Molecular Screening of Rice Cultivated in Benin for the Identification of <i>Xanthomonas oryzae</i> Pv. <i>oryzae</i> and Bacterial Leaf Blight Resistance Genes — Oak Academic Publishing
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Molecular Screening of Rice Cultivated in Benin for the Identification of <i>Xanthomonas oryzae</i> Pv. <i>oryzae</i> and Bacterial Leaf Blight Resistance Genes
Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnolo-gies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Plant, Horticultural and Forestry Sciences, National University of Agriculture, Kétou, Benin
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Laboratory of Molécular Genetics and Genome Analysis, Department of Genetics and Biotechnology, Faculty of Science and Technology (FAST), University of Abomey-Calavi, Cotonou, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
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Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi, Benin
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Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
1 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnolo-gies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
2 Laboratory of Plant, Horticultural and Forestry Sciences, National University of Agriculture, Kétou, Benin
3 Laboratory of Molécular Genetics and Genome Analysis, Department of Genetics and Biotechnology, Faculty of Science and Technology (FAST), University of Abomey-Calavi, Cotonou, Benin
4 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
5 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
6 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
7 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
8 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
9 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
10 Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi, Benin
11 Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National School of Applied Biosciences and Biotechnologies, National University of Science, Technology, Engineering and Mathematics, Dassa-Zoumè, Benin
One of the most devastating diseases of rice worldwide is bacterial blight (BLB) caused by Xanthomonas oryzae pv. Oryzae (Xoo). In Benin, Xoo was first described in 2013 on wild rice Oryzae longistaminata . So far, no study has been done on Beninese Xoo strains. We do not know whether the pathogen has already passed into the rice varieties grown, or if they are exposed to other bacteria. Whereas the use of resistant varieties, carrying resistance genes, is the only highly effective and environmentally friendly way to control this disease, no information is available on these Xoo resistance genes in rice varieties grown in Benin apart from the one we recently. This study aims to identify Beninese Xoo strains, causing BLB and screen rice varieties grown in Benin for the main resistance genes. Diseased rice leaves showing typical symptoms of fire blight collected from different rice fields in the three phytogeographic areas of Benin were analyzed by PCR for Xoo-specific sequence identification. Furthermore, seventy-five collected rice accessions were screened to identify xa5, Xa7, xa13, and Xa21 resistance genes to Xoo. The results reveal that Xantho monas oryzae was identified in two fields in Banikouara and one in Malanville. On the other hand, Sphingomonas sp. has been identified in several other rice fields in Benin. Forty-seven of seventy-five rice accessions examined (62.66%) carried Xoo resistance genes with 3 (4%) and 40 (53.33%) of xa5 and Xa21 respectively. None of the accessions had either Xa7 or xa13 resistance genes. Three accessions possess both xa5 and Xa21 genes. Isogenic lines IRBB60 a nd IRBB21, supposed to be a positive control, presented a Xoo sensitivity allele. These results indicate that Xoo has moved from the wild rice variety to the cultivated v ariety in northern Benin and varietal improvement programs must be implemented with varieties having several resistance genes for the efficient response against a possible BLB pandemic in Benin.
Mew, T.W., Alvarez, A.M., Leach, J.E. and Swings, J. (1993) Focus on Bacterial Blight of Rice. Plant Disease, 77, 5-12. https://doi.org/10.1094/PD-77-0005
Sere, Y., Onasanya, A., Verdier, V., Akator, K., Ouedraogo, L.S., Segda, Z., Mbare, M.M., Sido, A.Y. and Baso, A. (2005) Rice Bacterial Leaf Blight in West Africa: Preliminary Studies on Disease in Farmer’s Field and Screening. Asian Journal of Plant Sciences, 4, 577-579. https://doi.org/10.3923/ajps.2005.577.579
Gonzalez, C., Szurek, B., Manceau, C., Mathieu, T., Séré, Y. and Verdier, V. (2007) Molecular and Pathotypic Characterization of New Xanthomonas oryzae Strains from West Africa. Molecular Plant-Microbe Interactions, 20, 534-546. https://doi.org/10.1094/MPMI-20-5-0534
Willocquet, L., Elazegui, F.A., Castilla, N., Fernandez, L., Fischer, K.S., Peng, S.B., Teng, P.S., Srivastava, R.K., Singh, H.M., Zhu, D.F. and Savary, S. (2004) Research Priorities for Rice Pest Management in Tropical Asia: A Simulation Analysis of Yield Losses and Management Efficiencies. Phytopathology, 94, 672-682. https://doi.org/10.1094/PHYTO.2004.94.7.672
FAO (2020). https://www.fao.org.com
Pandey, M.K., Shobha, R.N., Sundaram, R., Laha, G., Madhav, M., Srinivasa, R.K., Sudharshan, I., Hari, Y., Varaprasad, G. and Subba, R.L. (2013) Improvement of Two Traditional Basmati Rice Varieties for Bacterial Blight Resistance and Plant Stature through Morphological and Marker-Assisted Selection. Molecular Breeding, 31, 239-246. https://doi.org/10.1007/s11032-012-9779-7
Afolabi, O., Amoussa, R., Bilé, M., Oludare, A., Gbogbo, V., Poulin, L., Koebnik, R., Szurek, B. and Silué, D. (2016) First Report of Bacterial Leaf Blight of Rice Caused by Xanthomonas oryzae pv. oryzae in Benin. Plant Disease, 10, 515. https://doi.org/10.1094/PDIS-07-15-0821-PDN
Islam, Md.R., Alam, Md.S., Khan, A.I., Hossain, I., Adam, L.R. and Daayf, F. (2016) Analyses of Genetic Diversity of Bacterial Blight Pathogen, Xanthomonas oryzae pv. oryzae Using IS1112 in Bangladesh. Comptes Rendus Biologies, 339, 399-407. https://doi.org/10.1016/j.crvi.2016.06.002
Mundt, C.C. (2014) Durable Resistance: A Key to Sustainable Management of Pathogens and Pests. Infection, Genetics and Evolution, 27, 446-455. https://doi.org/10.1016/j.meegid.2014.01.011
Verdier, V. (2020) Characterization of New Races of Xanthomonas oryzae pv. oryzae in Mali Informs Resistance Gene Deployment. Phytopathology, 110, 267-277. https://doi.org/10.1094/PHYTO-02-19-0070-R
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Molecular Characterization
Resistance Genes
Gu, K., Yang, B., Tian, D., Wu, L., Wang, D., Sreekala, C., Yang, F., Chu, Z., Wang, G.L., White, F.F. and Yin, Z.R. (2005) Gene Expression Induced by a Type-III Effector Triggers Disease Resistance in Rice. Nature, 435, 1122-1125. https://doi.org/10.1038/nature03630
Chu, Z., Fu, B., Yang, H., Xu, C., Li, Z. and Sanchez, A. (2006) Targeting xa13, a Recessive Gene for Bacterial Blight Resistance in Rice. Theoretical and Applied Genetics, 12, 455-461. https://doi.org/10.1007/s00122-005-0145-6
Mohiuddin, M.S., Rao, Y.P., Mohan, S.K. and Verma, J.P. (1976) Role of Leptocorisa acuta Thun in the Spread of Bacterial Blight of Rice. Current Science, 45, 426-427.
Furuya, N., Taura, S., Goto, T., Thuy, B.T., Ton, P.H., Tsuchiya, K. and Yoshimura, A. (2012) Diversity in Virulence of Xanthomonas oryzae pv. oryzae from Northern Vietnam. Japan Agricultural Research Quarterly, 46, 329-338. https://doi.org/10.6090/jarq.46.329
Petpisit, V., Khush, G.S. and Kauffman, H.E. (1977) Inheritance of Resistance to Bacterial-Blight in Rice. Crop Science, 17, 551-554. https://doi.org/10.2135/cropsci1977.0011183X001700040018x
Blair, M.W., Garris, A.J., Iyer, A.S., Chapman, B., Kresovich, S. and McCouch, S.R. (2003) High-Resolution Genetic Mapping and Candidate Gene Identification at the xa5 Locus for 44 Bacterial Blight Resistance in Rice (Oryza sativa L.). Theoretical and Applied Genetics, 107, 62-73. https://doi.org/10.1007/s00122-003-1231-2
Jiang, G.H., Xia, Z.H., Zhou, Y.L., Wan, J., Li, D.Y., Chen, R.S., Zhai, W.X. and Zhu, L.H. (2006) Testifying the Rice Bacterial Blight Resistance Gene xa5 by Genetic Complementation and Further Analyzing xa5 (Xa5) in Comparison with Its Homolog TFIIAγ1. Molecular Genetics and Genomics, 275, 354-366. https://doi.org/10.1007/s00438-005-0091-7
Chen, X., Liu, P., Mei, L., He, X., Chen, L., Liu, H., Shen, S., Ji, Z., Zheng, X. and Zhang, Y. (2021) Xa7, a New Executor R Gene That Confers Durable and Broad-Spectrum Resistance to Bacterial Blight Disease in Rice. Plant Communications, 2, Article ID: 100143. https://doi.org/10.1016/j.xplc.2021.100143
Dossa, G.S., Quibod, I., Atienza-Grande, G., Oliva, R., Maiss, E., Vera Cruz, C. and Wydra, K. (2020) Rice Pyramided Line IRBB67 (Xa4/Xa7) Homeostasis under Combined Stress of High Temperature and Bacterial Blight. Scientific Reports, 10, Article No. 683. https://doi.org/10.1038/s41598-020-57499-5
Khan, M.A., Naeem, M. and Iqbal, M. (2014) Breeding Approaches for Bacterial Leaf Blight Resistance in Rice (Oryza sativa L.), Current Status and Future Directions. European Journal of Plant Pathology, 139, 27-37. https://doi.org/10.1007/s10658-014-0377-x
Vikal, Y. and Bhatia, D. (2017) Genetics and Genomics of Bacterial Blight Resistance in Rice. Advances in International Rice Research, 10, 175-213. https://doi.org/10.5772/67361
Moumouni, B. (2007) Le flétrissement bactérien du riz au Niger: Diversité pathologique d’isolats collectés sur les périmètres irrigués. Journal of Applied Biosciences, 38, 2551-2563.
Priya, L.B., Ujjal, K.N., Sharmistha, G., Gayatri, G., Shalim, U., Omar, M.A., Arafat, A.H., Alison, M.L., Yong-Ming, G. and Akbar, H. (2021) Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xan-thomonas oryzae pv. oryzae in the F6 Generation. Plants, 10, Article No. 2048. https://doi.org/10.3390/plants10102048
Djèdatin, G., Nanoukon, C., Missihoun, A., Lomou, M., Sedah, P. and Agbangla, C. (2022) Molecular Identification of Xa4 Resistance Gene to Xanthomonas oryzae pv. oryzae in Cultivated Rice in Northwest Benin. Journal of Agricultural and Horticultural Research, 15, 11-22. https://doi.org/10.9734/arja/2022/v15i430162
Lang, J.M., Hamilton, J.P., Diaz, M.G.Q., Van Sluys, M.A.M., Burgos, R.G., Vera Cruz, C.M., Buell, Tisserat, C.R. and Leach, N.A. (2010) Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. Plant Disease, 94, 311-319. https://doi.org/10.1094/PDIS-94-3-0311
Kini, K., Agnimonhan, R., Dossa, R., Soglonou, B., Gbogbo, V., Ouedraogo, I., Kpemoua, K., Traoré, M. and Silue, D. (2017) First Report of Sphingomonas sp. Causing Bacterial Leaf Blight of Rice in Benin, Burkina Faso, the Gambia, Ivory Coast, Mali, Nigeria, Tanzania and Togo. New Disease Reports. 35, 32. https://doi.org/10.5197/j.2044-0588.2017.035.032
Fanou, A.A., Missihoun, A.A., Sovegnon, P., Behoundja-Kotoko, O., Baimey, H. and Agbangla, C. (2019) Molecular Genetic Identification of Viruses Affecting Pepper Crop (Capsicum spp.) in Western North of Benin. International Journal of Current Research, 6, 9-14. https://doi.org/10.20546/ijcrbp.2019.603.002
Chen, X., Temnykh, S., Xu, Y., Cho, Y. and McCouch, S. (2017) Development of a Microsatellite Framework Map Providing Genome-Wide Coverage in Rice (Oryza sativa L.). Theoretical and Applied Genetics, 95, 553-567. https://doi.org/10.1007/s001220050596
Porter, B., Chittoor, J., Yano, M., Sasaki, T. and White, F. (2023) Development and Mapping of Markers Linked to the Rice Bacterial Blight Resistance Gene Xa7. Crop Science, 43, 1484-1492. https://doi.org/10.2135/cropsci2003.1484
Hajira, S.K., Sundaram, R.M., Laha, G.S., Yugander, A., Balachandran, S.M., Viraktamath, B.C., Sujatha, K., Balachi-ranjeevi, C.H., Pranathi, K. and Anila, M. (2016) A Single-Tube, Functional Marker-Based Multiplex PCR Assay for Simultaneous Detection of Major Bacterial Blight Resistance Genes Xa21, xa13 and xa5 in Rice. Rice Science, 23, 144-151. https://doi.org/10.1016/j.rsci.2015.11.004
Luo, Y.-C., Wang, S.-H., Li, C.-Q., et al. (2004) Improvement of Resistance to Bacterial Blight by Marker-Assisted Selection in a Wide Compatibility Restorer Line of Hybrid Rice. Rice Science, 11, 231.
Midha, S., Bansal, K., Sharma, S., Kumar, N., Patil, N.P., Chaudhry, V. and Patil, P.B. (2016) Genomic Resource of Rice Seed Associated Bacteria. Frontiers in Microbiology, 6, Article No. 1551. https://doi.org/10.3389/fmicb.2015.01551
Ullah, I., Jamil, S., Iqbal, M., Shaheen, H., Hasni, S., Jabeen, S., Mehmood, A. and Akhter, M. (2012) Detection of Bacterial Blight Resistance Genes in Basmati Rice Landraces. Genetics and Molecular Research, 11, 1960-1966. https://doi.org/10.4238/2012.July.20.1
Sabar, M., Bibi, T., Farooq, H.U., Haider, Z., Naseem, I., Mahmood, A. and Akhter, M. (2016) Molecular Screening of Rice (Oryza sativa L.) Germplasm for Xa4, xa5 and Xa21 Bacterial Leaf Blight (BLB) Resistant Genes Using Linked Marker Approach. African Journal of Biotechnology, 15, 2317-2324. https://doi.org/10.5897/AJB2016.15612
Kamhun, W., Phengam, S., Uppananchai, T., Ratanasut, K. and Rungrat, T. (2022) Effects of Nitrogen Levels on Sucrose Content, Disease Severity of Xanthomonas oryzae pv. oryzae and Yield of Hybrid Rice (BC4F5). Journal of Agriculture and Natural Resources, 56, 909-916. https://doi.org/10.34044/j.anres.2022.56.5.05
Dossa, G.S., Oliva, R., Maiss, E., Vera Cruz, C. and Wydra, K. (2016) High Temperature Enhances the Resistance of Cultivated African Rice, Oryza glaberrima, to Bacterial Blight. Plant Disease, 100, 380-387. https://doi.org/10.1094/PDIS-05-15-0536-RE
Suh, J.P., Jeung, J.U., Noh, T.H., Cho, Y.C., Park, S.H., Park, H.S., Shin, M.S., Kim, C.K. and Jena, K.K. (2013) Development of Breeding Lines with Three Pyramided Resistance Genes That Confer Broad-Spectrum Bacterial Blight Resistance and Their Molecular Analysis in Rice. Rice, 6, Article No. 5. https://doi.org/10.1186/1939-8433-6-5
Chirinos, J., Olivares, B. and Guevara, E. (2013) Biological Effectiveness of Plant Extracts in in Vitro Control of the Phytopathogenic Xanthomonas Bacterium. Multiciencias, 13, 115-121. https://www.redalyc.org/pdf/904/90428841002.pdf
Paredes-Trejo, F., Campos, B., Movil Fuentes, Y., Arevalo-Groening, J. and Gil, A. (2023) Assessing the Spatiotemporal Patterns and Impacts of Droughts in the Orinoco River Basin Using Earth Observations Data and Surface Observations. Hydrology, 10, Article No. 195. https://doi.org/10.3390/hydrology10100195
Rodríguez-Yzquierdo, G., Olivares, O., Silva-Escobar, O., González-Ulloa, A., Soto-Suarez, M. and Betancourt-Vásquez, M. (2023) Mapping of the Susceptibility of Colombian Musaceae Lands to a Deadly Disease: Fusarium oxysporum f. sp. cubense Tropical Race 4. Horticulturae, 9, Article No. 757. https://doi.org/10.3390/horticulturae9070757
Vega, A., Orlando, O., Rueda Calderón, M.A., Montenegro-Gracia, E., Araya-Almán, M. and Marys, E. (2022) Prediction of Banana Production Using Epidemiological Parameters of Black Sigatoka: An Application with Random Forest. Sustainability, 14, Article No. 14123. https://doi.org/10.3390/su142114123
Olivares, B.O., Vega, A., Calderón, M.A.R., Rey, J.C., Lobo, D., Gómez, J.A. and Landa, B.B. (2022) Identification of Soil Properties Associated with the Incidence of Banana Wilt Using Supervised Methods. Plants, 11, Article No. 2070. https://doi.org/10.3390/plants11152070
Ronald, P.C., Albano, B., Tabien, R., Abenes, L., Wu, K., McCouch, S. and Tanksley, S.D. (1992) Genetic and Physical Analysis of the Rice Bacterial Blight Disease Resistance Locus, Xa21. Molecular Genetics and Genomics, 236, 113-120. https://doi.org/10.1007/BF00279649
Ramalingam, J., Raveendra, C., Savitha, P., Vidya, V., Chaithra, T.L., Velprabakaran, S., Saraswathi, R., Ramanathan, A., Arumugam Pillai, M.P. and Arumugachamy, S. (2020) Gene Pyramiding for Achieving Enhanced Resistance to Bacterial Blight, Blast, and Sheath Blight Diseases in Rice. Frontiers in Plant Science, 11, Article ID: 591457. https://doi.org/10.3389/fpls.2020.591457
Krishnakumar, R. and Kumaravadivel, N. (2018) Marker-Assisted Selection for Biotic Stress (Bacterial Leaf Blight and Gall Midge) Tolerance in Bc4F4 Generation of Rice (Oryza sativa L.). Electronic Journal of Plant Breeding, 9, 275-282. https://doi.org/10.5958/0975-928X.2018.00032.7