Plant Communications最新文献_第7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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897457/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

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

Agricultural landscape genomics to increase crop resilience. 农业景观基因组学提高作物抗灾能力。

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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897451/pdf/","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":"OA","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. U-box泛素连接酶TUD1促进油菜素类固醇诱导的水稻GSK2降解。

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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897461/pdf/","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":"OA","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

{"title":"The developments and prospects of plant super-pangenomes: Demands, approaches, and applications.","authors":"Wenchuang He, XiaoXia Li, Qian Qian, Lianguang Shang","doi":"10.1016/j.xplc.2024.101230","DOIUrl":"10.1016/j.xplc.2024.101230","url":null,"abstract":"By integrating genomes from different accessions, pangenomes provide a more comprehensive and reference-bias-free representation of genetic information within a population compared to a single reference genome. With the rapid accumulation of genomic sequencing data and the expanding scope of plant research, plant pangenomics has gradually evolved from single-species to multi-species studies. This shift has given rise to the concept of a super-pangenome that covers all genomic sequences within a genus-level taxonomic group. By incorporating both cultivated and wild species, the super-pangenome has greatly enhanced the resolution of research in various areas such as plant genetic diversity, evolution, domestication, and molecular breeding. In this review, we present a comprehensive overview of the plant super-pangenome, emphasizing its development requirements, construction strategies, potential applications, and notable achievements. We also highlight the distinctive advantages and promising prospects of super-pangenomes while addressing current challenges and future directions.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101230"},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Precise customization of plant architecture by combinatorial genetic modification of peptide ligands. 通过对多肽配体进行组合遗传修饰，精确定制植物结构。

IF 9.4 1区生物学

Plant Communications Pub Date : 2025-02-10 Epub Date: 2024-10-16 DOI: 10.1016/j.xplc.2024.101175

Myeong-Gyun Seo, Ho-Young Jeong, Yoonseo Lim, Seungpyo Hong, Jiwoo Lee, Woo-Jong Hong, Chanhui Lee, Soon Ju Park, Choon-Tak Kwon

引用次数: 0