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Akter A, Hassan L, Nihad SAI, Hasan MJ, Robin AHK, Khatun M, Tabassum A, Latif MA. Pyramiding of bacterial blight resistance genes into promising restorer BRRI31R line through marker-assisted backcross breeding and evaluation of agro-morphological and physiochemical characteristics of developed resistant restorer lines. PLoS One 2024; 19:e0301342. [PMID: 38865348 PMCID: PMC11168670 DOI: 10.1371/journal.pone.0301342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/13/2024] [Indexed: 06/14/2024] Open
Abstract
BRRI31R is one of the Bangladesh's most promising restorer lines due to its abundant pollen producing capacity, strong restoring ability, good combining ability, high outcrossing rate and genetically diverse from cytoplasmic male sterile (CMS) line. But the drawback of this line is that it is highly susceptible to bacterial blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae. The present study highlighted the pyramiding of effective BB resistance genes (xa5, xa13 and Xa21) into the background of BRRI31R, through marker-assisted backcrossing (MABC). Backcross progenies were confirmed and advanced based on the foreground selection of target genes. Pyramided lines were used for pathogenicity test against five Bangladeshi Xanthomonas oryzae (BXo) races (BXo93, BXo220, BXo822, BXo826, BXo887) and confirmed the dominant fertility restore genes, Rf3 and Rf4 and further validated against SNP markers for more confirmation of target resistance genes. All pyramided restorer lines consisted of Xa4 (in built), xa5, xa13, Xa21, and Chalk5 with two fertility restorer genes, Rf3, Rf4. and these restorer lines showed intermediate amylose content (<25%). Restorer lines BRRI31R-MASP3 and BRRI31R-MASP4 showed high levels of resistance against five virulent BXo races and SNP genotyping revealed that these lines also contained a blast resistance gene Pita races. Gene pyramided restorer lines, BRRI31R-MASP3 and BRRI31R-MASP4 can directly be used as a male parent for the development of new BB resistant hybrid rice variety or could be used as a replacement of restorer line of BRRI hybrid dhan5 and 7 to enhance the quality of hybrid seeds as well as rice production in Bangladesh.
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Affiliation(s)
- Anowara Akter
- Hybrid Rice Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Lutful Hassan
- Genetics and Plant Breeding, Bangladesh Agricultural University (BAU), Mymensingh, Bangladesh
| | | | - Md. Jamil Hasan
- Hybrid Rice Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Arif Hasan Khan Robin
- Genetics and Plant Breeding, Bangladesh Agricultural University (BAU), Mymensingh, Bangladesh
| | - Mahmuda Khatun
- Genetics and Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Anika Tabassum
- Plant Breeding Division, Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh
| | - Mohammad Abdul Latif
- Hybrid Rice Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
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Ahammad I, Jamal TB, Lamisa AB, Bhattacharjee A, Zinan N, Hasan Chowdhury MZ, Naimul Islam SM, Faruque KMO, Mahmud Chowdhury Z, Uzzal Hossain M, Chandra Das K, Ara Keya C, Salimullah M. Subtractive genomics study of Xanthomonas oryzae pv. Oryzae reveals repurposable drug candidate for the treatment of bacterial leaf blight in rice. J Genet Eng Biotechnol 2024; 22:100353. [PMID: 38494267 PMCID: PMC10980872 DOI: 10.1016/j.jgeb.2024.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/15/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against X. oryzae pv. oryzae, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants. RESULTS The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in Xoo proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time. CONCLUSION Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by X. oryzae pv. oryzae. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from in silico studies should be validated through further in vitro and in vivo investigation before approval.
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Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Tabassum Binte Jamal
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Anika Bushra Lamisa
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Nayeematul Zinan
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Zahid Hasan Chowdhury
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Shah Mohammad Naimul Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | | | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh.
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3
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Chowdhury AR, Kumar R, Mahanty A, Mukherjee K, Kumar S, Tribhuvan KU, Sheel R, Lenka S, Singh BK, Chattopadhyay C, Sharma TR, Bhadana VP, Sarkar B. Inhibitory role of copper and silver nanocomposite on important bacterial and fungal pathogens in rice (Oryza sativa). Sci Rep 2024; 14:1779. [PMID: 38245579 PMCID: PMC10799878 DOI: 10.1038/s41598-023-49918-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
Rice (Oryza sativa) being among the most important food crops in the world is also susceptible to various bacterial and fungal diseases that are the major stumbling blocks in the way of increased production and productivity. The bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae and the sheath blight disease caused by Rhizoctonia solani are among the most devastating diseases of the rice crop. In spite of the availability of array of chemical control, there are chances of development of resistance. Thus, there is a need for the nanotechnological intervention for management of disease in the form of copper and silver nano-composites. The copper (CuNPs) and silver nanoparticles (AgNPs) were synthesized using green route and characterized using different high throughput techniques, i.e., UV-Vis, FT-IR, DLS, XRD, FE-SEM, TEM. The particle size and zeta potential of synthesized CuNPs and AgNPs were found 273 nm and - 24.2 mV; 95.19 nm and - 25.5 mV respectively. The nanocomposite of CuNPs and AgNPs were prepared having particle size in the range of 375-306 nm with improved stability (zeta potential - 54.7 to - 39.4 mV). The copper and silver nanoparticle composites evaluated against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani were found to have higher antibacterial (inhibition zone 13 mm) and antifungal activities (77%) compared to only the copper nanoparticle (8 mm; 62% respectively). Net house trials of nano-composite formulations against the bacterial blight of rice also corroborated the potential of nanocomposite formulation. In silico studies were carried out selecting two disease-causing proteins, peptide deformylase (Xanthomonas oryzae) and pectate lyase (Rhizoctonia solani) to perform the molecular docking. Interaction studies indicatedthat both of these proteins generated better complex with CuNPs than AgNPs. The study suggested that the copper and silver nano-composites could be used for developing formulations to control these devastating rice diseases.
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Affiliation(s)
- Arnab Roy Chowdhury
- ICAR-National Institute of Secondary Agriculture, Namkum, Ranchi, 834 010, Jharkhand, India
| | - Rishikesh Kumar
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - Arabinda Mahanty
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Koel Mukherjee
- Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Sudhir Kumar
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - Kishor U Tribhuvan
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - Rishav Sheel
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
- Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Srikanta Lenka
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Binay K Singh
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - Chirantan Chattopadhyay
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - T R Sharma
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - Vijai Pal Bhadana
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India
| | - Biplab Sarkar
- ICAR-Indian Institute of Agricultural Biotechnology, GarhkhatangaRanchi, Jharkhand, 834 003, India.
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Diallo A, Wonni I, Sicard A, Blondin L, Gagnevin L, Vernière C, Szurek B, Hutin M. Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations. RICE (NEW YORK, N.Y.) 2023; 16:33. [PMID: 37523017 PMCID: PMC10390441 DOI: 10.1186/s12284-023-00648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980's. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.
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Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso.
| | - A Sicard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Blondin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Gagnevin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Vernière
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - B Szurek
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - M Hutin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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5
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My PDT, Vinh TQ, Ngoc TH, Anh PNQ, Duyen LTM, Thien NM, Tien LTT, Phuc VT, Oanh HN, Nga LP, Hoang HA. Complete genome sequence of a novel lytic phage of Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen in rice. Arch Virol 2023; 168:157. [PMID: 37160612 DOI: 10.1007/s00705-023-05788-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
Bacteriophage L522, which infects Xanthomonas oryzae pv. oryzae, was isolated from a paddy leaf sample collected in Long An province, Vietnam. The phage shows myovirus morphology based on transmission electron microscopy. It displays a latent period and burst size of approximately 3 h and 63 new virions per infected cell (PFU/infected cell), respectively. The genome of L522 is 44,497 bp in length, with 52% GC content. Of the 63 genes identified, functions were predicted for 26. No virulence or antibiotic-resistance genes were detected. The results of a BLASTn search showed similarity to a previously reported Xanthomonas phage, with 85% average nucleotide sequence identity and 87.15% query coverage. Thus, this L522 is a representative of a new species in the genus Xipdecavirus.
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Affiliation(s)
- Pham D T My
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Tu Q Vinh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - To H Ngoc
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Pham N Q Anh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Le T M Duyen
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Nguyen M Thien
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Le T T Tien
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Vo T Phuc
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Huynh N Oanh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Le P Nga
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Hoang A Hoang
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam.
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam.
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6
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Zang HY, Yang X, Gu CY, Sun JZ, Pan R, Wang YX, Gao TC, Yuan SK, Chen Y. A Specific High Toxicity of Xinjunan (Dioctyldiethylenetriamine) to Xanthomonas by Affecting the Iron Metabolism. Microbiol Spectr 2023; 11:e0438222. [PMID: 36877068 PMCID: PMC10100656 DOI: 10.1128/spectrum.04382-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
Xanthomonas spp. encompass a wide range of phytopathogens that brings great economic losses to various crops. Rational use of pesticides is one of the effective means to control the diseases. Xinjunan (Dioctyldiethylenetriamine) is structurally unrelated to traditional bactericides, and is used to control fungal, bacterial, and viral diseases with their unknown mode of actions. Here, we found that Xinjunan had a specific high toxicity toward Xanthomonas spp., especially to the Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial leaf blight. Transmission electron microscope (TEM) confirmed its bactericidal effect by morphological changes, including cytoplasmic vacuolation and cell wall degradation. DNA synthesis was significantly inhibited, and the inhibitory effect enhanced with the increase of the chemical concentration. However, the synthesis of protein and EPS was not affected. RNA-seq revealed differentially expressed genes (DEGs) particularly enriched in iron uptake, which was subsequently confirmed by siderophore detection, intracellular Fe content and iron-uptake related genes transcriptional level. The laser confocal scanning microscopy and growth curve monitoring of the cell viability in response to different Fe condition proved that the Xinjunan activity relied on the addition of iron. Taken together, we speculated that Xinjunan exerted bactericidal effect by affecting cellular iron metabolism as a novel mode of action. IMPORTANCE Sustainable chemical control for rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae need to be developed due to limited bactericides with high efficiency, low cost, and low toxicity in China. This present study verified a broad-spectrum fungicide named Xinjunan possessing a specific high toxicity to Xanthomonas pathogens, which were further confirmed by affecting the cellular iron metabolism of Xoo as a novel mode of action. These findings will contribute to the application of the compound in the field control of Xanthomonas spp.-caused diseases, and be directive for future development of novel specific drugs for the control of severe bacterial diseases based on this novel mode of action.
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Affiliation(s)
- Hao-Yu Zang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xue Yang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Jia-Zhi Sun
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Rui Pan
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yong-Xing Wang
- Shandong Vicome Greenland Chemical Co. Ltd., Jinan, China
| | - Tong-Chun Gao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shan-Kui Yuan
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yu Chen
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Engineering Laboratory for Green Pesticide Development and Application of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
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7
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Zhu M, Li Y, Chen DP, Li CP, Ouyang GP, Wang ZC. Allicin-inspired disulfide derivatives containing quinazolin-4(3H)-one as a bacteriostat against Xanthomonas oryzae pv. oryzae. PEST MANAGEMENT SCIENCE 2023; 79:537-547. [PMID: 36193761 DOI: 10.1002/ps.7221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant bacterial diseases have seriously affected the yield and quality of crops, among which rice bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae has seriously affected the yield of rice. As plant-pathogenic bacteria gradually become resistant to existing bactericides, it is necessary to find effective bactericides with novel structures. RESULTS Herein, a series of compounds containing quinazolin-4(3H)-one and disulfide moieties were designed and synthesized using a facile synthetic method. The bioassay results revealed that most target compounds possessed noticeable antibacterial activity against Xanthomonas oryzae pv. oryzae. Particularly, compound 2-(butyldisulfanyl) quinazolin-4(3H)-one (1) exhibited remarkable antibacterial activity with the half effective concentration (EC50 ) of 0.52 μg mL-1 . Additionally, compound 1 was confirmed to inhibit the growth of the bacteria, change the bacterial morphology, and increase the level of reactive oxygen species. Proteomics, and RT-qPCR analysis results indicated that compound 1 could downregulate the expression of Pil-Chp histidine kinase chpA encoded by the pilL gene, and the potting experiments proved that compound 1 exhibits significant protective activity against BLB. CONCLUSIONS Compound 1 may weaken the pathogenicity of Xanthomonas oryzae pv. oryzae by inhibiting the bacterial growth and blocking the pili-mediated twitching motility without inducing the bacterial apoptosis. This study indicates that such derivatives could be a promising scaffold to develop a bacteriostat to control BLB. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Mei Zhu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yan Li
- College of Pharmacy, Guizhou University, Guiyang, China
| | - Dan-Ping Chen
- College of Pharmacy, Guizhou University, Guiyang, China
| | - Cheng-Peng Li
- College of Pharmacy, Guizhou University, Guiyang, China
| | - Gui-Ping Ouyang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals of Guizhou University, Guiyang, China
- College of Pharmacy, Guizhou University, Guiyang, China
| | - Zhen-Chao Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals of Guizhou University, Guiyang, China
- College of Pharmacy, Guizhou University, Guiyang, China
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8
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Sciallano C, Auguy F, Boulard G, Szurek B, Cunnac S. The Complete Genome Resource of Xanthomonas oryzae pv. oryzae CIX2779 Includes the First Sequence of a Plasmid for an African Representative of This Rice Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:73-77. [PMID: 36537805 DOI: 10.1094/mpmi-09-22-0191-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bacterial blight disease. Genetically contrasted, continent-specific, sublineages of this species can cause important damages to rice production both in Asia and Africa. We report on the genome of the CIX2779 strain of this pathogen, previously named NAI1 and originating from Niger. Oxford Nanopore long reads assembly and Illumina short reads polishing produced a genome sequence composed of a 4,725,792-bp circular chromosome and a 39,798-bp-long circular plasmid designated pCIX2779_1. The chromosome structure and base-level sequence are highly related to reference strains of African X. oryzae pv. oryzae and encode identical transcription activator-like effectors for virulence. Importantly, our in silico analysis strongly indicates that pCIX2779_1 is a genuine conjugative plasmid, the first indigenous one sequenced from an African strain of the X. oryzae species. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Coline Sciallano
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gabriel Boulard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sébastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Zhou Q, Li L, Liu F, Hu J, Cao Y, Qiao S, Zhou Y, Wang B, Jia Y, Chen Y, Xu S, Feng X. Mining and characterization of oxidative stress-related binding proteins of parthenolide in Xanthomonas oryzae pv. oryzae. PEST MANAGEMENT SCIENCE 2022; 78:3345-3355. [PMID: 35491536 DOI: 10.1002/ps.6961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Lack of control agents and development of bacterial resistance are emergent problems in the chemical control of rice bacterial blight, therefore novel bactericides against Xanthomonas oryzae pv. oryzae (Xoo, the causal agent of rice bacterial blight) are urgently needed. We previously found that parthenolide (PTL) is a potential lead against Xoo, and PTL inhibits Xoo growth via oxidative stress. However, the mechanism of action of PTL against Xoo needs further elucidation. RESULTS In this study, a biotinylated PTL probe was synthesized, and two important subunits in the respiratory chain (NuoF of complex I and SdhB of complex II) of Xoo were captured with the probe and identified with liquid chromatography tandem mass spectrometry (LC-MS/MS). The binding between them was verified with pull-down and drug affinity responsive target stability technologies. In addition, purified proteins of NuoF and SdhB greatly lowered the antibacterial activity of PTL, and PTL evidently inhibited the enzyme activities of complexes I and II. Moreover, knockout of nuoF and sdhB in Xoo caused elevated reactive oxygen species (ROS) levels and increased sensitivity to PTL. Furthermore, molecular simulations indicated that PTL may form covalent bonds with Cys105 and Cys187 in NuoF and Cys106 in SdhB. CONCLUSION PTL can directly bind to NuoF and SdhB, which impairs the enzyme functions of complexes I and II in the respiratory chain, leading to ROS accumulation in Xoo. This study will provide deep insight into the mechanism of action of PTL against Xoo. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Qian Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Province Engineering Research Center of Eco-cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Linwei Li
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Province Engineering Research Center of Eco-cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jun Hu
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yan Cao
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Siwei Qiao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Province Engineering Research Center of Eco-cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuxin Zhou
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Province Engineering Research Center of Eco-cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yihe Jia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China
| | - Yu Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Province Engineering Research Center of Eco-cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Province Engineering Research Center of Eco-cultivation and High-Value Utilization of Chinese Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xu Feng
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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10
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Jiang D, Zhang D, Li S, Liang Y, Zhang Q, Qin X, Gao J, Qiu J. Highly efficient genome editing in Xanthomonas oryzae pv. oryzae through repurposing the endogenous type I-C CRISPR-Cas system. MOLECULAR PLANT PATHOLOGY 2022; 23:583-594. [PMID: 34954876 PMCID: PMC8916207 DOI: 10.1111/mpp.13178] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Efficient and modular genome editing technologies that manipulate the genome of bacterial pathogens will facilitate the study of pathogenesis mechanisms. However, such methods are yet to be established for Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight. We identified a single type I-C CRISPR-Cas system in the Xoo genome and leveraged this endogenous defence system for high-efficiency genome editing in Xoo. Specifically, we developed plasmid components carrying a mini-CRISPR array, donor DNA, and a phage-derived recombination system to enable the efficient and programmable genome editing of precise deletions, insertions, base substitutions, and gene replacements. Furthermore, the type I-C CRISPR-Cas system of Xoo cleaves target DNA unidirectionally, and this can be harnessed to generate large genomic deletions up to 212 kb efficiently. Therefore, the genome-editing strategy we have developed can serve as an excellent tool for functional genomics of Xoo, and should also be applicable to other CRISPR-harbouring bacterial plant pathogens.
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Affiliation(s)
- Dandan Jiang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Dandan Zhang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Shengnan Li
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yueting Liang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Qianwei Zhang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Xu Qin
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Jinlan Gao
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jin‐Long Qiu
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
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11
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Diversity of transcription activator-like effectors and pathogenicity in strains of Xanthomonas oryzae pv. oryzicola from Yunnan. World J Microbiol Biotechnol 2022; 38:71. [PMID: 35258706 DOI: 10.1007/s11274-022-03230-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 01/07/2022] [Indexed: 10/18/2022]
Abstract
The present study aimed to evaluate transcriptional activator-like effector (TALE) genes in 86 Xanthomonas oryzae pv. oryzicola strains collected from 8 rice-growing regions in Yunnan, and to examine the relationship between TALE genotypes and virulence in 6 differential rice lines. Besides, the geographical areas, distribution of these genotypes were studied in detail. Genetic diversity was analyzed through the number and size of putative TALE genes based on TALE gene avrXa3 as a probe. We found that X. oryzae pv. oryzicola strains consist of variable number (13-27) of avrXa3-hybridizing fragments (putative TALE genes). Test strains were classified into 8 genotypes (G1-G8) with major genotypes G3 and G7 widely distributed in Yunnan. Pathogenicity of X. oryzae pv. oryzicola was evaluated by inoculating 6 differential rice lines with a single resistance gene into 9 pathotypes clusters (I-IX), the dominant Genotypes G3 and G7 consist of pathotypes I, II, and IV. Furthermore, we also detected the known TALE target genes expression in susceptible rice cultivar (cv. nipponbare) after inoculating 8 genotypes-representative X. oryzae pv. oryzicola strain. Correlation between the numbers of putative TALE genes of X. oryzae pv. oryzicola and relevant target genes in nipponbare confirmed up-regulation. Altogether, this study has given insights into the population structure of X. oryzae pv. oryzicola that may inform strategies to control BLS in rice.
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12
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Abstract
Xanthomonas is a notorious plant pathogen causing serious diseases in hundreds of plant hosts. Xanthomonas species are equipped with an array of signal transduction systems that regulate gene expression to survive in various harsh environments and successfully infect hosts. Although certain pathogenicity-associated regulators have been functionally characterized, signal transduction systems always function as a regulatory network which remains to be elucidated in Xanthomonas. This study used a systematic approach to characterize all identified pathogenicity-associated regulators in Xanthomonas oryzae pv. oryzae (Xoo), including a transcriptional regulator with unknown function, and their interactive regulatory network. RNA sequencing was used in elucidating the patterns of the 10 pathogenicity-associated regulators identified. Results revealed that each pathogenicity-associated regulator has cross talk with others and all these regulators function as a regulatory network, with VemR and PXO_RS20790 being the master pathogenicity-associated regulators and HrpX being the final executant. Moreover, regulome analysis showed that numerous genes other than genes in pathogenicity islands are finely regulated within the regulatory network. Given that most of the pathogenicity-associated regulators are conserved in Xanthomonadales, our findings suggest a global network of gene regulation in this evolutionarily conserved pathogen. In conclusion, our study provides essential basic information about the regulatory network in Xoo, suggesting that this complicated regulatory network is one of the reasons for the robustness and fitness of Xanthomonas spp. IMPORTANCE The host plant infection process of pathogenic bacteria is a coordinating cellular behavior, which requires dynamic regulation at several levels in response to variations in host plants or fluctuations in the external environment. As one of the most important genera of plant-pathogenic bacteria, Xanthomonas has been studied as a model. Although certain pathogenicity-associated regulators have been functionally characterized, interactions among them remain to be elucidated. This study systematically characterized pathogenicity-associated regulators in Xoo and revealed that cross talk exists among pathogenicity-associated regulators and function as a regulatory network in which a hierarchy exists among the regulators. Our study elucidated the landscape of the pathogenicity-associated regulatory network in Xanthomonas, promoting understanding of the infection process of pathogenic bacteria.
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13
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Yadav S, Sandhu N, Dixit S, Singh VK, Catolos M, Mazumder RR, Rahman MA, Kumar A. Genomics-assisted breeding for successful development of multiple-stress-tolerant, climate-smart rice for southern and southeastern Asia. THE PLANT GENOME 2021; 14:e20074. [PMID: 33438317 DOI: 10.1002/tpg2.20074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 06/12/2023]
Abstract
Rice (Oryza sativa L.) in rainfed marginal environments is prone to multiple abiotic and biotic stresses, which can occur in combination in a single cropping season and adversely affect rice growth and yield. The present study was undertaken to develop high-yielding, climate-resilient rice that can provide tolerance to multiple biotic and abiotic stresses. An assembled first-crossing scheme was employed to transfer 15 quantitative trait loci (QTL) and genes-qDTY1.1 , qDTY2.1 , qDTY3.1 , qDTY12.1 (drought), Sub1 (submergence), Gm4 (gall midge), Pi9, Pita2 (blast), Bph3, Bph17 (brown plant hoppers), Xa4, xa5, xa13, Xa21, and Xa23 (bacterial leaf blight)-from eight different parents using genomics-assisted breeding. A funnel mating design was employed to assemble all the targeted QTL and genes into a high-yielding breeding line IR 91648-B-1-B-3-1. Gene-based linked markers were used in each generation from intercrossing to the F6 generation for tracking the presence of desirable alleles of targeted QTL and genes. Single-plant selections were performed from F2 onwards to select desirable recombinants possessing alleles of interest with suitable phenotypes. Phenotyping of 95 homozygous F6 lines carrying six to 10 QTL and genes was performed for nonstress, reproductive-stage (RS) drought, blast, bacterial leaf blight (BLB), gall midge (GM), and for grain quality parameters such as chalkiness, amylose content (AC), gelatinization temperature (GT), and head rice recovery (HRR). Finally, 56 F7 homozygous lines were found promising for multiple-location evaluation for grain yield (GY) and other traits. These multiple-stress-tolerant lines with the desired grain quality profiling can be targeted for varietal release in southern and southeastern Asia through national release systems.
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Affiliation(s)
- Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
- Punjab Agricultural University, Ludhiana, Punjab, India
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
| | - Ratna Rani Mazumder
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
- IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, 221106, India
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14
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Kini K, Agnimonhan R, Wonni I, Silue D. An Efficient Inoculation Technique to Assess the Pathogenicity of Pantoea Species Associated to Bacterial Blight of Rice. Bio Protoc 2020; 10:e3740. [PMID: 33659400 PMCID: PMC7842767 DOI: 10.21769/bioprotoc.3740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 06/17/2020] [Accepted: 07/14/2020] [Indexed: 11/02/2022] Open
Abstract
Bacteria blight diseases of rice due to several genera of pathogenic bacteria are one of the major constraints worldwide for rice production. The disease can be best managed through host plant resistance sources. For most of these bacteria such as Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae, specific diagnostic techniques that include molecular and pathogenicity tests have been developed. However, for Pantoea spp., information on pathogenicity assay is very limited and protocols used are not uniform. Most authors use the leaf clipping method. In this paper, we describe the protocol for mechanical inoculation of rice seedlings aged 35 days. The method consists of infiltrating bacterial suspensions at concentrations of 108 CFU/ml, with a needleless syringe into the intercellular and interveinal spaces of rice leaves underside at about 4-5 cm below the leaf tip. This method can be used for a standardized pathogenicity assessment, germplasm resistance evaluation for identifying and characterizing resistance sources.
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Affiliation(s)
- Kossi Kini
- Plant Pathology Unit, AfricaRice, Cotonou, Benin
| | | | - Issa Wonni
- Plant Pathology, Institut de l'Environnement et de Recherches Agricoles (INERA), Bobo Dioulasso, Burkina Faso
| | - Drissa Silue
- Plant Pathology Unit, AfricaRice, Cotonou, Benin
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15
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Angeles-Shim RB, Shim J, Vinarao RB, Lapis RS, Singleton JJ. A novel locus from the wild allotetraploid rice species Oryza latifolia Desv. confers bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in rice (O. sativa). PLoS One 2020; 15:e0229155. [PMID: 32084193 PMCID: PMC7034821 DOI: 10.1371/journal.pone.0229155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/30/2020] [Indexed: 11/19/2022] Open
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major limiting factor to rice productivity worldwide. Genetic control through the identification of novel sources of bacterial blight resistance and their utilization in resistance breeding remains the most effective and economical strategy to manage the disease. Here we report the identification of a novel locus from the wild Oryza species, Oryza latifolia, conferring a race-specific resistance to Philippine Xoo race 9A (PXO339). The locus was identified from two introgression lines i.e. WH12-2252 and WH12-2256 that segregated from O. latifolia monosomic alien addition lines (MAALs). The discrete segregation ratio of susceptible and resistant phenotypes in the F2 (χ2[3:1] = 0.22 at p>0.05) and F3 (χ2[3:1] = 0.36 at p>0.05) populations indicates that PXO339 resistance in the MAAL-derived introgression lines (MDILs) is controlled by a single, recessive gene. Genotyping of a total of 216 F2, 1130 F3 and 288 F4 plants derived from crossing either of the MDILs with the recurrent parent used to generate the MAALs narrowed the candidate region to a 1,817 kb locus that extends from 10,425 to 12,266 kb in chromosome 12. Putative candidate genes that were identified by data mining and comparative sequence analysis can provide targets for further studies on mapping and cloning of the causal gene for PXO339 resistance in the MDILs. To our knowledge, this is the first report of a genetic locus from the allotetraploid wild rice, O. latifolia conferring race-specific resistance to bacterial blight.
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Affiliation(s)
| | - Junghyun Shim
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
| | - Ricky B. Vinarao
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
| | - Ruby S. Lapis
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
| | - Joshua J. Singleton
- Plant Breeding Division, International Rice Research Institute, Manila, Philippines
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16
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Nelson R. International Plant Pathology: Past and Future Contributions to Global Food Security. PHYTOPATHOLOGY 2020; 110:245-253. [PMID: 31680649 DOI: 10.1094/phyto-08-19-0300-ia] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The challenge of feeding the current and future world population is widely recognized, and the management of plant diseases has an important role in overcoming this. This paper explores the ways in which international plant pathology has contributed and continues to support efforts to secure adequate, safe and culturally appropriate nourishment and livelihoods for present and future generations. For the purposes of this paper, "international plant pathology" refers to the work that plant pathologists do when they work across international borders, with a focus on enhancing food security in tropical regions. Significant efforts involve public and philanthropic resources from the global North for addressing plant disease concerns in the global South, where food security is a legitimate and pressing concern. International disease management efforts are also aimed at protecting domestic food security, for example when pathogens of major staples migrate across national borders. In addition, some important crops are largely produced in tropical countries and consumed globally, including in industrialized countries; the diseases of these crops are of international interest, and they are largely managed by the private sector. Finally, host-microbe interactions are fascinating biological systems, and basic research on plant diseases of international relevance has often yielded insights and technologies with both scientific and practical implications.
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Affiliation(s)
- Rebecca Nelson
- School of Integrative Plant Sciences, Cornell University
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17
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Abd-El-Khair H. Biological Control of Phyto-pathogenic Bacteria. COTTAGE INDUSTRY OF BIOCONTROL AGENTS AND THEIR APPLICATIONS 2020:299-336. [DOI: 10.1007/978-3-030-33161-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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18
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Kim SM, Reinke RF. A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS, confirmed by QTL mapping using a bi-parental population. PLoS One 2019; 14:e0211775. [PMID: 30753229 PMCID: PMC6372157 DOI: 10.1371/journal.pone.0211775] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/21/2019] [Indexed: 11/18/2022] Open
Abstract
Bacterial blight (BB) caused by the Xanthomonas oryzae pv. oryzae (Xoo) pathogen is a significant disease in most rice cultivation areas. The disease is estimated to cause annual rice production losses of 20–30 percent throughout rice-growing countries in Asia. The discovery and deployment of durable resistance genes for BB is an effective and sustainable means of mitigating production losses. In this study QTL analysis and fine mapping were performed using an F2 and a BC2F2 population derived from a cross with a new R-donor having broad spectrum resistance to Korean BB races. The QTL qBB11 was identified by composite interval mapping and explained 31.25% of the phenotypic variation (R2) with LOD values of 43.44 harboring two SNP markers. The single major R-gene was designated Xa43 (t). Through dissection of the target region we were able to narrow the region to within 27.83–27.95 Mbp, a physical interval of about 119-kb designated by the two flanking markers IBb27os11_14 and S_BB11.ssr_9. Of nine ORFs in the target region two ORFs revealed significantly different expression levels of the candidate genes. From these results we developed a marker specific to this R-gene, which will have utility for future BB resistance breeding and/or R-gene pyramiding using marker assisted selection. Further characterization of the R-gene would be helpful to enhance understanding of mechanisms of BB resistance in rice.
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Affiliation(s)
- Suk-Man Kim
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
- IRRI-Korea Office, National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Russell F. Reinke
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
- * E-mail:
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19
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Vemanna RS, Bakade R, Bharti P, Kumar MKP, Sreeman SM, Senthil-Kumar M, Makarla U. Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:193. [PMID: 30894866 PMCID: PMC6415615 DOI: 10.3389/fpls.2019.00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Due to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.
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Affiliation(s)
- Ramu S. Vemanna
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
- Regional Center for Biotechnology, Faridabad, India
- *Correspondence: Ramu S. Vemanna, ;
| | - Rahul Bakade
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | - Pooja Bharti
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | | | | | - Udayakumar Makarla
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
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20
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Xu S, Zhao X, Liu F, Cao Y, Wang B, Wang X, Yin M, Wang Q, Feng X. Crucial role of oxidative stress in bactericidal effect of parthenolide against Xanthomonas oryzae pv. oryzae. PEST MANAGEMENT SCIENCE 2018; 74:2716-2723. [PMID: 29808556 DOI: 10.1002/ps.5091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) causes rice bacterial blight, which is one of the most devastating diseases on rice. Parthenolide (PTL) is a sesquiterpene lactone possessing multiple bioactivities. In the preliminary study, we found PTL can totally inhibit the growth of Xoo at 10 mg L-1 in vitro. In this study, we aim to further evaluate the anti-bacterial activity of PTL against Xoo and discern the role of oxidative stress in its bactericidal effect. RESULTS PTL was effective against Xoo both in vitro and in vivo. PTL induced reactive oxygen species (ROS) accumulation in Xoo, leading to cell death, while exogenous catalase can fully abolish its bactericidal effect. PTL sensitivity of catalase deletion mutants of Xoo increased significantly compared with that of wild-type Xoo strain. In addition, PTL treatment increased glutathione peroxidase activity and decreased glutathione (GSH) reductase activity in Xoo, but had no effect on its catalase and superoxide dismutase activities. Interestingly, PTL dramatically reduced the GSH level in Xoo, resulting in disturbed GSH/GSSG balance. Moreover, PTL rapidly reacted with GSH by a nucleophilic addition reaction. CONCLUSION PTL is a promising lead compound for developing bactericide against Xoo. PTL rapidly reacts with GSH, resulting in disturbed GSH/GSSG balance in Xoo, which causes ROS accumulation, leading to cell death. Oxidative stress plays a critical role in the bactericidal effect of PTL against Xoo. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Shu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xingzeng Zhao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yan Cao
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiangyun Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Min Yin
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Qizhi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xu Feng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Zheng D, Xue B, Shao Y, Yu H, Yao X, Ruan L. Activation of PhoBR under phosphate-rich conditions reduces the virulence of Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2018; 19:2066-2076. [PMID: 29575480 PMCID: PMC6638161 DOI: 10.1111/mpp.12680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 05/20/2023]
Abstract
The two-component signal transduction system PhoBR regulates the adaptation to phosphate limitation and the virulence of many animal bacterial pathogens. However, PhoBR in phytopathogens has rarely been investigated. In this study, we found that PhoBR in Xanthomonas oryzae pv. oryzae (Xoo), the pathogen of rice bacterial leaf blight, also regulates the adaptation to phosphate starvation. Unexpectedly, rice leaves infected by the phoBR-deleted mutant and wild-type PXO99A showed similar lesions, indicating that PhoBR is unnecessary for the virulence of Xoo. phoBR was found to be silenced during host infection, whereas artificially constitutive PhoBR expression attenuated virulence on host rice and growth in phosphate-rich media. RNA-sequencing (RNA-seq) was then performed to investigate the global effect caused by constitutive PhoBR activation. RNA-seq and further experiments revealed that the PhoBR regulon in Xoo comprised a wide range of genes. Nutrient transport and metabolism readjustments that resulted from PhoBR regulon activation may be responsible for growth attenuation. Our findings suggest that growth reduction regulated by PhoBR is a fitness cost of adaptation to phosphate starvation. PhoBR in Xoo is activated under phosphate-limited conditions, which could exist in epiphytic and saprophytic surviving phases, and is strictly repressed within phosphate-rich host plants to minimize fitness costs.
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Affiliation(s)
- Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
| | - Bingbing Xue
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
| | - Yanan Shao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
| | - Haoquan Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
| | - Xiaoyan Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan 430070China
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22
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Long JJ, Jahn CE, Sánchez-Hidalgo A, Wheat W, Jackson M, Gonzalez-Juarrero M, Leach JE. Interactions of free-living amoebae with rice bacterial pathogens Xanthomonas oryzae pathovars oryzae and oryzicola. PLoS One 2018; 13:e0202941. [PMID: 30142182 PMCID: PMC6108499 DOI: 10.1371/journal.pone.0202941] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/23/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Free-living amoebae (FLA) are voracious feeders, consuming bacteria and other microbes during colonization of the phytobiome. FLA are also known to secrete bacteriocidal or bacteriostatic compounds into their growth environment. METHODOLOGY AND PRINCIPAL FINDINGS Here, we explore the impacts of co-cultivation of five FLA species, including Acanthamoeba castellanii, A. lenticulata, A. polyphaga, Dictyostelium discoideum and Vermamoeba vermiformis, on survival of two devastating bacterial pathogens of rice, Xanthomonas oryzae pathovars (pv.) oryzae and oryzicola. In co-cultivation assays, the five FLA species were either bacteriostatic or bactericidal to X. oryzae pv. oryzae and X. oryzae pv. oryzicola. Despite these effects, bacteria were rarely detected inside amoebal cells. Furthermore, amoebae did not disrupt X. oryzae biofilms. The bactericidal effects persisted when bacteria were added to a cell-free supernatant from amoebal cultures, suggesting some amoebae produce an extracellular bactericidal compound. CONCLUSIONS/SIGNIFICANCE This work establishes novel, basal dynamics between important plant pathogenic bacteria and diverse amoebae, and lays the framework for future mechanistic studies.
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Affiliation(s)
- John J. Long
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
| | - Courtney E. Jahn
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
| | - Andrea Sánchez-Hidalgo
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - William Wheat
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
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23
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Doucouré H, Pérez-Quintero AL, Reshetnyak G, Tekete C, Auguy F, Thomas E, Koebnik R, Szurek B, Koita O, Verdier V, Cunnac S. Functional and Genome Sequence-Driven Characterization of tal Effector Gene Repertoires Reveals Novel Variants With Altered Specificities in Closely Related Malian Xanthomonas oryzae pv. oryzae Strains. Front Microbiol 2018; 9:1657. [PMID: 30127769 PMCID: PMC6088199 DOI: 10.3389/fmicb.2018.01657] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Rice bacterial leaf blight (BLB) is caused by Xanthomonas oryzae pv. oryzae (Xoo) which injects Transcription Activator-Like Effectors (TALEs) into the host cell to modulate the expression of target disease susceptibility genes. Xoo major-virulence TALEs universally target susceptibility genes of the SWEET sugar transporter family. TALE-unresponsive alleles of OsSWEET genes have been identified in the rice germplasm or created by genome editing and confer resistance to BLB. In recent years, BLB has become one of the major biotic constraints to rice cultivation in Mali. To inform the deployment of alternative sources of resistance in this country, rice lines carrying alleles of OsSWEET14 unresponsive to either TalF (formerly Tal5) or TalC, two important TALEs previously identified in West African Xoo, were challenged with a panel of strains recently isolated in Mali and were found to remain susceptible to these isolates. The characterization of TALE repertoires revealed that talF and talC specific molecular markers were simultaneously present in all surveyed Malian strains, suggesting that the corresponding TALEs are broadly deployed by Malian Xoo to redundantly target the OsSWEET14 gene promoter. Consistent with this, the capacity of most Malian Xoo to induce OsSWEET14 was unaffected by either talC- or talF-unresponsive alleles of this gene. Long-read sequencing and assembly of eight Malian Xoo genomes confirmed the widespread occurrence of active TalF and TalC variants and provided a detailed insight into the diversity of TALE repertoires. All sequenced strains shared nine evolutionary related tal effector genes. Notably, a new TalF variant that is unable to induce OsSWEET14 was identified. Furthermore, two distinct TalB variants were shown to have lost the ability to simultaneously induce two susceptibility genes as previously reported for the founding members of this group from strains MAI1 and BAI3. Yet, both new TalB variants retained the ability to induce one or the other of the two susceptibility genes. These results reveal molecular and functional differences in tal repertoires and will be important for the sustainable deployment of broad-spectrum and durable resistance to BLB in West Africa.
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Affiliation(s)
- Hinda Doucouré
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | | | - Ganna Reshetnyak
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Cheick Tekete
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Florence Auguy
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Emilie Thomas
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Boris Szurek
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Valérie Verdier
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Sébastien Cunnac
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
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24
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Yin X, Zou B, Hong X, Gao M, Yang W, Zhong X, He Y, Kuai P, Lou Y, Huang J, Hua J, He Z. Rice copine genes OsBON1 and OsBON3 function as suppressors of broad-spectrum disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1476-1487. [PMID: 29356349 PMCID: PMC6041448 DOI: 10.1111/pbi.12890] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 05/21/2023]
Abstract
Breeding for disease resistance is the most effective strategy to control diseases, particularly with broad-spectrum disease resistance in many crops. However, knowledge on genes and mechanism of broad-spectrum resistance and trade-off between defence and growth in crops is limited. Here, we show that the rice copine genes OsBON1 and OsBON3 are critical suppressors of immunity. Both OsBON1 and OsBON3 changed their protein subcellular localization upon pathogen challenge. Knockdown of OsBON1 and dominant negative mutant of OsBON3 each enhanced resistance to rice bacterial and fungal pathogens with either hemibiotrophic or necrotrophic lifestyles. The defence activation in OsBON1 knockdown mutants was associated with reduced growth, both of which were largely suppressed under high temperature. In contrast, overexpression of OsBON1 or OsBON3 decreased disease resistance and promoted plant growth. However, neither OsBON1 nor OsBON3 could rescue the dwarf phenotype of the Arabidopsis BON1 knockout mutant, suggesting a divergence of the rice and Arabidopsis copine genes. Our study therefore shows that the rice copine genes play a negative role in regulating disease resistance and their expression level and protein location likely have a large impact on the balance between immunity and agronomic traits.
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Affiliation(s)
- Xin Yin
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Baohong Zou
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Xuexue Hong
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Mingjun Gao
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Weibing Yang
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Xiangbin Zhong
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yang He
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Peng Kuai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Yonggen Lou
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jirong Huang
- College of Life and Environmental SciencesShanghai Normal UniversityShanghaiChina
| | - Jian Hua
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
- Plant Biology SectionSchool of Integrated Plant ScienceCornell UniversityIthacaNYUSA
| | - Zuhua He
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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25
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Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice. PLoS Pathog 2018; 14:e1007092. [PMID: 29864161 PMCID: PMC6037387 DOI: 10.1371/journal.ppat.1007092] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 07/09/2018] [Accepted: 05/12/2018] [Indexed: 11/19/2022] Open
Abstract
Most Xanthomonas species translocate Transcription Activator-Like (TAL) effectors into plant cells where they function like plant transcription factors via a programmable DNA-binding domain. Characterized strains of rice pathogenic X. oryzae pv. oryzae harbor 9–16 different tal effector genes, but the function of only a few of them has been decoded. Using sequencing of entire genomes, we first performed comparative analyses of the complete repertoires of TAL effectors, herein referred to as TALomes, in three Xoo strains forming an African genetic lineage different from Asian Xoo. A phylogenetic analysis of the three TALomes combined with in silico predictions of TAL effector targets showed that African Xoo TALomes are highly conserved, genetically distant from Asian ones, and closely related to TAL effectors from the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Nine clusters of TAL effectors could be identified among the three TALomes, including three showing higher levels of variation in their repeat variable diresidues (RVDs). Detailed analyses of these groups revealed recombination events as a possible source of variation among TAL effector genes. Next, to address contribution to virulence, nine TAL effector genes from the Malian Xoo strain MAI1 and four allelic variants from the Burkinabe Xoo strain BAI3, thus representing most of the TAL effector diversity in African Xoo strains, were expressed in the TAL effector-deficient X. oryzae strain X11-5A for gain-of-function assays. Inoculation of the susceptible rice variety Azucena lead to the discovery of three TAL effectors promoting virulence, including two TAL effectors previously reported to target the susceptibility (S) gene OsSWEET14 and a novel major virulence contributor, TalB. RNA profiling experiments in rice and in silico prediction of EBEs were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. Use of designer TAL effectors demonstrated that induction of either gene resulted in greater susceptibility to strain X11-5A. The induction of OsERF#123 by BAI3Δ1, a talB knockout derivative of BAI3, carrying these designer TAL effectors increased virulence of BAI3Δ1, validating OsERF#123 as a new, bacterial blight S gene. The ability of most Xanthomonas plant pathogenic bacteria to infect their hosts relies on the action of a specific family of proteins called TAL effectors, which are transcriptional activators injected into the plant by the bacteria. TAL effectors enter the plant cell nucleus and bind to the promoters of specific plant genes. Genes that when induced can benefit pathogen multiplication or disease development are called susceptibility (S) genes. Here, we perform a comparative analysis of the TAL effector repertoires of three strains of X. oryzae pv. oryzae, which causes bacterial leaf blight of rice, a major yield constraint in this staple crop. Using sequencing of entire genomes, we compared the large repertoires of TAL effectors in three African Xoo strains which form a genetic lineage distinct from Asian strains. We assessed the individual contribution to pathogen virulence of 13 TAL effector variants represented in the three strains, and identified one that makes a major contribution. By combining host transcriptome profiling and TAL effector binding sites prediction, we identified two targets of this TAL effector that function as S genes, one previously identified, and one, new S gene. We validated the new S gene by functional characterization using designer TAL effectors. Both S genes encode transcription factors and can therefore be considered as susceptibility hubs for pathogen manipulation of the host transcriptome. Our results provide new insights into the diversified strategies underlying the roles of TAL effectors in promoting plant disease.
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26
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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27
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Li N, Wei S, Chen J, Yang F, Kong L, Chen C, Ding X, Chu Z. OsASR2 regulates the expression of a defence-related gene, Os2H16, by targeting the GT-1 cis-element. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:771-783. [PMID: 28869785 PMCID: PMC5814579 DOI: 10.1111/pbi.12827] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/23/2017] [Indexed: 05/11/2023]
Abstract
The GT-1 cis-element widely exists in many plant gene promoters. However, the molecular mechanism that underlies the response of the GT-1 cis-element to abiotic and biotic stresses remains elusive in rice. We previously isolated a rice short-chain peptide-encoding gene, Os2H16, and demonstrated that it plays important roles in both disease resistance and drought tolerance. Here, we conducted a promoter assay of Os2H16 and identified GT-1 as an important cis-element that mediates Os2H16 expression in response to pathogen attack and osmotic stress. Using the repeated GT-1 as bait, we characterized an abscisic acid, stress and ripening 2 (ASR2) protein from yeast-one hybridization screening. Sequence alignments showed that the carboxy-terminal domain of OsASR2 containing residues 80-138 was the DNA-binding domain. Furthermore, we identified that OsASR2 was specifically bound to GT-1 and activated the expression of the target gene Os2H16, as well as GFP driven by the chimeric promoter of 2 × GT-1-35S mini construct. Additionally, the expression of OsASR2 was elevated by pathogens and osmotic stress challenges. Overexpression of OsASR2 enhanced the resistance against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani, and tolerance to drought in rice. These results suggest that the interaction between OsASR2 and GT-1 plays an important role in the crosstalk of the response of rice to biotic and abiotic stresses.
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Affiliation(s)
- Ning Li
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Shutong Wei
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Jing Chen
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Fangfang Yang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Lingguang Kong
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Cuixia Chen
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Xinhua Ding
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Zhaohui Chu
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
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28
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Busungu C, Taura S, Sakagami JI, Anai T, Ichitani K. High-resolution mapping and characterization of xa42, a resistance gene against multiple Xanthomonas oryzae pv. oryzae races in rice ( Oryza sativa L.). BREEDING SCIENCE 2018; 68:188-199. [PMID: 29875602 PMCID: PMC5982184 DOI: 10.1270/jsbbs.17094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/29/2017] [Indexed: 06/01/2023]
Abstract
Improvement of resistance against rice bacterial blight (BB) disease is an important breeding strategy in breeding programs across the world, especially in Africa and southern Asia where BB is more prevalent. This report describes a high-resolution map and characterization of xa42 at XA42 locus, a rice BB resistance gene in XM14, a mutant line originating from IR24. The candidate gene region was narrowed down from 582 kb, which had been obtained in our previous study, to 57 kb. XM14 shows brown spots in its leaves like lesion mimic mutants. This line also shows a shorter stature than the original cultivar IR24. In XA42 gene segregating populations, homozygotes of xa42 allele were consistently resistant to the six Japanese Xanthomonas oryzae pv. oryzae races used for this study. They also showed brown spots and markedly short stature compared with the other genotypes, suggesting that xa42 gene exhibits pleiotropic effects.
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Affiliation(s)
- Constantine Busungu
- United Graduate School of Agricultural Sciences, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
| | - Satoru Taura
- Institute of Gene Research, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
| | - Jun-Ichi Sakagami
- United Graduate School of Agricultural Sciences, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
- Faculty of Agriculture, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
| | - Toyoaki Anai
- United Graduate School of Agricultural Sciences, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Katsuyuki Ichitani
- United Graduate School of Agricultural Sciences, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
- Faculty of Agriculture, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
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29
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Bossa‐Castro AM, Tekete C, Raghavan C, Delorean EE, Dereeper A, Dagno K, Koita O, Mosquera G, Leung H, Verdier V, Leach JE. Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1559-1568. [PMID: 29406604 PMCID: PMC6097120 DOI: 10.1111/pbi.12895] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/22/2018] [Accepted: 01/26/2018] [Indexed: 05/19/2023]
Abstract
Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub-Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar-specific QTL. The most promising BSR QTL (qXO-2-1, qXO-4-1 and qXO-11-2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes.
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Affiliation(s)
- Ana M. Bossa‐Castro
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
| | - Cheick Tekete
- IRDCiradIPMEUniv MontpellierMontpellierFrance
- Faculté des Sciences et TechniquesLBMAUniversité des Sciences Techniques et TechnologiquesBamakoMali
| | - Chitra Raghavan
- Division of Plant Breeding, Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
- Present address:
Horticulture and Forestry SciencesQueensland Department of Agriculture and FisheriesCairnsQLDAustralia
| | - Emily E. Delorean
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | | | - Karim Dagno
- Plant ProtectionInstitute of Rural EconomySotubaMali
| | - Ousmane Koita
- Faculté des Sciences et TechniquesLBMAUniversité des Sciences Techniques et TechnologiquesBamakoMali
| | | | - Hei Leung
- Division of Plant Breeding, Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
| | | | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
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Jeger M, Candresse T, Chatzivassiliou E, Dehnen-Schmutz K, Gilioli G, Grégoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Rossi V, Urek G, Van Bruggen A, Van der Werf W, West J, Winter S, Bragard C, Szurek B, Hollo G, Caffier D. Pest categorisation of Xanthomonas oryzae pathovars oryzae and oryzicola. EFSA J 2018; 16:e05109. [PMID: 32625664 PMCID: PMC7009692 DOI: 10.2903/j.efsa.2018.5109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The EFSA Panel on Plant Health performed a pest categorisation for Xanthomonas oryzae pathovars oryzae (Xoo) and oryzicola (Xoc), the causal agents of the bacterial blight and the bacterial leaf streak of rice, respectively. These pathovars are widely distributed in Asia, Africa and Australia. Xoo is also reported in some states of the USA and in some other countries of America. The identity of both pathovars is well established and efficient identification methods are available. The major host is cultivated rice (Oryza sativa), but different Oryza spp. as well as Poaceae weeds are reported as alternative hosts, with some uncertainty concerning the actual host range. Both pathovars are seed associated, despite the fact that seed transmission is still controversial for Xoo. Both pathovars are already regulated in Directives 2000/29/EC, on harmful organisms for plants, and 66/402/EEC, on the marketing of cereal seeds. The main pathway for entry is seed. Should these pathovars enter into EU, they may establish and spread, and they may have an impact on the rice crops, with uncertainties. The knowledge gaps identified are (1) the quantity of EU importation of rice seeds, (2) the risk of introduction through unprocessed rice for consumption, (3) the suitability of the EU growing climate conditions for the bacteria to establish and spread, (4) role of seed transmission (Xoo), (5) the role of weeds in the epidemiology and especially in seed transmission and dispersal, (6) host range of weeds. As none of the pathovars is known to occur in the EU, they do not meet one of the criteria for being considered as Union regulated non-quarantine pests. Nevertheless, both pathovars meet the criteria assessed by EFSA for consideration as Union quarantine pest.
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Dilla-Ermita CJ, Tandayu E, Juanillas VM, Detras J, Lozada DN, Dwiyanti MS, Vera Cruz C, Mbanjo EGN, Ardales E, Diaz MG, Mendioro M, Thomson MJ, Kretzschmar T. Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm. RICE (NEW YORK, N.Y.) 2017; 10:8. [PMID: 28321828 PMCID: PMC5359197 DOI: 10.1186/s12284-017-0147-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/23/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding. RESULTS A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes. CONCLUSIONS The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.
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Affiliation(s)
- Christine Jade Dilla-Ermita
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Erwin Tandayu
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Venice Margarette Juanillas
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Jeffrey Detras
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Dennis Nicuh Lozada
- Crop, Soil, and Environmental Science, University of Arkansas, Fayettevile, AR, USA
| | - Maria Stefanie Dwiyanti
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Casiana Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Edwige Gaby Nkouaya Mbanjo
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Edna Ardales
- Crop Protection Cluster, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Maria Genaleen Diaz
- Institute of Biological Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Merlyn Mendioro
- Institute of Biological Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Tobias Kretzschmar
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
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A Transcription Activator-Like Effector Tal7 of Xanthomonas oryzae pv. oryzicola Activates Rice Gene Os09g29100 to Suppress Rice Immunity. Sci Rep 2017; 7:5089. [PMID: 28698641 PMCID: PMC5505973 DOI: 10.1038/s41598-017-04800-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/23/2017] [Indexed: 11/09/2022] Open
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo) cause bacterial leaf streak (BLS) and bacterial leaf blight (BLB) in rice, respectively. Unlike Xoo, endogenous avirulence-resistance (avr-R) gene interactions have not been identified in the Xoc-rice pathosystem; however, both pathogens possess transcription activator-like effectors (TALEs) that are known to modulate R or S genes in rice. The transfer of individual tal genes from Xoc RS105 (hypervirulent) into Xoc YNB0-17 (hypovirulent) led to the identification of tal7, which suppressed avrXa7-Xa7 mediated defense in rice containing an Xa7 R gene. Mobility shift and microscale thermophoresis assays showed that Tal7 bound two EBE sites in the promoters of two rice genes, Os09g29100 and Os12g42970, which encode predicted Cyclin-D4-1 and GATA zinc finger family protein, respectively. Assays using designer TALEs and a TALE-free strain of Xoo revealed that Os09g29100 was the biologically relevant target of Tal7. Tal7 activates the expression of rice gene Os09g29100 that suppresses avrXa7-Xa7 mediated defense in Rice. TALEN editing of the Tal7-binding site in the Os09g29100 gene promoter further enhanced resistance to the pathogen Xoc RS105. The suppression of effector-trigger immunity (ETI) is a phenomenon that may contribute to the scarcity of BLS resistant cultivars.
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Blanvillain‐Baufumé S, Reschke M, Solé M, Auguy F, Doucoure H, Szurek B, Meynard D, Portefaix M, Cunnac S, Guiderdoni E, Boch J, Koebnik R. Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:306-317. [PMID: 27539813 PMCID: PMC5316920 DOI: 10.1111/pbi.12613] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 05/04/2023]
Abstract
As a key virulence strategy to cause bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo) injects into the plant cell DNA-binding proteins called transcription activator-like effectors (TALEs) that bind to effector-binding elements (EBEs) in a sequence-specific manner, resulting in host gene induction. TALEs AvrXa7, PthXo3, TalC and Tal5, found in geographically distant Xoo strains, all target OsSWEET14, thus considered as a pivotal TALE target acting as major susceptibility factor during rice-Xoo interactions. Here, we report the generation of an allele library of the OsSWEET14 promoter through stable expression of TALE-nuclease (TALEN) constructs in rice. The susceptibility level of lines carrying mutations in AvrXa7, Tal5 or TalC EBEs was assessed. Plants edited in AvrXa7 or Tal5 EBEs were resistant to bacterial strains relying on the corresponding TALE. Surprisingly, although indels within TalC EBE prevented OsSWEET14 induction in response to BAI3 wild-type bacteria relying on TalC, loss of TalC responsiveness failed to confer resistance to this strain. The TalC EBE mutant line was, however, resistant to a strain expressing an artificial SWEET14-inducing TALE whose EBE was also edited in this line. This work offers the first set of alleles edited in TalC EBE and uncovers a distinct, broader range of activities for TalC compared to AvrXa7 or Tal5. We propose the existence of additional targets for TalC beyond SWEET14, suggesting that TALE-mediated plant susceptibility may result from induction of several, genetically redundant, host susceptibility genes by a single effector.
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Affiliation(s)
- Servane Blanvillain‐Baufumé
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
- Present address: LabEx CeMEBUniversité de MontpellierMontpellierFrance
| | - Maik Reschke
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Montserrat Solé
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Sustainable Agro Solutions S.A.Almacelles (Lleida)Spain
| | - Florence Auguy
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Hinda Doucoure
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Donaldo Meynard
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Murielle Portefaix
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Sébastien Cunnac
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Emmanuel Guiderdoni
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Jens Boch
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Ralf Koebnik
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
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Djedatin G, Ndjiondjop MN, Sanni A, Lorieux M, Verdier V, Ghesquiere A. Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2016; 9:18. [PMID: 27107993 PMCID: PMC4842194 DOI: 10.1186/s12284-016-0090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 03/20/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains. RESULTS The reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map. CONCLUSION We characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease.
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Affiliation(s)
| | | | | | - Mathias Lorieux
- UMR Diversité, Adaptation et Développement des plantes (DIADE), Institut de Recherche pour le Développement, 911 Avenue Agropolis BP 64501, 34394, Montpellier Cedex 5, France
| | - Valérie Verdier
- IPME Interactions Plantes Microorganismes, Environnement, IRD - Cirad - University Montpellier, 34394, Montpellier, France
| | - Alain Ghesquiere
- UMR Diversité, Adaptation et Développement des plantes (DIADE), Institut de Recherche pour le Développement, 911 Avenue Agropolis BP 64501, 34394, Montpellier Cedex 5, France
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Triplett LR, Cohen SP, Heffelfinger C, Schmidt CL, Huerta A, Tekete C, Verdier V, Bogdanove AJ, Leach JE. A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL effectors with diverse predicted targets and is effective against African strains of Xanthomonas oryzae pv. oryzicola. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:472-83. [PMID: 27197779 PMCID: PMC5030141 DOI: 10.1111/tpj.13212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 05/19/2023]
Abstract
The rice pathogens Xanthomonas oryzae pathovar (pv.) oryzae and pv. oryzicola produce numerous transcription activator-like (TAL) effectors that increase bacterial virulence by activating expression of host susceptibility genes. Rice resistance mechanisms against TAL effectors include polymorphisms that prevent effector binding to susceptibility gene promoters, or that allow effector activation of resistance genes. This study identifies, in the heirloom variety Carolina Gold Select, a third mechanism of rice resistance involving TAL effectors. This resistance manifests through strong suppression of disease development in response to diverse TAL effectors from both X. oryzae pathovars. The resistance can be triggered by an effector with only 3.5 central repeats, is independent of the composition of the repeat variable di-residues that determine TAL effector binding specificity, and is independent of the transcriptional activation domain. We determined that the resistance is conferred by a single dominant locus, designated Xo1, that maps to a 1.09 Mbp fragment on chromosome 4. The Xo1 interval also confers complete resistance to the strains in the African clade of X. oryzae pv. oryzicola, representing the first dominant resistance locus against bacterial leaf streak in rice. The strong phenotypic similarity between the TAL effector-triggered resistance conferred by Xo1 and that conferred by the tomato resistance gene Bs4 suggests that monocots and dicots share an ancient or convergently evolved mechanism to recognize analogous TAL effector epitopes.
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Affiliation(s)
- Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
| | - Stephen P. Cohen
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
| | - Clarice L. Schmidt
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Alejandra Huerta
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
| | - Cheick Tekete
- Université des Sciences Techniques et Technologiques, Faculté des Sciences et Techniques, LBMA, Bamako, Mali
| | - Valerie Verdier
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
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Busungu C, Taura S, Sakagami JI, Ichitani K. Identification and linkage analysis of a new rice bacterial blight resistance gene from XM14, a mutant line from IR24. BREEDING SCIENCE 2016; 66:636-645. [PMID: 27795689 PMCID: PMC5010315 DOI: 10.1270/jsbbs.16062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/17/2016] [Indexed: 05/21/2023]
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a chief factor limiting rice productivity worldwide. XM14, a rice mutant line resistant to Xoo, has been obtained by treating IR24, which is susceptible to six Philippine Xoo races and six Japanese Xoo races, with N-methyl-N-nitrosourea. XM14 showed resistance to six Japanese Xoo races. The F2 population from XM14 × IR24 clearly showed 1 resistant : 3 susceptible segregation, suggesting control of resistance by a recessive gene. The approximate chromosomal location of the resistance gene was determined using 10 plants with shortest lesion length in the F2 population from XM14 × Koshihikari, which is susceptible to Japanese Xoo races. DNA marker-assisted analysis revealed that the gene was located on chromosome 3. IAS16 line carries IR24 genetic background with a Japonica cultivar Asominori segment of chromosome 3, on which the resistance gene locus was thought to be located. The F2 population from IAS16 × XM14 showed a discrete distribution. Linkage analysis indicated that the gene is located around the centromeric region. The resistance gene in XM14 was a new gene, named XA42. This gene is expected to be useful for resistance breeding programs and for genetic analysis of Xoo resistance.
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Affiliation(s)
- Constantine Busungu
- United Graduate School of Agricultural Sciences, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
| | - Satoru Taura
- Institute of Gene Research, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
| | - Jun-Ichi Sakagami
- Faculty of Agriculture, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
| | - Katsuyuki Ichitani
- Faculty of Agriculture, Kagoshima University,
1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065,
Japan
- Corresponding author (e-mail: )
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Analysis of the Proteins Secreted from the Oryza meyeriana Suspension-Cultured Cells Induced by Xanthomonas oryzae pv. oryzae. PLoS One 2016; 11:e0154793. [PMID: 27196123 PMCID: PMC4873123 DOI: 10.1371/journal.pone.0154793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/19/2016] [Indexed: 01/18/2023] Open
Abstract
Oryza meyeriana, a wild species of rice from China, shows high resistance to Xanthomonas oryzae pv. oryzae (Xoo), the cause of rice bacterial blight, one of the most serious rice pathogens. To better understand the resistance mechanism, a proteomic study was conducted to identify changes in the proteins secreted in embryo cell suspension cultures in response to Xoo. After two-dimensional difference gel electrophoresis (2D-DIGE), 72 differentially expressed protein spots corresponding to 34 proteins were identified by Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry. Of the 34 proteins, 10 were up regulated and 24 down regulated. The secreted proteins identified were predicted to be involved in various biological processes, including signal transduction, defense, ROS and cell wall modification. 77% of the 34 proteins were predicted to have a signal peptide by Signal P. Quantitative Real-Time PCR showed that transcript levels of 14 secreted proteins were not well correlated with secreted protein levels. Peroxidase activity was up regulated in both O. meyriana and susceptible rice but was about three times higher in O. meyeriana. This suggests that peroxidases may play an important role in the early response to Xoo in O. meyeriana. These results not only provide a better understanding of the resistance mechanism of O. meyeriana, but have implications for studies of the interactions between other plants and their pathogens.
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Zheng D, Yao X, Duan M, Luo Y, Liu B, Qi P, Sun M, Ruan L. Two overlapping two-component systems in Xanthomonas oryzae pv. oryzae contribute to full fitness in rice by regulating virulence factors expression. Sci Rep 2016; 6:22768. [PMID: 26957113 PMCID: PMC4783713 DOI: 10.1038/srep22768] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/19/2016] [Indexed: 01/17/2023] Open
Abstract
Two-component signal transduction systems (TCSs) are widely used by bacteria to adapt to the environment. In the present study, StoS (stress tolerance-related oxygen sensor) and SreKRS (salt response kinase, regulator, and sensor) were found to positively regulate extracellular polysaccharide (EPS) production and swarming in the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo). Surprisingly, the absence of stoS or sreKRS did not attenuate virulence. To better understand the intrinsic functions of StoS and SreKRS, quantitative proteomics isobaric tags for relative and absolute quantitation (iTRAQ) was employed. Consistent with stoS and sreK mutants exhibiting a similar phenotype, the signalling circuits of StoS and SreKRS overlapped. Carbohydrate metabolism proteins and chemotaxis proteins, which could be responsible for EPS and swarming regulation, respectively, were reprogrammed in stoS and sreK mutants. Moreover, StoS and SreKRS demonstrated moderate expression of the major virulence factor, hypersensitive response and pathogenicity (Hrp) proteins through the HrpG-HrpX circuit. Most importantly, Xoo equipped with StoS and SreKRS outcompetes strains without StoS or SreKRS in co-infected rice and grows outside the host. Therefore, we propose that StoS and SreKRS adopt a novel strategy involving the moderation of Hrp protein expression and the promotion of EPS and motility to adapt to the environment.
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Affiliation(s)
- Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiaoyan Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Meng Duan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yufeng Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Biao Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Pengyuan Qi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Kim SI, Song JT, Jeong JY, Seo HS. Niclosamide inhibits leaf blight caused by Xanthomonas oryzae in rice. Sci Rep 2016; 6:21209. [PMID: 26879887 PMCID: PMC4754756 DOI: 10.1038/srep21209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/19/2016] [Indexed: 01/24/2023] Open
Abstract
Rice leaf blight, which is caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), results in huge losses in grain yield. Here, we show that Xoo-induced rice leaf blight is effectively controlled by niclosamide, an oral antihelminthic drug and molluscicide, which also functions as an anti-tumor agent. Niclosamide directly inhibited the growth of the three Xoo strains PXO99, 10208 and K3a. Niclosamide moved long distances from the site of local application to distant rice tissues. Niclosamide also increased the levels of salicylate and induced the expression of defense-related genes such as OsPR1 and OsWRKY45, which suppressed Xoo-induced leaf wilting. Niclosamide had no detrimental effects on vegetative/reproductive growth and yield. These combined results indicate that niclosamide can be used to block bacterial leaf blight in rice with no negative side effects.
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Affiliation(s)
- Sung-Il Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea
| | - Jin-Yong Jeong
- Department of Convergence Medicine and Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Hak Soo Seo
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
- Bio-MAX Institute, Seoul National University, Seoul 151-818, Korea
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Chen X, Deng Z, Yu C, Yan C, Chen J. Secretome analysis of rice suspension-cultured cells infected by Xanthomonas oryzae pv.oryza (Xoo). Proteome Sci 2016; 14:2. [PMID: 26839515 PMCID: PMC4735954 DOI: 10.1186/s12953-016-0091-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/17/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Rice bacterial blight (BB) caused by Xanthomonas oryzae pv.oryzae (Xoo) is one of the most devastating bacterial diseases in rice-growing regions worldwide. The rice-Xoo interaction is a classical model for studying the interaction between plants and pathogens. Secreted proteins play important roles in plant-bacterial interactions, but are poorly studied in the rice-Xoo system. Rice cv. Nipponbare is highly susceptible to Xoo. Here, we used two-dimensional difference gel electrophoresis (2D-DIGE) coupled with MALDI-TOF/TOF mass spectrometry (MS), to investigate secreted proteins in Nipponbare embryo cell suspension culture infected by Xoo. RESULTS A total of 32 protein spots changed significantly (p < 0.05) by more than 1.5 fold in gel intensity after Xoo inoculation, and were identified by MS. They represent protein products of 11 unique genes, seven from rice and four from Xoo. Of the rice proteins, six up-regulated proteins are involved in cell wall modification, the TCA cycle, glycolysis and redox, while a down-regulated protein, CHIT16, is involved in plant defense. Quantitative Real-Time PCR showed that transcript levels were not correlated with secreted protein levels. Of the Xoo proteins, three of them were possibly located in the extracellular space as shown by transient expression assays in rice protoplasts. Two of the Xoo proteins were previously reported to be likely involved in pathogenicity, and the third gene, Xoo3654, is likely a negative regulator of Xoo virulence as its overexpression reduced Xoo pathogenicity in our study. CONCLUSION Among the secreted proteins that responded to Xoo inoculation, we identified rice proteins involved in cell defense and Xoo proteins involved in pathogenicity. Our study also showed that Xoo3654 (X2) protein is likely a novel negative regulator of Xoo virulence. These results not only help us better understand the interaction between susceptible rice and Xoo, but also serve as a reference for studying the interaction between other plants and their pathogens.
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Affiliation(s)
- Xian Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China ; State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Zhiping Deng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Chulang Yu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MOA Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021 China
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Hou Y, Wang L, Wang L, Liu L, Li L, Sun L, Rao Q, Zhang J, Huang S. JMJ704 positively regulates rice defense response against Xanthomonas oryzae pv. oryzae infection via reducing H3K4me2/3 associated with negative disease resistance regulators. BMC PLANT BIOLOGY 2015; 15:286. [PMID: 26646110 PMCID: PMC4673860 DOI: 10.1186/s12870-015-0674-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/03/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND Jumonji C (JmjC) domain-containing proteins are a group of functionally conserved histone lysine demethylases in Eukaryotes. Growing evidences have shown that JmjCs epigenetically regulate various biological processes in plants. However, their roles in plant biotic stress, especially in rice bacterial blight resistance have been barely studied so far. RESULTS In this study, we found that the global di- and tri-methylation levels on multiple lysine sites of histone three were dramatically altered after being infected by bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). Xoo infection induced the transcription of 15 JmjCs, suggesting these JmjCs are involved in rice bacterial blight defense. Further functional characterization of JmjC mutants revealed that JMJ704 is a positive regulator of rice bacterial blight resistance as the jmj704 became more susceptible to Xoo than the wild-type. In jmj704, the H3K4me2/3 levels were significantly increased; suggesting JMJ704 may be involved in H3K4me2/3 demethylation. Moreover, JMJ704 suppressed the transcription of the rice defense negative regulator genes, such as NRR, OsWRKY62 and Os-11N3, by reducing the activation marks H3K4me2/3 on them. CONCLUSIONS JMJ704 may be a universal switch controlling multiple genes of the bacterial blight resistance pathway. JMJ704 positively regulates rice defense by epigenetically suppressing master negative defense regulators, presenting a novel mechanism distinct from its homolog JMJ705 which also positively regulates rice defense but via activating positive defense regulators.
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Affiliation(s)
- Yuxuan Hou
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Liyuan Wang
- School of Agricultural and Food Science, Zhejiang A & F University, Lin'an, 311300, China.
| | - Ling Wang
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Lianmeng Liu
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Lu Li
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Lei Sun
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Qiong Rao
- School of Agricultural and Food Science, Zhejiang A & F University, Lin'an, 311300, China.
| | - Jian Zhang
- State key lab of rice biology, China National Rice Research Insititute, Hangzhou, 311400, China.
| | - Shiwen Huang
- China National Rice Research Institute, Hangzhou, 311400, China.
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42
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Kim SM, Suh JP, Qin Y, Noh TH, Reinke RF, Jena KK. Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1933-43. [PMID: 26081948 DOI: 10.1007/s00122-015-2557-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/05/2015] [Indexed: 05/20/2023]
Abstract
A new bacterial blight resistance gene has been identified through fine-mapping, which confers high levels of resistance to all Korean Xanthomonas oryzae pv. oryzae (Xoo) races, including the new Xoo race K3a. Rice bacterial leaf blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious constraint to rice production in Asia and Africa. The japonica advanced backcross breeding lines derived from the indica line IR65482-7-216-1-2 in the background of cultivar Junam are resistant to all Korean BB races, including K3a. To identify the gene(s) involved in resistance to Korean Xoo races, the association of genotypic and phenotypic variations was examined in two F2 populations derived from the crosses between 11325 (IR83261-3-7-23-6-2-1-1-2-1-2)/Anmi and 11325/Ilpum. The segregation ratios of F2 individuals from the crosses of 11325/Anmi and 11325/Ilpum were 578 resistant:209 susceptible and 555 resistant:241 susceptible, respectively, which is consistent with the expected allelic frequency of a 3:1 ratio. Genetic analysis using graphical mapping indicated that resistance (R) was controlled by a new resistance gene linked with the flanking markers RM27320 and ID55.WA18-5 within an approximately 80-kb region between 28.14 and 28.22 Mbp on chromosome 11. The eight candidate genes functionally predicted were included in the target region. Examination of the candidate genes by RT-PCR analysis only corroborated with the significant difference in transcript levels of the WAK3 gene in the presence or absence of pathogen infection. Allelism tests performed with other known BB R-genes revealed that the allele was distinct from others having a similar chromosomal location.
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Affiliation(s)
- Suk-Man Kim
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- C/o IRRI-Korea Office, National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Wanju-gun, Jeollabuk-do, 565-851, Republic of Korea
| | - Jung-Pil Suh
- Central Area Crop Breeding Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, 441-857, Republic of Korea
| | - Yang Qin
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea
| | - Tae-Hwan Noh
- National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Wanju-gun, Jeollabuk-do, 565-851, Republic of Korea
| | - Russell F Reinke
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- C/o IRRI-Korea Office, National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Wanju-gun, Jeollabuk-do, 565-851, Republic of Korea
| | - Kshirod K Jena
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Poulin L, Grygiel P, Magne M, Gagnevin L, Rodriguez-R LM, Forero Serna N, Zhao S, El Rafii M, Dao S, Tekete C, Wonni I, Koita O, Pruvost O, Verdier V, Vernière C, Koebnik R. New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Appl Environ Microbiol 2015; 81:688-98. [PMID: 25398857 PMCID: PMC4277570 DOI: 10.1128/aem.02768-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/04/2014] [Indexed: 12/12/2022] Open
Abstract
Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.
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Affiliation(s)
- L Poulin
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - P Grygiel
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - M Magne
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - L Gagnevin
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - L M Rodriguez-R
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - N Forero Serna
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - S Zhao
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - M El Rafii
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - S Dao
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - C Tekete
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - I Wonni
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France Institut de l'Environnement et de Recherches Agricoles, Bobo Dioulasso, Burkina Faso
| | - O Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - O Pruvost
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - V Verdier
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - C Vernière
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - R Koebnik
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
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44
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Lang JM, Langlois P, Nguyen MHR, Triplett LR, Purdie L, Holton TA, Djikeng A, Vera Cruz CM, Verdier V, Leach JE. Sensitive detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by loop-mediated isothermal amplification. Appl Environ Microbiol 2014; 80:4519-30. [PMID: 24837384 PMCID: PMC4148787 DOI: 10.1128/aem.00274-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/06/2014] [Indexed: 11/20/2022] Open
Abstract
Molecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 10(4) to 10(5) CFU ml(-1), while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens.
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Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Paul Langlois
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | | | - Lindsay R. Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Laura Purdie
- Biosciences eastern and central Africa, Nairobi, Kenya
| | | | | | | | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs, IRD-CIRAD-UM2, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
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45
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Ichida H, Sun X, Imanaga S, Ito Y, Yoneyama K, Kuwata S, Ohsato S. Construction and characterization of a copy number-inducible fosmid library of Xanthomonas oryzae pathovar oryzae MAFF311018. Gene 2014; 546:68-72. [PMID: 24835513 DOI: 10.1016/j.gene.2014.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 11/30/2022]
Abstract
A fosmid library of Xanthomonas oryzae pathovar oryzae MAFF311018 (T7174), the causative agent of bacterial blight on rice, was constructed and characterized. The average fosmid library insert size was >34kb, and 967 clones were uniquely positioned on its sequenced genome. The entire Xoo MAFF311018 genome was covered by end-sequenced clones with at least 5kb of overlap. The fosmid vector contains both the single-copy Escherichia coli fertility factor origin, which enhances fosmid stability, and the multi-copy IncPα origin, allowing amplification of copy number upon induction with l-arabinose. Real-time quantitative PCR on 12 randomly picked fosmid library clones determined that fosmid copy number increased 8- to 58-fold after 5hour induction. This library provides a new resource for complementation experiments and systematic functional studies in Xoo and related species.
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Affiliation(s)
- Hiroyuki Ichida
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Xiaoying Sun
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Suguru Imanaga
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yasuhiro Ito
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Katsuyoshi Yoneyama
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Shigeru Kuwata
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Shuichi Ohsato
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.
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Ji ZY, Zakria M, Zou LF, Xiong L, Li Z, Ji GH, Chen GY. Genetic diversity of transcriptional activator-like effector genes in Chinese isolates of Xanthomonas oryzae pv. oryzicola. PHYTOPATHOLOGY 2014; 104:672-82. [PMID: 24423401 DOI: 10.1094/phyto-08-13-0232-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Xanthomonas oryzae pv. oryzicola causes bacterial leaf streak (BLS), a devastating disease of rice in Asia countries. X. oryzae pv. oryzicola utilizes repertoires of transcriptional activator-like effectors (TALEs) to manipulate host resistance or susceptibility; thus, TALEs can determine the outcome of BLS. In this report, we studied genetic diversity in putative tale genes of 65 X. oryzae pv. oryzicola strains that originated from nine provinces of southern China. Genomic DNAs from the 65 strains were digested with BamHI and hybridized with an internal fragment of avrXa3, a tale gene originating from the related pathogen, X. oryzae pv. oryzae, which causes bacterial leaf blight (BLB). Southern blot analysis indicated that the strains contained a variable number (9 to 22) of avrXa3-hybridizing fragments (e.g., putative tale genes). Based on the number and size of hybridizing bands, strains were classified into 14 genotypes (designated 1 to 14), and genotypes 3 and 10 represented 29.23 and 24.64% of the total, respectively. A high molecular weight BamHI fragment (HMWB; ≈6.0 kb) was present in 12 of the 14 genotypes, and sequence analysis of the HMWB revealed the presence of a C-terminally truncated tale, an insertion element related to IS1403, and genes encoding phosphoglycerate mutase and endonuclease V. Primers were developed from the 6.0-kb HMWB fragment and showed potential in genotyping X. oryzae pv. oryzicola strains by polymerase chain reaction. Virulence of X. oryzae pv. oryzicola strains was assessed on 23 rice cultivars containing different resistance genes for BLB. The X. oryzae pv. oryzicola strains could be grouped into 14 pathotypes (I to XIV), and the grouping of strains was almost identical to the categories determined by genotypic analysis. In general, strains containing higher numbers of putative tale genes were more virulent on rice than strains containing fewer tales. The results also indicate that there are no gene-for-gene relationships between the tested rice lines and X. oryzae pv. oryzicola strains. To our knowledge, this is the first description of genetic diversity of X. oryzae pv. oryzicola strains based on tale gene analysis.
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47
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Wonni I, Cottyn B, Detemmerman L, Dao S, Ouedraogo L, Sarra S, Tekete C, Poussier S, Corral R, Triplett L, Koita O, Koebnik R, Leach J, Szurek B, Maes M, Verdier V. Analysis of Xanthomonas oryzae pv. oryzicola population in Mali and Burkina Faso reveals a high level of genetic and pathogenic diversity. PHYTOPATHOLOGY 2014; 104:520-31. [PMID: 24199713 DOI: 10.1094/phyto-07-13-0213-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola was first reported in Africa in the 1980s. Recently, a substantial reemergence of this disease was observed in West Africa. Samples were collected at various sites in five and three different rice-growing regions of Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv. oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six housekeeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effector avrXa7 as probe resulted in the identification of 18 haplotypes. Polymerase chain reaction-based analyses of two conserved type III effector (T3E) genes (xopAJ and xopW) differentiated the strains into distinct groups, with xopAJ not detected in most African X. oryzae pv. oryzicola strains. XopAJ functionality was confirmed by leaf infiltration on 'Kitaake' rice Rxo1 lines. Sequence analysis of xopW revealed four groups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains. Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and another one that may have evolved from an Asian strain.
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48
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Tran HT, Pham TV, Ngo HPT, Hong MK, Kim JG, Lee SH, Ahn YJ, Kang LW. Crystallization and preliminary X-ray crystallographic analysis of the XoGroEL chaperonin from Xanthomonas oryzae pv. oryzae. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:604-7. [PMID: 24817719 DOI: 10.1107/s2053230x14006591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/25/2014] [Indexed: 11/11/2022]
Abstract
Along with the co-chaperonin GroES, the chaperonin GroEL plays an essential role in enhancing protein folding or refolding and in protecting proteins against misfolding and aggregation in the cellular environment. The XoGroEL gene (XOO_4288) from Xanthomonas oryzae pv. oryzae was cloned and the protein was expressed, purified and crystallized. The purified XoGroEL protein was crystallized using the hanging-drop vapour-diffusion method and a crystal diffracted to a resolution of 3.4 Å. The crystal belonged to the orthorhombic space group P212121 with 14 monomers in the asymmetric unit, with a corresponding VM of 2.7 Å(3) Da(-1) and a solvent content of 54.5%.
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Affiliation(s)
- Huyen Thi Tran
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Tan Viet Pham
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Ho Phuong Thuy Ngo
- Department of Biological Sciences, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Myoung Ki Hong
- Department of Biological Sciences, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Jeong Gu Kim
- Genomics Division, National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Yeh Jin Ahn
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 110-743, Republic of Korea
| | - Lin Woo Kang
- Department of Biological Sciences, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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A TAL effector repeat architecture for frameshift binding. Nat Commun 2014; 5:3447. [PMID: 24614980 DOI: 10.1038/ncomms4447] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/13/2014] [Indexed: 11/08/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are important Xanthomonas virulence factors that bind DNA via a unique tandem 34-amino-acid repeat domain to induce expression of plant genes. So far, TALE repeats are described to bind as a consecutive array to a consecutive DNA sequence, in which each repeat independently recognizes a single DNA base. This modular protein architecture enables the design of any desired DNA-binding specificity for biotechnology applications. Here we report that natural TALE repeats of unusual amino-acid sequence length break the strict one repeat-to-one base pair binding mode and introduce a local flexibility to TALE-DNA binding. This flexibility allows TALEs and TALE nucleases to recognize target sequence variants with single nucleotide deletions. The flexibility also allows TALEs to activate transcription at allelic promoters that otherwise confer resistance to the host plant.
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