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Annual review of plant biology最新文献

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Deep Learning in Image-Based Plant Phenotyping. 基于图像的植物表型分析中的深度学习
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-070523-042828
Katherine M Murphy, Ella Ludwig, Jorge Gutierrez, Malia A Gehan
{"title":"Deep Learning in Image-Based Plant Phenotyping.","authors":"Katherine M Murphy, Ella Ludwig, Jorge Gutierrez, Malia A Gehan","doi":"10.1146/annurev-arplant-070523-042828","DOIUrl":"10.1146/annurev-arplant-070523-042828","url":null,"abstract":"<p><p>A major bottleneck in the crop improvement pipeline is our ability to phenotype crops quickly and efficiently. Image-based, high-throughput phenotyping has a number of advantages because it is nondestructive and reduces human labor, but a new challenge arises in extracting meaningful information from large quantities of image data. Deep learning, a type of artificial intelligence, is an approach used to analyze image data and make predictions on unseen images that ultimately reduces the need for human input in computation. Here, we review the basics of deep learning, assessments of deep learning success, examples of applications of deep learning in plant phenomics, best practices, and open challenges.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"771-795"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Molecular Phenology and Climate Feedbacks Mediated by BVOCs. 由 BVOCs 介导的植物分子物候学和气候反馈。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-060223-032108
Akiko Satake, Tomika Hagiwara, Atsushi J Nagano, Nobutoshi Yamaguchi, Kanako Sekimoto, Kaori Shiojiri, Kengo Sudo
{"title":"Plant Molecular Phenology and Climate Feedbacks Mediated by BVOCs.","authors":"Akiko Satake, Tomika Hagiwara, Atsushi J Nagano, Nobutoshi Yamaguchi, Kanako Sekimoto, Kaori Shiojiri, Kengo Sudo","doi":"10.1146/annurev-arplant-060223-032108","DOIUrl":"10.1146/annurev-arplant-060223-032108","url":null,"abstract":"<p><p>Climate change profoundly affects the timing of seasonal activities of organisms, known as phenology. The impact of climate change is not unidirectional; it is also influenced by plant phenology as plants modify atmospheric composition and climatic processes. One important aspect of this interaction is the emission of biogenic volatile organic compounds (BVOCs), which link the Earth's surface, atmosphere, and climate. BVOC emissions exhibit significant diurnal and seasonal variations and are therefore considered essential phenological traits. To understand the dynamic equilibrium arising from the interplay between plant phenology and climate, this review presents recent advances in comprehending the molecular mechanisms underpinning plant phenology and its interaction with climate. We provide an overview of studies investigating molecular phenology, genome-wide gene expression analyses conducted in natural environments, and how these studies revolutionize the concept of phenology, shifting it from observable traits to dynamic molecular responses driven by gene-environment interactions. We explain how this knowledge can be scaled up to encompass plant populations, regions, and even the globe by establishing connections between molecular phenology, changes in plant distribution, species composition, and climate.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"605-627"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Physiological Responses of C4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints. C4 多年生生物能源草对气候变化的生理反应：原因、后果和制约因素。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-070623-093952
Robert W Heckman, Caio Guilherme Pereira, Michael J Aspinwall, Thomas E Juenger
{"title":"Physiological Responses of C<sub>4</sub> Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints.","authors":"Robert W Heckman, Caio Guilherme Pereira, Michael J Aspinwall, Thomas E Juenger","doi":"10.1146/annurev-arplant-070623-093952","DOIUrl":"10.1146/annurev-arplant-070623-093952","url":null,"abstract":"<p><p>C<sub>4</sub> perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C<sub>4</sub> perennial bioenergy grasses are predicted to thrive under climate change-C<sub>4</sub> photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO<sub>2</sub>], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C<sub>4</sub> perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C<sub>4</sub> physiology with recent advances in crop improvement, especially genomic selection.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"737-769"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
The Plant Mediator Complex in the Initiation of Transcription by RNA Polymerase II. RNA 聚合酶 II 启动转录过程中的植物中介复合物
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-070623-114005
Santiago Nicolás Freytes, María Laura Gobbini, Pablo D Cerdán
{"title":"The Plant Mediator Complex in the Initiation of Transcription by RNA Polymerase II.","authors":"Santiago Nicolás Freytes, María Laura Gobbini, Pablo D Cerdán","doi":"10.1146/annurev-arplant-070623-114005","DOIUrl":"10.1146/annurev-arplant-070623-114005","url":null,"abstract":"<p><p>Thirty years have passed since the discovery of the Mediator complex in yeast. We are witnessing breakthroughs and advances that have led to high-resolution structural models of yeast and mammalian Mediators in the preinitiation complex, showing how it is assembled and how it positions the RNA polymerase II and its C-terminal domain (CTD) to facilitate the CTD phosphorylation that initiates transcription. This information may be also used to guide future plant research on the mechanisms of Mediator transcriptional control. Here, we review what we know about the subunit composition and structure of plant Mediators, the roles of the individual subunits and the genetic analyses that pioneered Mediator research, and how transcription factors recruit Mediators to regulatory regions adjoining promoters. What emerges from the research is a Mediator that regulates transcription activity and recruits hormonal signaling modules and histone-modifying activities to set up an off or on transcriptional state that recruits general transcription factors for preinitiation complex assembly.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"211-237"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139566338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining. 通过植物生物学和生物炼制的综合进展实现木质素的价值化。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 DOI: 10.1146/annurev-arplant-062923-022602
Richard A Dixon, Allen Puente-Urbina, Gregg T Beckham, Yuriy Román-Leshkov
{"title":"Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining.","authors":"Richard A Dixon, Allen Puente-Urbina, Gregg T Beckham, Yuriy Román-Leshkov","doi":"10.1146/annurev-arplant-062923-022602","DOIUrl":"https://doi.org/10.1146/annurev-arplant-062923-022602","url":null,"abstract":"<p><p>Despite lignin having long been viewed as an impediment to the processing of biomass for the production of paper, biofuels, and high-value chemicals, the valorization of lignin to fuels, chemicals, and materials is now clearly recognized as a critical element for the lignocellulosic bioeconomy. However, the intended application for lignin will likely require a preferred lignin composition and form. To that end, effective lignin valorization will require the integration of plant biology, providing optimal feedstocks, with chemical process engineering, providing efficient lignin transformations. Recent advances in our understanding of lignin biosynthesis have shown that lignin structure is extremely diverse and potentially tunable, while simultaneous developments in lignin refining have resulted in the development of several processes that are more agnostic to lignin composition. Here, we review the interface between in planta lignin design and lignin processing and discuss the advances necessary for lignin valorization to become a feature of advanced biorefining.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"75 1","pages":"239-263"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Intercellular Communication in Shoot Meristems. 嫩枝分生组织中的细胞间通信
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-070523-035342
Edgar Demesa-Arevalo, Madhumitha Narasimhan, Rüdiger Simon
{"title":"Intercellular Communication in Shoot Meristems.","authors":"Edgar Demesa-Arevalo, Madhumitha Narasimhan, Rüdiger Simon","doi":"10.1146/annurev-arplant-070523-035342","DOIUrl":"10.1146/annurev-arplant-070523-035342","url":null,"abstract":"<p><p>The shoot meristem of land plants maintains the capacity for organ generation throughout its lifespan due to a group of undifferentiated stem cells. Most meristems are shaped like a dome with a precise spatial arrangement of functional domains, and, within and between these domains, cells interact through a network of interconnected signaling pathways. Intercellular communication in meristems is mediated by mobile transcription factors, small RNAs, hormones, and secreted peptides that are perceived by membrane-localized receptors. In recent years, we have gained deeper insight into the underlying molecular processes of the shoot meristem, and we discuss here how plants integrate internal and external inputs to control shoot meristem activities.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"319-344"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Environmental Control of Hypocotyl Elongation. 下胚轴伸长的环境控制。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-062923-023852
Johanna Krahmer, Christian Fankhauser
{"title":"Environmental Control of Hypocotyl Elongation.","authors":"Johanna Krahmer, Christian Fankhauser","doi":"10.1146/annurev-arplant-062923-023852","DOIUrl":"10.1146/annurev-arplant-062923-023852","url":null,"abstract":"<p><p>The hypocotyl is the embryonic stem connecting the primary root to the cotyledons. Hypocotyl length varies tremendously depending on the conditions. This developmental plasticity and the simplicity of the organ explain its success as a model for growth regulation. Light and temperature are prominent growth-controlling cues, using shared signaling elements. Mechanisms controlling hypocotyl elongation in etiolated seedlings reaching the light differ from those in photoautotrophic seedlings. However, many common growth regulators intervene in both situations. Multiple photoreceptors including phytochromes, which also respond to temperature, control the activity of several transcription factors, thereby eliciting rapid transcriptional reprogramming. Hypocotyl growth often depends on sensing in green tissues and interorgan communication comprising auxin. Hypocotyl auxin, in conjunction with other hormones, determines epidermal cell elongation. Plants facing cues with opposite effects on growth control hypocotyl elongation through intricate mechanisms. We discuss the status of the field and end by highlighting open questions.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"489-519"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138443673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Using Synthetic Biology to Understand the Function of Plant Specialized Metabolites. 利用合成生物学了解植物特化代谢物的功能。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-060223-013842
Yuechen Bai, Xinyu Liu, Ian T Baldwin
{"title":"Using Synthetic Biology to Understand the Function of Plant Specialized Metabolites.","authors":"Yuechen Bai, Xinyu Liu, Ian T Baldwin","doi":"10.1146/annurev-arplant-060223-013842","DOIUrl":"10.1146/annurev-arplant-060223-013842","url":null,"abstract":"<p><p>Plant specialized metabolites (PSMs) are variably distributed across taxa, tissues, and ecological contexts; this variability has inspired many theories about PSM function, which, to date, remain poorly tested because predictions have outpaced the available data. Advances in mass spectrometry-based metabolomics have enabled unbiased PSM profiling, and molecular biology techniques have produced PSM-free plants; the combination of these methods has accelerated our understanding of the complex ecological roles that PSMs play in plants. Synthetic biology techniques and workflows are producing high-value, structurally complex PSMs in quantities and purities sufficient for both medicinal and functional studies. These workflows enable the reengineering of PSM transport, externalization, structural diversity, and production in novel taxa, facilitating rigorous tests of long-standing theoretical predictions about why plants produce so many different PSMs in particular tissues and ecological contexts. Plants use their chemical prowess to solve ecological challenges, and synthetic biology workflows are accelerating our understanding of these evolved functions.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"629-653"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Cryopreservation: Principles, Applications, and Challenges of Banking Plant Diversity at Ultralow Temperatures. 植物低温保存：在超低温下保存植物多样性的原理、应用和挑战。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-070623-103551
Manuela Nagel, Valerie Pence, Daniel Ballesteros, Maurizio Lambardi, Elena Popova, Bart Panis
{"title":"Plant Cryopreservation: Principles, Applications, and Challenges of Banking Plant Diversity at Ultralow Temperatures.","authors":"Manuela Nagel, Valerie Pence, Daniel Ballesteros, Maurizio Lambardi, Elena Popova, Bart Panis","doi":"10.1146/annurev-arplant-070623-103551","DOIUrl":"10.1146/annurev-arplant-070623-103551","url":null,"abstract":"<p><p>Progressive loss of plant diversity requires the protection of wild and agri-/horticultural species. For species whose seeds are extremely short-lived, or rarely or never produce seeds, or whose genetic makeup must be preserved, cryopreservation offers the only possibility for long-term conservation. At temperatures below freezing, most vegetative plant tissues suffer severe damage from ice crystal formation and require protection. In this review, we describe how increasing the concentration of cellular solutes by air drying or adding cryoprotectants, together with rapid cooling, results in a vitrified, highly viscous state in which cells can remain viable and be stored. On this basis, a range of dormant bud-freezing, slow-cooling, and (droplet-)vitrification protocols have been developed, but few are used to cryobank important agricultural/horticultural/timber and threatened species. To improve cryopreservation efficiency, the effects of cryoprotectants and molecular processes need to be understood and the costs for cryobanking reduced. However, overall, the long-term costs of cryopreservation are low, while the benefits are huge.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"797-824"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139429031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Polyamines: Their Role in Plant Development and Stress. 多胺：多胺：它们在植物发育和胁迫中的作用
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2024-07-01 Epub Date: 2024-07-02 DOI: 10.1146/annurev-arplant-070623-110056
Miguel A Blázquez
{"title":"Polyamines: Their Role in Plant Development and Stress.","authors":"Miguel A Blázquez","doi":"10.1146/annurev-arplant-070623-110056","DOIUrl":"10.1146/annurev-arplant-070623-110056","url":null,"abstract":"<p><p>This review focuses on the intricate relationship between plant polyamines and the genetic circuits and signaling pathways that regulate various developmental programs and the defense responses of plants when faced with biotic and abiotic aggressions. Particular emphasis is placed on genetic evidence supporting the involvement of polyamines in specific processes, such as the pivotal role of thermospermine in regulating xylem cell differentiation and the significant contribution of polyamine metabolism in enhancing plant resilience to drought. Based on the numerous studies describing effects of the manipulation of plant polyamine levels, two conceptually different mechanisms for polyamine activity are discussed: direct participation of polyamines in translational regulation and the indirect production of hydrogen peroxide as a defensive mechanism against pathogens. By describing the multifaceted functions of polyamines, this review underscores the profound significance of these compounds in enabling plants to adapt and thrive in challenging environments.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"95-117"},"PeriodicalIF":21.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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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