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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 insights.We 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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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 crops.However,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking.In 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 regulation.wGRN 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 experiments.We 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 studies.In addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks.We 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 accessions.Finally,we developed an interactive webserver,wGRN(http://***/wGRN),for the community to explore gene regulation and discover trait-associated genes.Collectively,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

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/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2021年第4期22卷 253-284页

作者： Chao LI Eleanor BRANT Hikmet BUDAK Baohong ZHANG Oil crops Research Institute Chinese Academy of Agricultural SciencesKey Laboratory for Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062China Agronomy Department University of FloridaGainesvilleFL 32611USA Montana Bio Agriculture Inc.MissoulaMT 59802USA Department of Biology East Carolina UniversityGreenvilleNC 27858USA

Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010 s,clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)has rapidly been developed into a robust,multifunctional genome editing tool with many uses.Following the discovery of the initial CRISPR/Cas-based system,the technology has been advanced to facilitate a multitude of different functions.These include development as a base editor,prime editor,epigenetic editor,and CRISPR interference(CRISPRi)and CRISPR activator(CRISPRa)gene regulators.It can also be used for chromatin and RNA targeting and imaging.Its applications have proved revolutionary across numerous biological fields,especially in biomedical and agricultural improvement.As a diagnostic tool,CRISPR has been developed to aid the detection and screening of both human and plant diseases,and has even been applied during the current coronavirus disease 2019(COVID-19)pandemic.CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases,including cancers,and has aided drug development.In terms of agricultural breeding,precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins,starch,oil,and other functional components for crop improvement.Adding to this,CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators.Looking to the future,increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology.This review provides an in-depth overview of current CRISPR development,including the advantages and disadvantages of the technology,recent applications,and future considerations.

关键词： Genome editing Clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas) Coronavirus disease 2019(COVID-19) Cancer Precision breeding crop improvement Gene knock-out/in Gene repair/replacement

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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 protein.Major CD processes governing genetic flow include the cell cycle,DNA replication,chromosome packaging,epigenetic changes,transcription,posttranscriptional alterations,translation,and posttranslational modifications.The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation.Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population.CRISPR technology enables programmable editing of CD processes to alter DNA,RNA,or protein,which would have been impossible in the past.Here,an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided.Furthermore,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 described.Finally,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

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

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 mitochondria.Plastid transformation has emerged as an attractive platformfor the generation of transgenic plants,also referred to as transplastomic plants.Plastid genomes have been genetically engineered to improve crop yield,nutritional quality,and resistance to abiotic and biotic stresses,as well as for recombinant protein production.Despite many promising proof-of-concept applications,transplastomic plants have not been commercialized to date.Sequence-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 editing.Unlike plastid transformation,successful genetic transformation of higher plant mitochondrial genome transformation was tested in several research group,but not successful to date.However,stepwise progress has been made in modifying mitochondrial genes and their transcripts,thus enabling the study of their functions.Here,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

Integrating artificial intelligence and high-throughput phenotyping for crop improvement

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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 University Council of Scientific&Industrial Research Indian Institute of Integrative Medicine Animal and Dairy Science University of Wisconsin Division of Fruit Science Faculty of HorticultureSher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir

crop improvement is crucial for addressing the global challenges of food security and sustainable agriculture.Recent 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 scale. The integration of AI and machine learning algorithms with HTP data has unlocked new opportunities for crop improvement. AI algorithms can analyze and interpret large datasets, and extract meaningful patterns and correlations between phenotypic traits and genetic factors. These 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 development. However, further research and collaboration are needed to overcome the existing challenges and fully unlock the power of HTP and AI in crop improvement. By leveraging AI algorithms, researchers can efficiently analyze phenotypic data, uncover complex patterns, and establish predictive models that enable precise trait selection and crop breeding. The aim of this review is to explore the transformative potential of integrating HTP and AI in crop improvement. This 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

High-Throughput Phenotyping:A Platform to Accelerate crop improvement

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Phenomics 2021年第2期1卷 31-53页

作者： Sumit Jangra Vrantika Chaudhary Ram C.Yadav Neelam R.Yadav Department of Molecular Biology Biotechnologyand BioinformaticsCCS Haryana Agricultural UniversityHisar 125004India

Development of high-throughput phenotyping technologies has progressed considerably in the last 10 years.These technologies provide precise measurements of desired traits among thousands of field-grown plants under diversified environments;this is a critical step towards selection of better performing lines as to yield,disease resistance,and stress tolerance to accelerate crop improvement programs.High-throughput phenotyping techniques and platforms help unrave-ling the genetic basis of complex traits associated with plant growth and development and targeted traits.This review focuses on the advancements in technologies involved in high-throughput,field-based,aerial,and unmanned platforms.Development of user-friendly data management tools and softwares to better understand phenotyping will increase the use of field-based high-throughput techniques,which have potential to revolutionize breeding strategies and meet the future needs of stakeholders.

关键词： High-throughput phenotyping Imaging Technologies Platform crop improvement Biotic and abiotic stress