调节因子。传统上,每个修饰被视为一个独立的信号,标记特定的染色质状态。然而,表观基因组分析、基因组编辑和蛋白质组学的最新进展表明,组蛋白标记通常以组合方式起作用,参与分层、合作和对抗关系。特别是,对拟南芥的研究揭示了激活和抑制修饰之间的动态相互作用,以及它们与DNA甲基化、组蛋白变异和RNA修饰的协调。其中,H3K4和H3K36甲基化已成为将发育和环境信号整合到上下文依赖性转录反应中的关键调控枢纽。越来越多的证据表明,染色质调节并不涉及孤立的修饰,而是一个相互依赖的标记的复杂网络。在这篇综述中,我们讨论了最近组蛋白修饰和其他调控层之间的串扰,以强调组合染色质调控及其潜在的分子机制如何促进植物的转录控制和表观遗传反应。这些关键的见解扩展了我们对组蛋白修饰在植物生物学中的多样性和环境依赖性作用的理解。
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引用次数: 0
Cell biology features and gene expression programs modulating cell expansion during root organ growth 根器官生长过程中调节细胞扩增的细胞生物学特性和基因表达程序
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-08-16 DOI: 10.1016/j.pbi.2025.102766
Camila Goldy , Virginia Barrera , Mariana Sotelo-Silveira , Ramiro E. Rodriguez
Diffuse cell expansion mainly in the longitudinal axis of the organ significantly contributes to root organ growth. Root cell expansion is a diverse, plastic, and dynamic process, as each cell expands at specific rates and directions according to its developmental stage and in response to different ambient conditions, helping to shape the root system architecture. In this review, we focus on Arabidopsis thaliana to summarize the modes and magnitudes of cell expansion in both meristematic and postmitotic root cells and assess recent advances in the understanding of the transitions required for cell expansion to occur. We also elaborate on the gene expression programs that control the forces, the biochemical and the molecular mechanisms that determine cell expansion, and finally, on how variations in the magnitude and distribution of this process contribute to root adaptation to the environment.
主要分布在器官纵轴的弥漫性细胞扩增对根器官的生长有显著的促进作用。根细胞的扩张是一个多样化、可塑性和动态的过程,每个细胞根据其发育阶段和不同的环境条件以特定的速度和方向扩张,帮助塑造根系结构。在这篇综述中,我们将重点介绍拟南芥分生组织和有丝分裂后根细胞的细胞扩增模式和大小,并评估细胞扩增发生所需转变的最新进展。我们还详细阐述了控制力量的基因表达程序,决定细胞扩增的生化和分子机制,最后,这一过程的大小和分布的变化如何促进根对环境的适应。
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引用次数: 0
Metabolic innovations: The study of the less ordinary 代谢创新:对不平凡事物的研究
IF 7.5 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-10-01 Epub Date: 2025-08-13 DOI: 10.1016/j.pbi.2025.102767
Alisdair R. Fernie, Shijuan Yan
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引用次数: 0
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Current opinion in plant biology
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