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Understanding plant-soil interactions underpins enhanced sustainability of crop production. 了解植物与土壤之间的相互作用有助于提高作物生产的可持续性。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-01 Epub Date: 2024-06-18 DOI: 10.1016/j.tplants.2024.05.008
Xin Wang, Lingyun Cheng, Chuanyong Xiong, William R Whalley, Anthony J Miller, Zed Rengel, Fusuo Zhang, Jianbo Shen

The Green Revolution transformed agriculture with high-yielding, stress-resistant varieties. However, the urgent need for more sustainable agricultural development presents new challenges: increasing crop yield, improving nutritional quality, and enhancing resource-use efficiency. Soil plays a vital role in crop-production systems and ecosystem services, providing water, nutrients, and physical anchorage for crop growth. Despite advancements in plant and soil sciences, our understanding of belowground plant-soil interactions, which impact both crop performance and soil health, remains limited. Here, we argue that a lack of understanding of these plant-soil interactions hinders sustainable crop production. We propose that targeted engineering of crops and soils can provide a fresh approach to achieve higher yields, more efficient sustainable crop production, and improved soil health.

绿色革命用高产、抗逆的品种改变了农业。然而,对更可持续农业发展的迫切需求带来了新的挑战:提高作物产量、改善营养质量和提高资源利用效率。土壤在作物生产系统和生态系统服务中发挥着至关重要的作用,为作物生长提供水分、养分和物理锚地。尽管植物和土壤科学取得了进步,但我们对影响作物生长和土壤健康的地下植物-土壤相互作用的了解仍然有限。在此,我们认为,缺乏对这些植物-土壤相互作用的了解会阻碍作物的可持续生产。我们建议,对作物和土壤进行有针对性的工程设计可以提供一种全新的方法来实现更高的产量、更高效的可持续作物生产以及更好的土壤健康。
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引用次数: 0
Non-B DNA in plant genomes: prediction, mapping, and emerging roles. 植物基因组中的非 B 型 DNA:预测、绘图和新出现的作用。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-01 Epub Date: 2024-07-29 DOI: 10.1016/j.tplants.2024.06.011
Lucía Ferrero, Wenli Zhang, Moussa Benhamed, Martin Crespi, Federico Ariel

Regulating gene expression in plant development and environmental responses is vital for mitigating the effects of climate change on crop growth and productivity. The eukaryotic genome largely shows the canonical B-DNA structure that is organized into nucleosomes with histone modifications shaping the epigenome. Nuclear proteins and RNA interactions influence chromatin conformations and dynamically modulate gene activity. Non-B DNA conformations and their transitions introduce novel aspects to gene expression modulation, particularly in response to environmental shifts. We explore the current understanding of non-B DNA structures in plant genomes, their interplay with epigenomics and gene expression, and advances in methods for their mapping and characterization. The exploration of so far uncharacterized non-B DNA structures remains an intriguing area in plant chromatin research and offers insights into their potential role in gene regulation.

调控植物发育和环境响应中的基因表达对于减轻气候变化对作物生长和生产力的影响至关重要。真核生物基因组在很大程度上显示出典型的 B-DNA 结构,这种结构被组织成核小体,并通过组蛋白修饰形成表观基因组。核蛋白和 RNA 相互作用影响染色质构象,并动态调节基因活性。非 B 型 DNA 构象及其转变为基因表达调控带来了新的方面,尤其是在响应环境变化时。我们探讨了目前对植物基因组中非 B 型 DNA 结构的理解、它们与表观基因组学和基因表达的相互作用,以及它们的绘图和表征方法的进展。对迄今尚未定性的非 B DNA 结构的探索仍然是植物染色质研究中一个引人入胜的领域,并为了解它们在基因调控中的潜在作用提供了启示。
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引用次数: 0
Unmasking complexities of combined stresses for creating climate-smart crops. 揭示综合压力的复杂性,创造气候智能型作物。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-01 Epub Date: 2024-08-10 DOI: 10.1016/j.tplants.2024.07.005
Prachi Pandey, Muthappa Senthil-Kumar

Understanding the complex challenges that plants face from multiple stresses is key to developing climate-ready crops. We highlight the significance of the Stress Combinations and their Interactions in Plants database (SCIPdb) for studying the impact of stress combinations on plants and the importance of aligning thematic research programs to create crops aligned with achieving sustainable development goals.

了解植物面临的多重胁迫的复杂挑战是开发适应气候的作物的关键。我们强调了植物胁迫组合及其相互作用数据库(SCIPdb)在研究胁迫组合对植物的影响方面的重要意义,以及调整专题研究计划以创造与实现可持续发展目标相一致的作物的重要性。
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引用次数: 0
Can a nitrogen-fixing organelle be engineered within plants? 能否在植物体内设计出固氮细胞器?
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-01 Epub Date: 2024-07-24 DOI: 10.1016/j.tplants.2024.07.001
Fang Liu, Alisdair R Fernie, Youjun Zhang

Given that crop yields are strongly limited by nitrogen, engineering crop plants with self-nitrogen-fertilization capacity holds great promise for sustainable agriculture. Recently, a nitrogen-fixing organelle has been characterized in the unicellular marine microalgae Braarudosphaera bigelowii. Engineering a nitrogen-fixing organelle into the non-nitrogen-fixing crops could benefit both environmental sustainability and global food security.

鉴于农作物产量受到氮的严重限制,对农作物进行工程改造使其具有自氮肥能力,为可持续农业带来了巨大希望。最近,一种固氮细胞器在单细胞海洋微藻 Braarudosphaera bigelowii 中得到了表征。将固氮细胞器工程化到非固氮作物中,既有利于环境的可持续发展,也有利于全球粮食安全。
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引用次数: 0
Single same-cell multiome for dissecting key plant traits. 用于剖析植物关键性状的单细胞多基因组
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-31 DOI: 10.1016/j.tplants.2024.10.008
Rohini Garg, Sunil Kumar Sahu, Mukesh Jain

Understanding molecular dynamics at the single cell level is crucial to understand plant traits. Recently, Liu et al. and Cui et al. reported multiome analysis in the same cell/nucleus to dissect the key plant traits (osmotic stress response and pod development). Their results provide novel insights into pathways and regulatory networks at a single cell resolution.

了解单细胞水平的分子动态对于了解植物性状至关重要。最近,Liu 等人和 Cui 等人报道了在同一细胞/核中进行多组分析,以剖析植物的关键性状(渗透胁迫响应和豆荚发育)。他们的研究结果提供了单细胞分辨率的通路和调控网络的新见解。
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引用次数: 0
Translational photobiology: towards dynamic lighting in indoor horticulture. 转化光生物学:实现室内园艺的动态照明。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-30 DOI: 10.1016/j.tplants.2024.10.006
Ulrike Bechtold, Meike Burow, Saijaliisa Kangasjärvi

Crop productivity depends on the ability of plants to thrive across different growth environments. In nature, light conditions fluctuate due to diurnal and seasonal changes in direction, duration, intensity, and spectrum. Laboratory studies, predominantly conducted with arabidopsis (Arabidopsis thaliana), have provided valuable insights into the metabolic and regulatory strategies that plants employ to cope with varying light intensities. However, there has been less focus on how horticultural crops tolerate dynamically changing light conditions during the photoperiod. In this review we connect insights from photobiology in model plants to the application of dynamic lighting in indoor horticulture. We explore how model species respond to fluctuating light intensities and discuss how this knowledge could be translated for new lighting solutions in controlled environment agriculture.

农作物的产量取决于植物在不同生长环境中茁壮成长的能力。在自然界中,光照条件因方向、持续时间、强度和光谱的昼夜变化和季节变化而波动。主要以拟南芥(Arabidopsis thaliana)为对象进行的实验室研究为了解植物应对不同光照强度所采用的代谢和调控策略提供了宝贵的资料。然而,园艺作物如何耐受光周期内动态变化的光照条件却鲜有人关注。在这篇综述中,我们将从模式植物的光生物学中获得的见解与室内园艺中动态光照的应用联系起来。我们探讨了模式物种如何对波动的光照强度做出反应,并讨论了如何将这些知识转化为可控环境农业中的新照明解决方案。
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引用次数: 0
Developing frameworks for nanotechnology-driven DNA-free plant genome-editing. 开发纳米技术驱动的无 DNA 植物基因组编辑框架。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-29 DOI: 10.1016/j.tplants.2024.09.014
Neelam Gogoi, Hendry Susila, Joan Leach, Markus Müllner, Brian Jones, Barry J Pogson

The bottlenecks of conventional plant genome-editing methods gave an innovative rise to nanotechnology as a delivery tool to manipulate gene(s) of interest. Studies suggest a strong correlation between the physicochemical properties of nanomaterials and their efficiency in gene delivery to different plant species/tissues. In this opinion article we highlight the need for a deeper understanding of plant-nanomaterial interactions to align their full capabilities with the strategic goals of plant genome-editing. Additionally, we emphasize DNA-free plant genome-editing approaches to potentially mitigate concerns surrounding genetically modified organisms (GMOs). Lastly, we propose a strategic integration of the principles of responsible research and innovation (RRI) in R&D. We aim to initiate a dialogue on developing collaborative and socio-technical frameworks for nanotechnology and DNA-free plant genome-editing.

由于传统植物基因组编辑方法存在瓶颈,纳米技术应运而生,成为操纵相关基因的一种传递工具。研究表明,纳米材料的理化特性与其向不同植物物种/组织传递基因的效率之间存在密切联系。在这篇观点文章中,我们强调需要更深入地了解植物与纳米材料之间的相互作用,使它们的全部能力与植物基因组编辑的战略目标相一致。此外,我们还强调了不含 DNA 的植物基因组编辑方法,以减轻人们对转基因生物的担忧。最后,我们建议将负责任的研究与创新(RRI)原则战略性地融入研发工作中。我们的目标是开展对话,为纳米技术和无 DNA 植物基因组编辑开发合作和社会技术框架。
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引用次数: 0
Engineering crop performance with upstream open reading frames. 利用上游开放阅读框改造作物性能。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-28 DOI: 10.1016/j.tplants.2024.10.005
Rui Mou, Ruixia Niu, Ruoying Yang, Guoyong Xu

Plants intricately regulate the expression of protein-coding genes at multiple stages - including mRNA transcription, translation, decay, and protein degradation - to control growth, development, and responses to environmental challenges. Recent research highlights the importance of translational reprogramming as a pivotal mechanism in regulating gene expression across diverse physiological scenarios. This regulatory mechanism bears practical implications, particularly in bolstering crop productivity by manipulating RNA regulatory elements (RREs) to modulate heterologous gene expression through transgene and endogenous gene expression through gene editing. Here, we elucidate the potential of upstream open reading frames (uORFs), a prominent and stringent class of RREs, in optimizing crop performance, exemplifying the efficacy of translational control in enhancing agricultural yields.

植物在多个阶段--包括 mRNA 转录、翻译、衰变和蛋白质降解--复杂地调控蛋白质编码基因的表达,以控制生长、发育和对环境挑战的反应。最近的研究突显了翻译重编程的重要性,它是调节各种生理情况下基因表达的关键机制。这种调控机制具有实际意义,特别是通过操纵 RNA 调控元件(RRE),通过转基因调控异源基因表达,通过基因编辑调控内源基因表达,从而提高作物产量。在这里,我们阐释了上游开放阅读框(uORFs)--一类突出而严格的 RREs--在优化作物表现方面的潜力,体现了转译控制在提高农业产量方面的功效。
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引用次数: 0
Machine learning algorithms translate big data into predictive breeding accuracy. 机器学习算法将大数据转化为预测育种的准确性。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-26 DOI: 10.1016/j.tplants.2024.09.011
José Crossa, Osval A Montesinos-Lopez, Germano Costa-Neto, Paolo Vitale, Johannes W R Martini, Daniel Runcie, Roberto Fritsche-Neto, Abelardo Montesinos-Lopez, Paulino Pérez-Rodríguez, Guillermo Gerard, Susanna Dreisigacker, Leonardo Crespo-Herrera, Carolina Saint Pierre, Morten Lillemo, Jaime Cuevas, Alison Bentley, Rodomiro Ortiz

Statistical machine learning (ML) extracts patterns from extensive genomic, phenotypic, and environmental data. ML algorithms automatically identify relevant features and use cross-validation to ensure robust models and improve prediction reliability in new lines. Furthermore, ML analyses of genotype-by-environment (G×E) interactions can offer insights into the genetic factors that affect performance in specific environments. By leveraging historical breeding data, ML streamlines strategies and automates analyses to reveal genomic patterns. In this review we examine the transformative impact of big data, including multi-trait genomics, phenomics, and environmental covariables, on genomic-enabled prediction in plant breeding. We discuss how big data and ML are revolutionizing the field by enhancing prediction accuracy, deepening our understanding of G×E interactions, and optimizing breeding strategies through the analysis of extensive and diverse datasets.

统计机器学习(ML)可从大量基因组、表型和环境数据中提取模式。ML 算法能自动识别相关特征,并利用交叉验证确保模型的稳健性,提高新品系的预测可靠性。此外,通过 ML 分析基因型与环境(G×E)的交互作用,可以深入了解影响特定环境中表现的遗传因素。通过利用历史育种数据,ML 简化了策略并使分析自动化,从而揭示基因组模式。在本综述中,我们探讨了大数据(包括多性状基因组学、表型组学和环境协变量)对植物育种中基因组预测的变革性影响。我们将讨论大数据和 ML 如何通过提高预测准确性、加深对 G×E 相互作用的理解以及通过分析广泛而多样的数据集优化育种策略来彻底改变这一领域。
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引用次数: 0
Redefining the role of sodium exclusion within salt tolerance. 重新定义排钠在盐耐受性中的作用。
IF 17.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-26 DOI: 10.1016/j.tplants.2024.10.002
Sebastian Garcia-Daga, Stuart J Roy, Matthew Gilliham

Salt contamination of soils and irrigation water is a significant environmental concern for crop production. Leaf sodium (Na+) exclusion is commonly proposed to be a key subtrait of salt tolerance for many crop plants. High-Affinity Potassium (K+) Transporter 1 (HKT1) proteins have previously been identified as major controllers of leaf Na+ exclusion across diverse species. However, leaf Na+ exclusion does not always correlate with salt tolerance. We discuss literature which shows leaf Na+ accumulation can, in some circumstances, be tolerated without a detrimental effect on yield when HKT1 still functions to exclude Na+ from reproductive tissues. We conclude that, by having an ultimate role in the protection of reproductive performance, HKT1s' role in adaptation to salinity warrants redefinition.

土壤和灌溉水的盐污染是农作物生产的一个重大环境问题。叶片排钠(Na+)通常被认为是许多作物植物耐盐性的一个关键特征。高亲和性钾(K+)转运体 1(HKT1)蛋白先前已被确定为不同物种叶片排斥 Na+ 的主要控制因子。然而,叶片对 Na+ 的排斥并不总是与耐盐性相关。我们讨论的文献表明,在某些情况下,如果 HKT1 仍能起到将 Na+ 排出生殖组织的作用,则可以耐受叶片 Na+ 积累,而不会对产量产生不利影响。我们的结论是,HKT1 在保护繁殖性能方面发挥着最终作用,因此其在适应盐度方面的作用需要重新定义。
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引用次数: 0
期刊
Trends in Plant Science
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