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Pangenomics combined with artificial intelligence and precision breeding can accelerate crop improvement 泛基因组学与人工智能和精准育种相结合，可以加速作物改良。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-11-16 DOI: 10.1016/j.pbi.2025.102825
Teng Li , Shameela Mohamedikbal , Mitchell Bestry , Jacqueline Batley , David Edwards
{"title":"Pangenomics combined with artificial intelligence and precision breeding can accelerate crop improvement","authors":"Teng Li ,&nbsp;Shameela Mohamedikbal ,&nbsp;Mitchell Bestry ,&nbsp;Jacqueline Batley ,&nbsp;David Edwards","doi":"10.1016/j.pbi.2025.102825","DOIUrl":"10.1016/j.pbi.2025.102825","url":null,"abstract":"<div><div>Pangenomics significantly expands our understanding of genetic diversity in plants beyond single reference genomes by capturing extensive genomic variations. In this review, we discuss recent methodological breakthroughs in pangenomics, including advances in long-read sequencing, graph-based pangenome tools, artificial intelligence, and multiomics approaches that have collectively enabled pangenomes to become more accurate and prevalent. We review the broad applications of pangenomics in plant science, particularly focusing on crop breeding, including haplotype-based selection, improved prediction for genomic selection, multiomics guided marker discovery, precise identification of genome-editing targets, association of genes with agronomic traits, understanding transposable element dynamics, and providing valuable insights to guide crop improvement. Furthermore, we discuss current challenges and future directions for pangenomics studies.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102825"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145539423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deciphering actomyosin functions in plant cytokinesis: A half-century odyssey 破译肌动球蛋白在植物细胞分裂中的功能：半个世纪的奥德赛。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-24 DOI: 10.1016/j.pbi.2025.102790
Bo Liu , Takumi Higaki , Yuh-Ru Julie Lee
{"title":"Deciphering actomyosin functions in plant cytokinesis: A half-century odyssey","authors":"Bo Liu ,&nbsp;Takumi Higaki ,&nbsp;Yuh-Ru Julie Lee","doi":"10.1016/j.pbi.2025.102790","DOIUrl":"10.1016/j.pbi.2025.102790","url":null,"abstract":"<div><div>Half a century ago, it was discovered that in somatic plant cells actin microfilaments play a critical role in division plane orientation but not in cell plate assembly during cytokinesis. Because plant cytokinesis is brought about by the microtubule-based phragmoplast, the actomyosin system must be required for the centrifugally expanding phragmoplast to recognize the cortical division zone established by the microtubular preprophase band (PPB). It has been intriguing to learn how the two cytoskeletal elements communicate with each other in the two temporally separated cytokinetic apparatuses of the PPB and the phragmoplast. Half a century later, it is now clear that the PPB recruits the actomyosin system to the cortical division zone where the Myosin XI motors form macromolecular assemblies with Kinesin-12 motors and other microtubule-associated proteins. These Cytoskeleton-Associated Motor assemblies at the PPB site (CAMPs) play critical roles in the maintenance of the division site established by the PPB. They receive microtubules emanating from the edge of the expanding phragmoplast so that the developing cell plate can be inserted into the spatially defined position. Therefore, the actomyosin system joins microtubules to orchestrate the recognition of the PPB-defined position by the phragmoplast in order to execute cytokinesis in a spatiotemporally regulated manner in somatic plant cells.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102790"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Telomeres: The EPI-Ending 端粒：epi的终结。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-11-05 DOI: 10.1016/j.pbi.2025.102823
Petra Procházková Schrumpfová , Miloslava Fojtová , Martina Dvořáčková
{"title":"Telomeres: The EPI-Ending","authors":"Petra Procházková Schrumpfová ,&nbsp;Miloslava Fojtová ,&nbsp;Martina Dvořáčková","doi":"10.1016/j.pbi.2025.102823","DOIUrl":"10.1016/j.pbi.2025.102823","url":null,"abstract":"<div><div>Telomeres are essential chromosomal structures that protect genome integrity and play a central role in aging and cell proliferation. In plants, the epigenetic landscape of telomeres and their adjacent subtelomeric regions has emerged as a critical component regulating telomere function and genome organization. This review summarizes current knowledge of chromatin modifications at plant telomeres, and the impact of chromatin-associated factors on telomere stability. We also discuss experimental tools for studying telomere epigenetics, and identify key open questions in the field.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102823"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145458039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Plant histone acetyltransferase complexes: Conserved and plant-specific characteristics 植物组蛋白乙酰转移酶复合物：保守和植物特异性特征。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-10-17 DOI: 10.1016/j.pbi.2025.102815
Xin Xu , Xin-Jian He
{"title":"Plant histone acetyltransferase complexes: Conserved and plant-specific characteristics","authors":"Xin Xu ,&nbsp;Xin-Jian He","doi":"10.1016/j.pbi.2025.102815","DOIUrl":"10.1016/j.pbi.2025.102815","url":null,"abstract":"<div><div>Histone acetyltransferase (HAT) complexes are pivotal regulators of chromatin dynamics, orchestrating transcriptional programs essential for plant development and stress responses in plants. This review synthesizes recent advances in the classification, subunit composition, and functional mechanisms of plant HAT complexes, emphasizing plant-specific characteristics compared to the conserved architecture of HAT complexes. By integrating genetic, biochemical, and structural studies, we delineate how these complexes modulate histone acetylation and coordinate with other chromatin modifications to regulate gene expression. Further research should focus on deciphering the spatiotemporal regulation of HAT complex composition and histone acetylation, and determining the targeting mechanisms of these complexes.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102815"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Plant trait variation shapes plant–microbe interactions in changing climate 植物性状变异决定了气候变化中植物与微生物的相互作用。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-30 DOI: 10.1016/j.pbi.2025.102801
Hyung-Woo Jeon , Yujeong Lim , Jong Hum Kim
{"title":"Plant trait variation shapes plant–microbe interactions in changing climate","authors":"Hyung-Woo Jeon ,&nbsp;Yujeong Lim ,&nbsp;Jong Hum Kim","doi":"10.1016/j.pbi.2025.102801","DOIUrl":"10.1016/j.pbi.2025.102801","url":null,"abstract":"<div><div>As the climate crisis intensifies, finding strategies to mitigate its cascading effects is now a pressing global priority for both scientists and policymakers. In agriculture and ecology, a key first step is to understand how changing environmental conditions affect plant–microbe interactions, especially given the knowledge gap between findings from controlled experiments and those from field studies. In this review, we highlight known fluctuations in host factors that mediate interactions with surrounding microorganisms under changing climate conditions and discuss potential future directions to alleviate the impacts of climate changes.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102801"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Position and identity, two separable but inseparable processes in floral meristem patterning 位置和身份，花分生组织形成过程中两个可分离但不可分割的过程
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-01 DOI: 10.1016/j.pbi.2025.102785
Ya Min
{"title":"Position and identity, two separable but inseparable processes in floral meristem patterning","authors":"Ya Min","doi":"10.1016/j.pbi.2025.102785","DOIUrl":"10.1016/j.pbi.2025.102785","url":null,"abstract":"<div><div>Early floral meristem (FM) patterning is one of the most intensively studied developmental programs in plants. While extensive work has uncovered the molecular networks underlying key processes such as organ initiation and identity specification, integrating this knowledge into a comprehensive framework remains challenging. Organ initiation is governed by auxin-mediated positioning and boundary formation, whereas organ identity is determined by the combinatorial activities of ABCE-class transcription factors. These processes have often been studied in isolation, even though proper flower development requires their coordination in space and time. This review synthesizes current insights into early floral organ initiation and identity determination, and potential molecular links bridging these two programs. I also discuss persistent gaps in our understanding, the challenges in addressing these knowledge gaps, and how emerging tools can help disentangle the complex crosstalk between initiation and identity, ultimately advancing a more integrated view of the regulatory networks that pattern the early FM.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102785"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144922520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Plant ribosomopathies: New insights and a critical re-evaluation of ribosomal protein gene mutants in plants 植物核糖体病：植物核糖体蛋白基因突变的新见解和关键的重新评估
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-27 DOI: 10.1016/j.pbi.2025.102791
Ryan E. Martinez, Katherine A. Klimpel, Michael Busche, Jacob O. Brunkard
{"title":"Plant ribosomopathies: New insights and a critical re-evaluation of ribosomal protein gene mutants in plants","authors":"Ryan E. Martinez,&nbsp;Katherine A. Klimpel,&nbsp;Michael Busche,&nbsp;Jacob O. Brunkard","doi":"10.1016/j.pbi.2025.102791","DOIUrl":"10.1016/j.pbi.2025.102791","url":null,"abstract":"<div><div>Ribosomes are essential cellular machines that translate genetic information into functional proteins. Ribosomes require massive nutrient investments, accounting for as much as 50 % of organic phosphorus and 25 % of organic nitrogen in leaves. Optimizing ribosome levels could therefore reduce crop plant fertilizer requirements, an urgent goal for agricultural sustainability. Disruptions to ribosome biogenesis often cause surprising developmental defects, however, and there is substantial confusion and debate among plant geneticists about how to interpret mutant phenotypes caused by defective ribosomes. Here, we propose to adopt the conceptual framework of “ribosomopathies”, human disorders caused by defects in ribosome biogenesis, to better appreciate why some plant developmental processes are more sensitive to ribosome levels than others. We argue that understanding plant ribosomopathies as a broad class of mutants that affect ribosome homeostasis, rather than a series of distinct cases impacting specialized, heterogeneous ribosomes, will encourage productive mechanistic studies of specific ribosome-sensitive developmental processes that could be engineered to circumvent the deleterious effects of restricting ribosome availability.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102791"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145154983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Stomatal patterning and development in grasses 禾本科植物的气孔模式和发育
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-10-10 DOI: 10.1016/j.pbi.2025.102808
Lea Sophie Berg , Michael Thomas Raissig
{"title":"Stomatal patterning and development in grasses","authors":"Lea Sophie Berg ,&nbsp;Michael Thomas Raissig","doi":"10.1016/j.pbi.2025.102808","DOIUrl":"10.1016/j.pbi.2025.102808","url":null,"abstract":"<div><div>Grass stomata provide an exemplary model of how form can improve functionality and promote the success of a plant family. The four-celled grass stomata are composed of dumbbell-shaped guard cells, each flanked by a single parallel subsidiary cell–arguably the most derived and fastest stomatal morphotype. The grasses' breathing pores develop in a strictly linear gradient within a stereotypically patterned epidermis, making it a highly accessible and spatiotemporally predictable developmental study system. Here, we highlight our current understanding of how vein-associated establishment of stomatal identity, tightly regulated asymmetric and symmetric cell division programs and extraordinary morphogenetic processes orchestrate the development of these uniquely shaped graminoid stomata. The innovative geometry and cellular composition of grass stomata have been repeatedly linked to rapid stomatal opening and closing kinetics, thus contributing to the grasses’ water-use-efficient photosynthesis. Therefore, besides revealing fundamental aspects of plant development and plant cell biology, the dissection of the developmental processes forming grass stomata can also highlight strategies to engineer stomatal morphology for improved plant-atmosphere gas exchange.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102808"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145262908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epigenetic processes involved in the activation of the DNA damage response in plants: A link to stress memory 参与植物DNA损伤反应激活的表观遗传过程：与应激记忆的联系。
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-17 DOI: 10.1016/j.pbi.2025.102789
Paula Casati
{"title":"Epigenetic processes involved in the activation of the DNA damage response in plants: A link to stress memory","authors":"Paula Casati","doi":"10.1016/j.pbi.2025.102789","DOIUrl":"10.1016/j.pbi.2025.102789","url":null,"abstract":"<div><div>Epigenetic memory refers to heritable information that is not encoded in the DNA sequence itself but is transmitted across generations through epigenetic modifications. These modifications can arise in response to environmental stimuli, such as heat stress or DNA-damaging conditions, and may persist across multiple generations. One of the primary epigenetic marks in plants is DNA methylation, whose role in stress memory is discussed in a separate review within this Special Issue. In this article, I will focus in one particular stress condition, genotoxic stress, that occurs after plants are exposed to internal or external agents that produce damage in the DNA. I will present and discuss various examples of the establishment, dynamics, and maintenance of epigenetic marks in plants that trigger the DNA damage response, along with their physiological consequences.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102789"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Interplay between Polycomb-group associated histone modifiers and accessory proteins in plant evolution Polycomb-group相关组蛋白修饰因子与辅助蛋白在植物进化中的相互作用
IF 7.5 2区 生物学
Current opinion in plant biology Pub Date : 2025-12-01 Epub Date: 2025-09-01 DOI: 10.1016/j.pbi.2025.102783
Ahamed Khan, Biswajit Ghosh, Daniel Schubert
{"title":"Interplay between Polycomb-group associated histone modifiers and accessory proteins in plant evolution","authors":"Ahamed Khan,&nbsp;Biswajit Ghosh,&nbsp;Daniel Schubert","doi":"10.1016/j.pbi.2025.102783","DOIUrl":"10.1016/j.pbi.2025.102783","url":null,"abstract":"<div><div>Epigenetic regulators are multiprotein complexes that modify chromatin architecture to control gene expression in response to developmental and environmental cues. These complexes function in a highly coordinated manner, often collaborating with various accessory proteins to precisely regulate the dynamic nature of chromatin states. However, our understanding of how these core histone-modifying regulators co-evolved with accessory proteins during plant evolution remains limited. Therefore, in this review, we summarize the evolution of major histone modification regulators, with a focus on Polycomb group complexes and their associated accessory proteins. We discuss how accessory proteins have evolved to modulate the activity of conserved core components, supporting key innovations during plant evolution. Lastly, we highlight the role of accessory proteins in mediating crosstalk between histone-modifying complexes, emerging as key evolutionary factors that shape the epigenetic landscape and influence plant development and environmental adaptation.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"88 ","pages":"Article 102783"},"PeriodicalIF":7.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144922519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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