Plant Communications最新文献_第2页

Synthetic biology and artificial intelligence in crop improvement. 合成生物学和人工智能在作物改良中的应用。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-12-12 DOI: 10.1016/j.xplc.2024.101220

Daolei Zhang, Fan Xu, Fanhua Wang, Liang Le, Li Pu

{"title":"Synthetic biology and artificial intelligence in crop improvement.","authors":"Daolei Zhang, Fan Xu, Fanhua Wang, Liang Le, Li Pu","doi":"10.1016/j.xplc.2024.101220","DOIUrl":"10.1016/j.xplc.2024.101220","url":null,"abstract":"Synthetic biology plays a pivotal role in improving crop traits and increasing bioproduction through the use of engineering principles that purposefully modify plants through \"design, build, test, and learn\" cycles, ultimately resulting in improved bioproduction based on an input genetic circuit (DNA, RNA, and proteins). Crop synthetic biology is a new tool that uses circular principles to redesign and create innovative biological components, devices, and systems to enhance yields, nutrient absorption, resilience, and nutritional quality. In the digital age, artificial intelligence (AI) has demonstrated great strengths in design and learning. The application of AI has become an irreversible trend, with particularly remarkable potential for use in crop breeding. However, there has not yet been a systematic review of AI-driven synthetic biology pathways for plant engineering. In this review, we explore the fundamental engineering principles used in crop synthetic biology and their applications for crop improvement. We discuss approaches to genetic circuit design, including gene editing, synthetic nucleic acid and protein technologies, multi-omics analysis, genomic selection, directed protein engineering, and AI. We then outline strategies for the development of crops with higher photosynthetic efficiency, reshaped plant architecture, modified metabolic pathways, and improved environmental adaptability and nutrient absorption; the establishment of trait networks; and the construction of crop factories. We propose the development of SMART (self-monitoring, adapted, and responsive technology) crops through AI-empowered synthetic biotechnology. Finally, we address challenges associated with the development of synthetic biology and offer potential solutions for crop improvement.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101220"},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819653","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

Genetic engineering, including genome editing, for enhancing broad-spectrum disease resistance in crops. 基因工程，包括基因组编辑，用于作物的广谱抗病性。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-11-20 DOI: 10.1016/j.xplc.2024.101195

Xinyu Han, Shumin Li, Qingdong Zeng, Peng Sun, Dousheng Wu, Jianguo Wu, Xiao Yu, Zhibing Lai, Ricky J Milne, Zhensheng Kang, Kabin Xie, Guotian Li

{"title":"Genetic engineering, including genome editing, for enhancing broad-spectrum disease resistance in crops.","authors":"Xinyu Han, Shumin Li, Qingdong Zeng, Peng Sun, Dousheng Wu, Jianguo Wu, Xiao Yu, Zhibing Lai, Ricky J Milne, Zhensheng Kang, Kabin Xie, Guotian Li","doi":"10.1016/j.xplc.2024.101195","DOIUrl":"10.1016/j.xplc.2024.101195","url":null,"abstract":"Plant diseases, caused by a wide range of pathogens, severely reduce crop yield and quality, posing a significant threat to global food security. Developing broad-spectrum resistance (BSR) in crops is a key strategy for controlling crop diseases and ensuring sustainable crop production. Cloning disease-resistance (R) genes and understanding their underlying molecular mechanisms provide new genetic resources and strategies for crop breeding. Novel genetic engineering and genome editing tools have accelerated the study and engineering of BSR genes in crops, which is the primary focus of this review. We first summarize recent advances in understanding the plant immune system, followed by an examination of the molecular mechanisms underlying BSR in crops. Finally, we highlight diverse strategies employed to achieve BSR, including gene stacking to combine multiple R genes, multiplexed genome editing of susceptibility genes and promoter regions of executor R genes, editing cis-regulatory elements to fine-tune gene expression, RNA interference, saturation mutagenesis, and precise genomic insertions. The genetic studies and engineering of BSR are accelerating the breeding of disease-resistant cultivars, contributing to crop improvement and enhancing global food security.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101195"},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683347","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 gap-free assembly of pepper genome reveals transposable-element-driven expansion and rapid evolution of pericentromeres. 辣椒无间隙基因组揭示了转座元件驱动的扩展和围中心粒的快速进化。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-10-24 DOI: 10.1016/j.xplc.2024.101177

Kang Zhang, Xiang Wang, Shumin Chen, Yuanhang Liu, Lingkui Zhang, Xiaolong Yang, Hailong Yu, Yacong Cao, Lei Zhang, Chengcheng Cai, Jue Ruan, Lihao Wang, Feng Cheng

引用次数: 0

Pentatricopeptide repeat proteins in plants: Cellular functions, action mechanisms, and potential applications. 植物中的五肽重复蛋白：细胞功能、作用机制和潜在应用。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-12-05 DOI: 10.1016/j.xplc.2024.101203

Yong Wang, Bao-Cai Tan

引用次数: 0

Agricultural landscape genomics to increase crop resilience.

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2025-01-22 DOI: 10.1016/j.xplc.2025.101260

Quinn Campbell, James A Bedford, Yue Yu, Anna Halpin-McCormick, Nora Castaneda-Alvarez, Bryan Runck, Jeffrey Neyhart, Patrick Ewing, Daniel Ortiz-Barrientos, Lexuan Gao, Diane Wang, Mark A Chapman, Loren H Rieseberg, Michael B Kantar

{"title":"Agricultural landscape genomics to increase crop resilience.","authors":"Quinn Campbell, James A Bedford, Yue Yu, Anna Halpin-McCormick, Nora Castaneda-Alvarez, Bryan Runck, Jeffrey Neyhart, Patrick Ewing, Daniel Ortiz-Barrientos, Lexuan Gao, Diane Wang, Mark A Chapman, Loren H Rieseberg, Michael B Kantar","doi":"10.1016/j.xplc.2025.101260","DOIUrl":"10.1016/j.xplc.2025.101260","url":null,"abstract":"Populations are continually adapting to their environment. Knowledge of which populations and individuals harbor unique and agriculturally useful variations has the potential to accelerate crop adaptation to the increasingly challenging environments predicted for the coming century. Landscape genomics, which identifies associations between environmental and genomic variation, provides a means for obtaining this knowledge. However, despite extensive efforts to assemble and characterize ex situ collections of crops and their wild relatives, gaps remain in the genomic and environmental datasets needed to robustly implement this approach. This article outlines the history of landscape genomics, which, to date, has mainly been used in conservation and evolutionary studies, provides an overview of crops and wild relative collections that have the necessary data for implementation and identifies areas where new data generation is needed. We find that 60% of the crops covered by the International Treaty on Plant Genetic Resources for Food and Agriculture lack the data necessary to conduct this kind of analysis, necessitating identification of crops in need of more collections, sequencing, or phenotyping. By highlighting these aspects, we aim to help develop agricultural landscape genomics as a sub-discipline that brings together evolutionary genetics, landscape ecology, and plant breeding, ultimately enhancing the development of resilient and adaptable crops for future environmental challenges.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101260"},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030312","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 U-box ubiquitin ligase TUD1 promotes brassinosteroid-induced GSK2 degradation in rice.

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2025-01-30 DOI: 10.1016/j.xplc.2025.101255

Dapu Liu, Xiaoxing Zhang, Qingliang Li, Yunhua Xiao, Guoxia Zhang, Wenchao Yin, Mei Niu, Wenjing Meng, Nana Dong, Jihong Liu, Yanzhao Yang, Qi Xie, Chengcai Chu, Hongning Tong

引用次数: 0

CRISPR-mediated targeted mutagenesis for improving nitrogen use efficiency in japonica rice. CRISPR-mediated Targeted Mutagenesis for Improving Nitrogen Use Efficiency of Japonica Rice.

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-11-05 DOI: 10.1016/j.xplc.2024.101189

Yajun Tao, Zhihui Chen, Yang Xu, Fangquan Wang, Yanjie Jiang, Fangjun Fan, Wenqi Li, Jianping Zhu, Xia Li, Jun Wang, Qian-Hao Zhu, Guohua Xu, Jie Yang

引用次数: 0

Breeding herbicide-resistant rice using CRISPR-Cas gene editing and other technologies. 利用 CRISPR/Cas 基因编辑和其他技术培育抗除草剂水稻（Oryza sativa）。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-10-12 DOI: 10.1016/j.xplc.2024.101172

Qiyu Luo, Yao-Guang Liu

引用次数: 0

RNA modifications in plant adaptation to abiotic stresses. RNA修饰在植物适应非生物胁迫中的作用。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-12-21 DOI: 10.1016/j.xplc.2024.101229

Jing Cai, Ling Shen, Hunseung Kang, Tao Xu

{"title":"RNA modifications in plant adaptation to abiotic stresses.","authors":"Jing Cai, Ling Shen, Hunseung Kang, Tao Xu","doi":"10.1016/j.xplc.2024.101229","DOIUrl":"10.1016/j.xplc.2024.101229","url":null,"abstract":"Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in the process of plant stress adaptation. Currently, over 170 distinct chemical modifications have been identified in mRNAs, tRNAs, rRNAs, microRNAs (miRNAs), and long noncoding RNAs (lncRNAs). Genetic and molecular studies have identified the genes responsible for addition and removal of chemical modifications from RNA molecules, which are known as \"writers\" and \"erasers,\" respectively. N6-methyladenosine (m6A) is the most prevalent chemical modification identified in eukaryotic mRNAs. Recent studies have identified m6A writers and erasers across different plant species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), cotton (Gossypium hirsutum), and tomato (Solanum lycopersicum). Accumulating discoveries have improved our understanding of the functions of RNA modifications in plant stress responses. This review highlights the latest research on RNA modification, emphasizing the biological and cellular roles of diverse chemical modifications of mRNAs, tRNAs, rRNAs, miRNAs, and lncRNAs in plant responses to environmental and hormonal signals. We also propose and discuss critical questions and future challenges for enhancing our understanding of the cellular and mechanistic roles of RNA modifications in plant stress responses. Integrating molecular insights into the regulatory roles of RNA modifications in stress responses with novel genome- and RNA-editing technologies will facilitate the breeding of stress-tolerant crops through precise engineering of RNA modifications.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101229"},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873368","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 developments and prospects of plant super-pangenomes: Demands, approaches, and applications. 植物超级泛基因组的研究进展与展望：需求、方法与应用

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-12-24 DOI: 10.1016/j.xplc.2024.101230

Wenchuang He, XiaoXia Li, Qian Qian, Lianguang Shang

引用次数: 0