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Radhika DH, Nandan M, Gunnaiah R, Doddaraju P, Dumble P, Manjunatha G, Vikram Singh N. Genome and transcriptome exploration reveals receptor-like kinases as potential resistance gene analogs against bacterial blight in pomegranate. Mol Biol Rep 2024; 51:735. [PMID: 38874770 DOI: 10.1007/s11033-024-09670-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/22/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Pomegranate (Punica granatum L.) is a tropical fruit crop of pharma-nutritional importance. However, it faces farming challenges due to pests and diseases, particularly bacterial blight and wilt. Developing resistant cultivars is crucial for sustainable pomegranate cultivation, and understanding resistance's genetic basis is essential. METHODS AND RESULTS We used an extensive resistance gene analogues (RGA) prediction tool to identify 958 RGAs, classified into Nucleotide Binding Site-leucine-rich repeat (NBS-LRR) proteins, receptor-like kinases (RLKs), receptor-like proteins (RLPs), Transmembrane coiled-coil (TM-CC), and nine non-canonical RGAs. RGAs were distributed across all eight chromosomes, with chromosome 02 containing the most RGAs (161), and chromosome 08 having the highest density (4.42 RGA/Mb). NBS-LRR genes were predominantly present on chromosomes 08 and 02, whereas RLKs and RLPs were primarily located on chromosomes 04 and 07. Gene ontology analysis revealed that 475 RGAs were associated with defence against various biotic stresses. Using RNAseq, we identified 120 differentially expressed RGAs, with RLKs (74) being prominent among the differentially expressed genes. CONCLUSION The discovery of these RGAs is a significant step towards breeding pomegranates for pest and disease resistance. The differentially expressed RLKs hold promise for developing resistant cultivars against bacterial blight, thereby contributing to the sustainability of pomegranate cultivation.
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Affiliation(s)
- Dattatraya Hegde Radhika
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, 587104, India
| | - M Nandan
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, 587104, India
| | - Raghavendra Gunnaiah
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, 587104, India.
| | - Pushpa Doddaraju
- Biocontrol Laboratory, Directorate of Research, University of Horticultural Sciences, Bagalkot, 587104, India
| | - Pavan Dumble
- Biocontrol Laboratory, Directorate of Research, University of Horticultural Sciences, Bagalkot, 587104, India
- Research and Development Division-Biodefense, Sea6Energy Private Limited, C-CAMP, NCBS-TIFR Campus, GKVK, Bengaluru, 560065, India
| | - Girigowda Manjunatha
- Biocontrol Laboratory, Directorate of Research, University of Horticultural Sciences, Bagalkot, 587104, India
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Cardoso JLS, Souza AA, Vieira MLC. Molecular basis for host responses to Xanthomonas infection. PLANTA 2022; 256:84. [PMID: 36114308 DOI: 10.1007/s00425-022-03994-0] [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: 03/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
This review highlights the most relevant and recent updated information available on the defense responses of selected hosts against Xanthomonas spp. Xanthomonas is one of the most important genera of Gram-negative phytopathogenic bacteria, severely affecting the productivity of economically important crops worldwide, colonizing either the vascular system or the mesophyll tissue of the host. Due to its rapid propagation, Xanthomonas poses an enormous challenge to farmers, because it is usually controlled using huge quantities of copper-based chemicals, adversely impacting the environment. Thus, developing new ways of preventing colonization by these bacteria has become essential. Advances in genomic and transcriptomic technologies have significantly elucidated at molecular level interactions between various crops and Xanthomonas species. Understanding how these hosts respond to the infection is crucial if we are to exploit potential approaches for improving crop breeding and cutting productivity losses. This review focuses on our current knowledge of the defense response mechanisms in agricultural crops after Xanthomonas infection. We describe the molecular basis of host-bacterium interactions over a broad spectrum with the aim of improving our fundamental understanding of which genes are involved and how they work in this interaction, providing information that can help to speed up plant breeding programs, namely using gene editing approaches.
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Affiliation(s)
- Jéssica L S Cardoso
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Alessandra A Souza
- Citrus Research Center "Sylvio Moreira", Agronomic Institute (IAC), Cordeirópolis, SP, 13490-000, Brazil
| | - Maria Lucia C Vieira
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Elliott K, Berry JC, Kim H, Bart RS. A comparison of ImageJ and machine learning based image analysis methods to measure cassava bacterial blight disease severity. PLANT METHODS 2022; 18:86. [PMID: 35729628 PMCID: PMC9210806 DOI: 10.1186/s13007-022-00906-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/16/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Methods to accurately quantify disease severity are fundamental to plant pathogen interaction studies. Commonly used methods include visual scoring of disease symptoms, tracking pathogen growth in planta over time, and various assays that detect plant defense responses. Several image-based methods for phenotyping of plant disease symptoms have also been developed. Each of these methods has different advantages and limitations which should be carefully considered when choosing an approach and interpreting the results. RESULTS In this paper, we developed two image analysis methods and tested their ability to quantify different aspects of disease lesions in the cassava-Xanthomonas pathosystem. The first method uses ImageJ, an open-source platform widely used in the biological sciences. The second method is a few-shot support vector machine learning tool that uses a classifier file trained with five representative infected leaf images for lesion recognition. Cassava leaves were syringe infiltrated with wildtype Xanthomonas, a Xanthomonas mutant with decreased virulence, and mock treatments. Digital images of infected leaves were captured overtime using a Raspberry Pi camera. The image analysis methods were analyzed and compared for the ability to segment the lesion from the background and accurately capture and measure differences between the treatment types. CONCLUSIONS Both image analysis methods presented in this paper allow for accurate segmentation of disease lesions from the non-infected plant. Specifically, at 4-, 6-, and 9-days post inoculation (DPI), both methods provided quantitative differences in disease symptoms between different treatment types. Thus, either method could be applied to extract information about disease severity. Strengths and weaknesses of each approach are discussed.
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Affiliation(s)
- Kiona Elliott
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
- Division of Biological and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO, 63110, USA
| | - Jeffrey C Berry
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Hobin Kim
- Army and Navy Academy, Carlsbad, CA, 92008, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA.
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Díaz-Tatis PA, Ochoa JC, Rico EM, Rodríguez C, Medina A, Szurek B, Chavarriaga P, López CE. RXam2, a NLR from cassava (Manihot esculenta) contributes partially to the quantitative resistance to Xanthomonas phaseoli pv. manihotis. PLANT MOLECULAR BIOLOGY 2022; 109:313-324. [PMID: 34757519 DOI: 10.1007/s11103-021-01211-2] [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: 02/22/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The overexpression of RXam2, a cassava NLR (nucleotide-binding leucine-rich repeat) gene, by stable transformation and gene expression induction mediated by dTALEs, reduce cassava bacterial blight symptoms. Cassava (Manihot esculenta) is a tropical root crop affected by different pathogens including Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of cassava bacterial blight (CBB). Previous studies have reported resistance to CBB as a quantitative and polygenic character. This study sought to validate the functional role of a NLR (nucleotide-binding leucine-rich repeat) associated with a QTL to Xpm strain CIO151 called RXam2. Transgenic cassava plants overexpressing RXam2 were generated and analyzed. Plants overexpressing RXam2 showed a reduction in bacterial growth to Xpm strains CIO151, 232 and 226. In addition, designer TALEs (dTALEs) were developed to specifically bind to the RXam2 promoter region. The Xpm strain transformed with dTALEs allowed the induction of the RXam2 gene expression after inoculation in cassava plants and was associated with a diminution in CBB symptoms. These findings suggest that RXam2 contributes to the understanding of the molecular basis of quantitative disease resistance.
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Affiliation(s)
- Paula A Díaz-Tatis
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Grupo de Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Cra1 #47a15, Bogotá D.C., Colombia
| | - Juan C Ochoa
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Department of Integrative Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Edgar M Rico
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
| | - Catalina Rodríguez
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Ludwig Maximilian University of Munich, Biozentrum Martinsried, Grosshaderner Strasse 4, Martinsried, Germany
| | - Adriana Medina
- Transformation Platform, Centro Internacional de Agricultura Tropical (CIAT), Km17 Cali-Palmira, Palmira, Colombia
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME), IRD-CIRAD-Université, Montpellier, France
| | - Paul Chavarriaga
- Transformation Platform, Centro Internacional de Agricultura Tropical (CIAT), Km17 Cali-Palmira, Palmira, Colombia
| | - Camilo E López
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia.
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Dinh HX, Singh D, Gomez de la Cruz D, Hensel G, Kumlehn J, Mascher M, Stein N, Perovic D, Ayliffe M, Moscou MJ, Park RF, Pourkheirandish M. The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei. Nat Commun 2022; 13:2386. [PMID: 35501307 PMCID: PMC9061838 DOI: 10.1038/s41467-022-29840-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 04/03/2022] [Indexed: 01/04/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is an economically significant disease of barley, but only a few major resistance genes to P. hordei (Rph) have been cloned. In this study, gene Rph3 was isolated by positional cloning and confirmed by mutational analysis and transgenic complementation. The Rph3 gene, which originated from wild barley and was first introgressed into cultivated Egyptian germplasm, encodes a unique predicted transmembrane resistance protein that differs from all known plant disease resistance proteins at the amino acid sequence level. Genetic profiles of diverse accessions indicated limited genetic diversity in Rph3 in domesticated germplasm, and higher diversity in wild barley from the Eastern Mediterranean region. The Rph3 gene was expressed only in interactions with Rph3-avirulent P. hordei isolates, a phenomenon also observed for transcription activator-like effector-dependent genes known as executors conferring resistance to Xanthomonas spp. Like known transmembrane executors such as Bs3 and Xa7, heterologous expression of Rph3 in N. benthamiana induced a cell death response. The isolation of Rph3 highlights convergent evolutionary processes in diverse plant-pathogen interaction systems, where similar defence mechanisms evolved independently in monocots and dicots. Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.
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Zárate‐Chaves CA, Gómez de la Cruz D, Verdier V, López CE, Bernal A, Szurek B. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae. MOLECULAR PLANT PATHOLOGY 2021; 22:1520-1537. [PMID: 34227737 PMCID: PMC8578842 DOI: 10.1111/mpp.13094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
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Affiliation(s)
| | | | - Valérie Verdier
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
| | - Camilo E. López
- Manihot Biotec, Departamento de BiologíaUniversidad Nacional de ColombiaBogotáColombia
| | - Adriana Bernal
- Laboratorio de Interacciones Moleculares de Microorganismos AgrícolasDepartamento de Ciencias BásicasUniversidad de los AndesBogotáColombia
| | - Boris Szurek
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
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Barrera ADP, Soto-Sedano J, López Carrascal CE. Identificación de polimorfismos en el gen <i>RXAM1</i> de yuca y su asociación con la resistencia a la bacteriosis vascular. ACTA BIOLÓGICA COLOMBIANA 2020. [DOI: 10.15446/abc.v25n2.77564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La yuca (Manihot esculenta Crantz) es un cultivo importante en regiones del trópico que proporciona alimento para cerca de 1000 millones de personas en todo el mundo. La enfermedad bacteriana más importante es la bacteriosis vascular causada por Xanthomonas axonopodis pv. manihotis (Xam). Recientemente se logró identificar un gen de resistencia denominado RXAM1, el cual codifica para una proteína que posee un dominio LRR (Leucine-Rich Repeat) extracelular y un dominio STK (Serine Threonine Kinase) citoplasmático. RXAM1 colocaliza con un QTL que explica el 13 % de la resistencia a la cepa CIO136 de Xam. En este trabajo se evaluó la respuesta a la infección con la cepa XamCIO136 en diez diferentes variedades de yuca lo cual permitió identificar que las variedades TMS60444, SG10735, MCOL1522, MCOL1505 y MCOL2215 fueron susceptibles, mientras que CM6438-14, CM523-7 y MBRA902 se comportaron como resistentes. Así mismo se identificaron polimorfismos tipo SNPs (Single Nucleotide Polymorphism) en el gen RXAM1 en el mismo grupo de variedades. Las variedades SG10735, CM6438-14, TMS6044 y MBRA685 presentaron el mayor nivel de polimorfismos, mientras que las variedades CM523-7, CM2177-2 y MCOL1522 fueron menos polimórficas para este gen. Los análisis estadísticos no permitieron identificar una asociación significativa entre el fenotipo y los polimorfismos identificados. Este estudio representa un primer esfuerzo con miras a asociar variantes alélicas con el fenotipo de respuesta a la bacteriosis vascular.
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Liu Y, Zhou X, Liu W, Huang J, Liu Q, Sun J, Cai X, Miao W. HpaXpm, a novel harpin of Xanthomonas phaseoli pv. manihotis, acts as an elicitor with high thermal stability, reduces disease, and promotes plant growth. BMC Microbiol 2020; 20:4. [PMID: 31906854 PMCID: PMC6945534 DOI: 10.1186/s12866-019-1691-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Harpins are proteins secreted by the type III secretion system of Gram-negative bacteria during pathogen-plant interactions that can act as elicitors, stimulating defense and plant growth in many types of non-host plants. Harpin-treated plants have higher resistance, quality and yields and, therefore, harpin proteins may potentially have many valuable agricultural applications. Harpins are characterized by high thermal stability at 100 °C. However, it is unknown whether harpins are still active at temperatures above 100 °C or whether different temperatures affect the activity of the harpin protein in different ways. The mechanism responsible for the heat stability of harpins is also unknown. RESULTS We identified a novel harpin, HpaXpm, from the cassava blight bacteria Xanthomonas phaseoli pv. manihotis HNHK. The predicted secondary structure and 3-D structure indicated that the HpaXpm protein has two β-strand domains and two major α-helical domains located at the N- and C-terminal regions, respectively. A phylogenetic tree generated using the maximum likelihood method grouped HpaXpm in clade I of the Hpa1 group along with harpins produced by other Xanthomonas spp. (i.e., HpaG-Xag, HpaG-Xcm, Hpa1-Xac, and Hpa1Xm). Phenotypic assays showed that HpaXpm induced the hypersensitive response (HR), defense responses, and growth promotion in non-host plants more effectively than Hp1Xoo (X. oryzae pv. oryzae). Quantitative real-time PCR analysis indicated that HpaXpm proteins subjected to heat treatments at 100 °C, 150 °C, or 200 °C were still able to stimulate the expression of function-related genes (i.e., the HR marker genes Hin1 and Hsr203J, the defense-related gene NPR1, and the plant growth enhancement-related gene NtEXP6); however, the ability of heat-treated HpaXpm to induce HR was different at different temperatures. CONCLUSIONS These findings add a new member to the harpin family. HpaXpm is heat-stable up to 200 °C and is able to stimulate powerful beneficial biological functions that could potentially be more valuable for agricultural applications than those stimulated by Hpa1Xoo. We hypothesize that the extreme heat resistance of HpaXpm is because the structure of harpin is very stable and, therefore, the HpaXpm structure is less affected by temperature.
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Affiliation(s)
- Yue Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Xiaoyun Zhou
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Wenbo Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Jiamin Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Qinghuan Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Jianzhang Sun
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Xinfeng Cai
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Weiguo Miao
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China.
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China.
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Gil J, López Carrascal CE. El dominio STK de la proteína de resistencia a la bacteriosis vascular de yuca RXAM1 interactúa con una E3 Ubiquitin Ligasa. ACTA BIOLÓGICA COLOMBIANA 2019. [DOI: 10.15446/abc.v24n1.70821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La yuca (Manihot esculenta) representa el pilar de la seguridad alimentaria para cerca de mil millones de personas, principalmente en las zonas tropicales. Uno de los factores limitantes de la producción de yuca es la bacteriosis vascular causada por la bacteria Xanthomonas axonopodis pv. manihotis (Xam). Recientemente se identificó el gen RXam1 el cual confiere resistencia parcial de yuca a cepas de Xam. RXam1 codifica una proteína con un dominio LRR (Leucine Rich Repeats) extracelular y un dominio STK (Serina Treonina Kinasa) citoplasmático; estas proteínas son conocidas como RLKs (Receptor Like Kinases). En este estudio se realizó el tamizaje de una librería de ADNc de yuca mediante doble híbrido de levadura para identificar las posibles proteínas que interactúan con el dominio STK de RXam1. El tamizaje de 3x108 clones permitió identificar y confirmar cinco clones de ellos los cuales corresponden al mismo gen, el cual codifica para una proteína que presenta un dominio central de dedos de zinc CHY, seguido por un dominio C-terminal “RING finger” y un “Zinc ribbon” el cual fue denominado CRFE3-1 (Cassava RING Finger E3 ligase). La interacción entre STK y CRFE3-1 fue altamente especifica ya que se demostró también por doble híbrido que STK no interactúa con una E3 ligasa de Arabidopsis, altamente similar a CRFE3-1, así como tampoco CRFE3-1 interactúa con el dominio STK de un RLK de lechuga similar a RXam1. La identificación de CRFE3-1 sugiere que mecanismos de degradación proteica son importantes para regular la actividad de RXam1.
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10
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Thibaut O, Claude B. Innate Immunity Activation and RNAi Interplay in Citrus Exocortis Viroid-Tomato Pathosystem. Viruses 2018; 10:E587. [PMID: 30373191 PMCID: PMC6266551 DOI: 10.3390/v10110587] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/18/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Although viroids are the smallest and simplest plant pathogens known, the molecular mechanisms underlying their pathogenesis remain unclear. To unravel these mechanisms, a dual approach was implemented consisting of in silico identification of potential tomato silencing targets of pospiviroids, and the experimental validation of these targets through the sequencing of small RNAs and RNA ends extracted from tomatoes infected with a severe isolate of Citrus exocortis viroid (CEVd). The generated RNA ends were also used to monitor the differentially-expressed genes. These analyses showed that when CEVd symptoms are well established: (i) CEVd are degraded by at least three Dicer-like (DCL) proteins and possibly by RNA-induced silencing complex (RISC), (ii) five different mRNAs are partially degraded through post-transcriptional gene silencing (PTGS), including argonaute 2a, which is further degraded in phasiRNAs, (iii) Dicer-like 2b and 2d are both upregulated and degraded in phasiRNAs, and (iv) CEVd infection induced a significant shift in gene expression allowing to explain the usual symptoms of pospiviroids on tomato and to demonstrate the constant activation of host innate immunity and systemic acquired resistance (SAR) by these pathogenic RNAs. Finally, based on in silico analysis, potential immunity receptor candidates of viroid-derived RNAs are suggested.
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Affiliation(s)
- Olivier Thibaut
- Life Sciences Department, Walloon agricultural research Centre, Rue de Liroux 4, 5030 Gembloux, Belgium.
- UCLouvain, Earth&Life Institute, Croix du Sud 2bte L7.05.03, 1348 Louvain-la-Neuve, Belgium.
| | - Bragard Claude
- UCLouvain, Earth&Life Institute, Croix du Sud 2bte L7.05.03, 1348 Louvain-la-Neuve, Belgium.
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Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, Śmiech M, Zhao K, Rahman M, Islam T. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges. FRONTIERS IN PLANT SCIENCE 2018; 9:617. [PMID: 29868073 PMCID: PMC5952327 DOI: 10.3389/fpls.2018.00617] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/18/2018] [Indexed: 05/19/2023]
Abstract
The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.
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Affiliation(s)
- Effi Haque
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Md. Mahmudul Hassan
- Division of Genetics, Genomics and Development School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Pankaj Bhowmik
- National Research Council of Canada, Saskatoon, SK, Canada
| | - M. Rezaul Karim
- Department of Biotechnology and Genetic Engineering Jahangirnagar University Savar, Dhaka, Bangladesh
| | - Magdalena Śmiech
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mahfuzur Rahman
- Extension Service, West Virginia University, Morgantown, WV, United States
| | - Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
- Extension Service, West Virginia University, Morgantown, WV, United States
- *Correspondence: Tofazzal Islam
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