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Kababji AM, Butt H, Mahfouz M. Synthetic directed evolution for targeted engineering of plant traits. FRONTIERS IN PLANT SCIENCE 2024; 15:1449579. [PMID: 39286837 PMCID: PMC11402689 DOI: 10.3389/fpls.2024.1449579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 08/12/2024] [Indexed: 09/19/2024]
Abstract
Improving crop traits requires genetic diversity, which allows breeders to select advantageous alleles of key genes. In species or loci that lack sufficient genetic diversity, synthetic directed evolution (SDE) can supplement natural variation, thus expanding the possibilities for trait engineering. In this review, we explore recent advances and applications of SDE for crop improvement, highlighting potential targets (coding sequences and cis-regulatory elements) and computational tools to enhance crop resilience and performance across diverse environments. Recent advancements in SDE approaches have streamlined the generation of variants and the selection processes; by leveraging these advanced technologies and principles, we can minimize concerns about host fitness and unintended effects, thus opening promising avenues for effectively enhancing crop traits.
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Affiliation(s)
- Ahad Moussa Kababji
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Wu B, Luo H, Chen Z, Amin B, Yang M, Li Z, Wu S, Salmen SH, Alharbi SA, Fang Z. Rice Promoter Editing: An Efficient Genetic Improvement Strategy. RICE (NEW YORK, N.Y.) 2024; 17:55. [PMID: 39212859 PMCID: PMC11364747 DOI: 10.1186/s12284-024-00735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Gene expression levels in rice (Oryza sativa L.) and other plant species are determined by the promoters, which directly control phenotypic characteristics. As essential components of genes, promoters regulate the intensity, location, and timing of gene expression. They contain numerous regulatory elements and serve as binding sites for proteins that modulate transcription, including transcription factors and RNA polymerases. Genome editing can alter promoter sequences, thereby precisely modifying the expression patterns of specific genes, and ultimately affecting the morphology, quality, and resistance of rice. This paper summarizes research on rice promoter editing conducted in recent years, focusing on improvements in yield, heading date, quality, and disease resistance. It is expected to inform the application of promoter editing and encourage further research and development in crop genetic improvement with promote.
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Affiliation(s)
- Bowen Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Hangfei Luo
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhongbo Chen
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Bakht Amin
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Manyu Yang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhenghan Li
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Shuai Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Saleh H Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Zhongming Fang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China.
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
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Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
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Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
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Pradhan M, Bastia D, Samal KC, Dash M, Sahoo JP. Pyramiding resistance genes for bacterial leaf blight (Xanthomonas oryzae pv. Oryzae) into the popular rice variety, Pratikshya through marker assisted backcrossing. Mol Biol Rep 2023; 50:9047-9060. [PMID: 37725285 DOI: 10.1007/s11033-023-08805-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Bacterial leaf blight (BLB) is one of the major biotic stress in rice cultivation. Management techniques, such as the development of BLB-resistant cultivars, are required to lessen the severity of the disease attack and yield losses. Pratikshya was selected in the present investigation as the recipient parent, as it is one of the popular high-yielding rice varieties of Odisha, India, which is having excellent grain as well as cooking quality. However, Pratikshya is highly susceptible to BLB which is prevalent in Eastern Indian region. METHODS AND RESULTS Three major BLB resistance genes xa5, xa13, and Xa21 from the donor source Swarna MAS (CR Dhan 800) were attempted to introduce into Pratikshya through a marker-assisted backcross breeding program. Those markers closely linked to the target genes were employed for foreground selection in the segregating generations till BC2F3. In each backcross generation, progenies containing all three targeted resistance genes and phenotypically more similar to the recipient parent, Pratikshya were selected and backcrossed. Screening of 1,598 plants of the BC2F2 population was conducted against BLB using Xoo inoculum and 35 resistant plants similar to Pratikshya were carried forward to the next generation. In the BC2F3 generation, 31 plants were found to possess all the three resistance genes. For background selection of plants carrying resistance genes 45 polymorphic SSR markers were employed. Evaluation of the pyramided lines at BC2F4 generation exhibited that, most pyramided lines were similar to Pratikshya in terms of morphological features and yield parameters, and some lines were superior to the recurrent parent in terms of morphological features and yield parameters. CONCLUSION The three-gene pyramided lines showed a high level of resistance to BLB infection and are anticipated to offer a significant yield advantage over the recipient parent Pratikshya. The pyramided lines can further be used for multi-location trial, so as to be released as a variety or can be used as a potential donor for BLB resistance genes.
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Affiliation(s)
- Madhuri Pradhan
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, 753001, India
- Department of Agriculture and Allied Sciences, C. V. Raman Global University, Bhubaneswar, 752054, India
| | - Debendranath Bastia
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, 753001, India
| | - Kailash Chandra Samal
- Department of Molecular Biology and Biotechnology, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, 753001, India
- College of Horticulture, Odisha University of Agriculture and Technology, Chiplima, 768025, India
| | - Manasi Dash
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, 753001, India
| | - Jyoti Prakash Sahoo
- Department of Agriculture and Allied Sciences, C. V. Raman Global University, Bhubaneswar, 752054, India.
- Department of Molecular Biology and Biotechnology, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, 753001, India.
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Chen YH, Lu J, Yang X, Huang LC, Zhang CQ, Liu QQ, Li QF. Gene editing of non-coding regulatory DNA and its application in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6158-6175. [PMID: 37549968 DOI: 10.1093/jxb/erad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.
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Affiliation(s)
- Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xia Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
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Shaheen N, Ahmad S, Alghamdi SS, Rehman HM, Javed MA, Tabassum J, Shao G. CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review. RICE (NEW YORK, N.Y.) 2023; 16:39. [PMID: 37688677 PMCID: PMC10492775 DOI: 10.1186/s12284-023-00652-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/11/2023]
Abstract
Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.
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Affiliation(s)
- Nabeel Shaheen
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz Mamoon Rehman
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China.
- Zhejiang Lab, 310006, Hangzhou, China.
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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Sanya DRA, Syed-Ab-Rahman SF, Jia A, Onésime D, Kim KM, Ahohuendo BC, Rohr JR. A review of approaches to control bacterial leaf blight in rice. World J Microbiol Biotechnol 2022; 38:113. [PMID: 35578069 DOI: 10.1007/s11274-022-03298-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 01/16/2023]
Abstract
The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
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Affiliation(s)
| | | | - Aiqun Jia
- School of Environmental & Biological Engineering, Nanjing University of Science and Technology, Xiaolingwei No. 200, Xuanwu District, 210014, Nanjing, Jiangsu, China
| | - Djamila Onésime
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kyung-Min Kim
- School of Applied BioSciences, College of Agriculture & Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-Gu, 41566, Daegu, Korea
| | - Bonaventure Cohovi Ahohuendo
- Faculty of Agricultural Sciences, University of Abomey-Calavi, 526 Recette Principale, Cotonou 01, 01 BP, Abomey-Calavi, Benin
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Eck Institute of Global Health, Environmental Change Initiative, 178 Galvin Life Science Center, 46556, Notre Dame, IN, USA
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Doucouré H, Auguy F, Blanvillain-Baufumé S, Fabre S, Gabriel M, Thomas E, Dambreville F, Sciallano C, Szurek B, Koita O, Verdier V, Cunnac S. The Rice ILI2 Locus Is a Bidirectional Target of the African Xanthomonas oryzae pv. oryzae Major Transcription Activator-like Effector TalC but Does Not Contribute to Disease Susceptibility. Int J Mol Sci 2022; 23:ijms23105559. [PMID: 35628368 PMCID: PMC9142087 DOI: 10.3390/ijms23105559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependent fashion. Gain-of-function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain defective for SWEET gene activation. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target locus but nonetheless documents the first example of divergent transcription activation by a native TALE during infection.
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Affiliation(s)
- Hinda Doucouré
- LBMA, Faculté des Sciences et Techniques, University des Sciences Techniques et Technologiques, Bamako E 3206, Mali; (H.D.); (O.K.)
| | - Florence Auguy
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Servane Blanvillain-Baufumé
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Sandrine Fabre
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Marc Gabriel
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Emilie Thomas
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Fleur Dambreville
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Coline Sciallano
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Boris Szurek
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Ousmane Koita
- LBMA, Faculté des Sciences et Techniques, University des Sciences Techniques et Technologiques, Bamako E 3206, Mali; (H.D.); (O.K.)
| | - Valérie Verdier
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Sébastien Cunnac
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
- Correspondence:
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