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Integrating artificial intelligence and high-throughput phenotyping for crop improvement

Journal of Integrative Agriculture 2024年第6期23卷 1787-1802页

作者： Mansoor Sheikh Farooq Iqra Hamadani Ambreen Kumar A Pravin Manzoor Ikra Yong Suk Chung Phenomics Laboratory Department of Plant Resources and EnvironmentJeju National UniversityJeju 63234Republic of Korea Council of Scientific&Industrial Research Indian Institute of Integrative MedicinePulwamaJ&K 192301India Animal and Dairy Science University of WisconsinMadisonWI 530706United States of America Division of Fruit Science Faculty of HorticultureSher-e-Kashmir University of Agricultural Sciences and Technology of KashmirSrinagar 190025India

crop improvement is crucial for addressing the global challenges of food security and sustainable *** advancements in high-throughput phenotyping(HTP)technologies and artificial intelligence(AI)have revolutionized the field,enabling rapid and accurate assessment of crop traits on a large *** integration of AI and machine learning algorithms with HTP data has unlocked new opportunities for crop *** algorithms can analyze and interpret large datasets,and extract meaningful patterns and correlations between phenotypic traits and genetic *** technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection,thereby reducing the time and cost required for variety ***,further research and collaboration are needed to overcome the existing challenges and fully unlock the power of HTP and AI in crop *** leveraging AI algorithms,researchers can efficiently analyze phenotypic data,uncover complex patterns,and establish predictive models that enable precise trait selection and crop *** aim of this review is to explore the transformative potential of integrating HTP and AI in crop *** review will encompass an in-depth analysis of recent advances and applications,highlighting the numerous benefits and challenges associated with HTP and AI.

关键词： artificial intelligence crop improvement data analysis high-throughput phenotyping machine learning precision agriculture trait selection

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A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

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Molecular Plant 2023年第2期16卷 393-414页

作者： Yongming Chen Yiwen Guo Panfeng Guan Yongfa Wang Xiaobo Wang Zihao Wang Zhen Qin Shengwei Ma Mingming Xin Zhaorong Hu Yingyin Yao Zhongfu Ni Qixin Sun Weilong Guo Huiru Peng Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Hainan Yazhou Bay Seed Laboratory SanyaHainanChina State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

Gene regulation is central to all aspects of organism growth,and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in ***,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still *** this study,we constructed a wheat integrative gene regulatory network(wGRN)by combining an updated genome annotation and diverse complementary functional datasets,including gene expression,sequence motif,transcription factor(TF)binding,chromatin accessibility,and evolutionarily conserved *** contains 7.2 million genome-wide interactions covering 5947 TFs and 127439 target genes,which were further verified using known regulatory relationships,condition-specific expression,gene functional information,and *** used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association *** addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution *** further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat ***,we developed an interactive webserver,wGRN(http://***/wGRN),for the community to explore gene regulation and discover trait-associated ***,this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

关键词： wheat integrative gene regulatory network functional gene discovery phenotype prediction crop improvement

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Plant synthetic epigenomic engineering for crop improvement

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Science China(Life Sciences) 2022年第11期65卷 2191-2204页

作者： Liwen Yang Pingxian Zhang Yifan Wang Guihua Hu Weijun Guo Xiaofeng Gu Li Pu Biotechnology Research Institute Chinese Academy of Agricultural SciencesBejing 10081China College of Life Science and Technology Huazhong Agriculural UniversityWuhan 430070China

Efforts have been directed to redesign crops with increased yield,stress adaptability,and nutritional value through synthetic biology—the application of engineering principles to biology.A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops,thus heralding the promise of“synthetic epigenetics.”In this review,we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques,epigenetic editing,and deep learning-driven predictive tools can rapidly extend these *** also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.

关键词： epigenetics synthetic biology synthetic epigenetics crop improvement

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Genome editing for plant research and crop improvement

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Journal of Integrative Plant Biology 2021年第1期63卷 3-33页

作者： Xiangqiang Zhan Yuming Lu Jian-Kang Zhu Jose Ramon Botella State Key Laboratory of crop Stress Biology for Arid Areas and College of Horticuture Northwest A&F UniversityXianyang 712100 Shanghai Center for Plant Stress Biology CAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIndiana 47907USA School of Agriculture and Food Sciences University of QueenslandBrisbaneQueensland 4072Australia

The advent of clustered regularly interspaced short palindromic repeat(CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel(insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.

关键词： CRISPR/Cas crop improvement genome editing plant research

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CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and crop improvement

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Molecular Plant 2021年第1期14卷 127-150页

作者： Dibyajyoti Pramanik Rahul Mahadev Shelake Mi Jung Kim Jae-Yean Kim Division of Applied Life Science(BK21 Four Program) Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 52828Korea These authors contributed equally to this article

The central dogma(CD)of molecular biology is the transfer of genetic information from DNA to RNA to *** CD processes governing genetic flow include the cell cycle,DNA replication,chromosome packaging,epigenetic changes,transcription,posttranscriptional alterations,translation,and posttranslational *** CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next *** of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world *** technology enables programmable editing of CD processes to alter DNA,RNA,or protein,which would have been impossible in the ***,an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is ***,CRISPR applications in major thriving areas of research,such as gene discovery(allele mining and cryptic gene activation),introgression(de novo domestication and haploid induction),and application of desired traits beneficial to farmers or consumers(biotic/abiotic stress-resilient crops,plant cell factories,and delayed senescence),are ***,the global regulatory policies,challenges,and prospects for CRISPR-mediated crop improvement are discussed.

关键词： central dogma CRISPR crop improvement gene regulation genome editing

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Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： Long Chen Guanqing Liu Tao Zhang Jiangsu Key Laboratory of crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops/Jiangsu Key Laboratory of crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing crop improvement Molecular design breeding

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Cultivating potential:Harnessing plant stem cells for agricultural crop improvement

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Molecular Plant 2024年第1期17卷 50-74页

作者： Penelope Lindsay Kyle W.Swentowsky David Jackson Cold Spring Harbor Laboratory Cold Spring HarborNY 11724USA National Key Laboratory of crop Genetic improvement Huazhong Agricultural UniversityWuhanHubei430070China

Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop *** regulators control the balance and rate of cell divisions within the *** these regulators impacts meristem architecture and,as a consequence,plant *** this review,we discuss genes involved in regulating the shoot apical meristem,inflorescence meristem,axillary meristem,root apical meristem,and vascular cambium in *** highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching *** transformation techniques are another innovation related to plant meristem research because they make crop genome engineering *** discuss recent advances on plant transformation made possible by studying genes controlling meristem ***,we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.

关键词： meristem crop improvement plant transformation plant breeding crop yield gene editing

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Advancing organelle genome transformation and editing for crop improvement

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Plant Communications 2021年第2期2卷 16-28页

作者： Shengchun Li Ling Chang Jiang Zhang State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan 430062China

Plant cells contain three organelles that harbor DNA:the nucleus,plastids,and *** transformation has emerged as an attractive platformfor the generation of transgenic plants,also referred to as transplastomic *** genomes have been genetically engineered to improve crop yield,nutritional quality,and resistance to abiotic and biotic stresses,as well as for recombinant protein *** many promising proof-of-concept applications,transplastomic plants have not been commercialized to ***-specific nuclease technologies are widely used to precisely modify nuclear genomes,but these tools have not been applied to edit organelle genomes because the efficient homologous recombination system in plastids facilitates plastid genome *** plastid transformation,successful genetic transformation of higher plant mitochondrial genome transformation was tested in several research group,but not successful to ***,stepwise progress has been made in modifying mitochondrial genes and their transcripts,thus enabling the study of their ***,we provide an overview of advances in organelle transformation and genome editing for crop improvement,and we discuss the bottlenecks and future development of these technologies.

关键词： organelle transformation genome editing homologous recombination crop improvement

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Revolutionize Genetic Studies and crop improvement with High-Throughput and Genome-Scale CRISPR/Cas9 Gene Editing Technology

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Molecular Plant 2017年第9期10卷 1141-1143页

作者： Yang, Ning Wang, Rongchen Zhao, Yunde Huazhong Agr Univ Natl Key Lab Crop Genet Improvement Wuhan 430070 Hubei Peoples R China Huazhong Agr Univ Natl Ctr Plant Gene Res Wuhan Wuhan 430070 Hubei Peoples R China Univ Calif San Diego Sect Cell & Dev Biol La Jolla CA 92093 USA

Forward genetic screens have been instrumental in deciphering the molecular mechanisms that control agriculturally important traits. Traditionally, crop mutant collections are generated by chemical mutagenesis such as ethyl methanesulfonate （EMS） treatment, physical irradiation, and insertional agents including T-DNAs and transposons （Wei et al., 2013; Li et al., 2016）.

关键词： Revolutionize Genetic Studies crop improvement High-Throughput

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A New Era for crop improvement： From Model- Guided Rationale Design to Practical Engineering

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Molecular Plant 2015年第9期8卷 1299-1301页

作者： Chengcai Chu The State Key Laboratory of Plant Genomics and National Center of Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academy of Sciences (CAS) Beijing 100101 China

Photosynthesis is the basis of plant productivity. There is still a big gap between the efficiency of theoretical maximal photosyn- thetic energy conversion and the efficiency realized in the field. It was estimated that for C3 plants, the theoretical maximal energy conversion efficiency is ca. 4.6%, the observed maximal season- long energy conversion efficiency is about 2.4%, while the typical season-long energy conversion efficiency is only 0.8% （Zhu et al., 2010）. Despite this, however, photosynthesis has not been effectively used as a breeding target for crop improvement so far. When plants grow under elevated CO2, the crop yields are higher, clearly showing that enhancing photosynthesis can be used to improve yields （Long et al., 2006; Zhu et al., 2010）. Two reasons underlie the failure of improving photosynthesis for greater yields. First, photosynthesis is difficult to phenotype compared with other traits such as flowering time, plant height, leaf erectness, etc.; second, canopy photosynthesis, instead of leaf photosynthesis, is related to crop biomass and yield, however, there is no effective way to measure canopy photosynthesis and to identify the factors controlling canopy photosynthetic energy conversion efficiency.

关键词： New Era crop improvement Model-Guided

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