Molecular Identification of Xa4 Resistance Gene to Xanthomonas oryzae pv. oryzae in Cultivated Rice in Northwest Benin
Asian Research Journal of Agriculture,
Page 11-22
DOI:
10.9734/arja/2022/v15i430162
Abstract
Aims: The aim of this study was to identify the cultivated rice varieties that were resistant to Xanthomonas oryzae pv. oryzae (Xoo) by molecular screening. Xanthomonas oryzae pv. oryzae (Xoo) was the causal agent of bacterial blight, in the department of Atacora in Benin.
Place and Duration of Study: Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, between July 2021 and November 2021.
Methodology: Thirty-two rice accessions were collected in the department of Atacora and the IRBB4 isogenic line carrying Xa4 resistance gene, as a positive control, were screened using SSR marker. Genomic DNA was extracted from plants leaves. PCR using a pair of MP12 primers linked to the Xa4 gene were performed and amplified products were analyzed by electrophoresis in a 2% agarose gel.
Results: Our results showed that a significant number of rice varieties grown in northern Benin were resistant to Xoo. 62.5% were resistant of which 70% were local varieties. Some of these resistant varieties (35%) were heterozygous (Xa4/xa4) and others were homozygous (Xa4/Xa4). 10% had specific genotypes other than those expected, which showed the probability of existence new resistance alleles that need to be characterized.
Conclusion: This is the first time that a bacterial blight resistance gene has been identified in Beninese rice cultivation. This result will be very useful to rice breeders for developing elites resistant varieties through markers assisted selection programs.
Keywords:
- Rice
- Bénin Xanthomonas oryzae pv oryzae
- bacterial blight
- Xa4 resistance gene
How to Cite
Djedatin, G., Nanoukon, C., Missihoun, A., Lomou, M., Sedah, P., & Agbangla, C. (2022). Molecular Identification of Xa4 Resistance Gene to Xanthomonas oryzae pv. oryzae in Cultivated Rice in Northwest Benin. Asian Research Journal of Agriculture, 15(4), 11-22. https://doi.org/10.9734/arja/2022/v15i430162
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DOI: 978-3-319-45021-6_20/s11032-012-9779-7
Priya LB, Ujjal KN, Sharmistha G, Gayatri G, Shalim U, Omar MA, Arafat AH, Alison ML, Yong-Ming G and Akbar H. Introgression of bacterial blight resistance genes in the rice cultivar ciherang: Response against Xanthomonas oryzae pv. oryzae in the F6 generation. Plants. 2021;10:2048.
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Tian D, Wang J, Zeng X, Gu K, Qiu C, Yang X, et al. The Rice TAL effector–dependent resistance protein XA10 Triggers cell death and calcium depletion in the endoplasmic reticulum. Plant Cell. 2014;26:497.
Hutin M, Sabot F, Ghesquière A, Koebnik R, Boris S. A knowledge-based molecular screen uncovers a broad spectrum OsSWEET14 resistance allele to bacterial blight from wild rice. Plant J. 2015;84:694–703
Wan C, Zhang X, Fan Y, Gao Y, Zhu Q, Zheng C, et al. XA23 is an executor r protein and confers broad-spectrum disease resistance in rice. Mol. Plant. 2015;8:290–302.
Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H et al. Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nat. Plants. 2017; 3:17009.
Bhupendra SP, Ruchi T, Rallapalli R, Chet R and Subhash N. Molecular marker-based screening for bacterial leaf blight resistance genes in landraces and cultivars of rice in Gujarat. Indian J. Plant Genet. Resour. 2018;31(1):51-56.
DOI: 10.5958/0976-1926.2018.00008.6
Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H, Xie W, Liu H, Cui Y, Cao Y, Sun X, Xiao J, Li X, Zhang Q and Wang S. Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nature Plants. 2017;3:17009.
DOI: 10.1038/nplants.2017.9 |
Kam H, Ndjiondjop MN, Laing MD and Ahmadi N. Molecular characterisation and diversity analysis of burkina faso rice landraces using 23microsatellite markers and establishment of a core collection. Int. J. Curr. Res. 2017;9(8):56222-56232.
Gawel NJ and Jarret RL. A modified CTAB DNA extraction procedure for Musa and Ipomoea. Plant Molecular Biology Reporter. 1991;9:262–266
Adje C, Achigan-Dako E and Agbangla C. Optimizing genomic DNA isolation in Pineapple (Ananas Comosus L.) J. Plant Breed. Genet. 2016;1:11-18.
Ma B, Wang W, Zhao B, Zhou Y, Zhu L, and Zhai W. Studies of PCR marker for the rice bacterial blight resistance gene Xa-4. Hereditas. 1999;21(3):9-12.
Santoni S, Faivre-Rampant P, Prado E and Prat D. Marqueurs moléculaires pour l'analyse des ressources génétiques et l'amélioration des plantes. Cahiers Agricultures. 2000;9:311-27.
Vishnu VN, Raveendran M, Sudhakar D, Rajeswari S, Balaji AP, Govinthraj P, Karthika G, Manonmani S, Suji K K and Robin S. Analysis of population structure and genetic diversity in rice germplasm using SSR markers: An initiative towards association mapping of agronomic traits in Oryza sativa. Rice. 2015;8:30.
Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK. Highly variable SSR markers suitable for rice genotyping using agarose gels. Molecular Breeding. 2010;25:359–364.
Kumar R, Singh AK, Kumar A and Radha. Evaluation of genetic diversity in rice using simple sequence repeats (SSR) markers. AJB. 2012;11(84):14956-14995.
Wang S, Liu W, Lu D, Lu Z, Wang X, Xue J and He X. Distribution of bacterial blight resistance genes in the main cultivars and application of Xa23 in rice breeding. Frontiers in Plant Science. 2020;11:555228.
DOI: 10.3389/fpls.2020.555228
Arif M, Jaffar M, Babar M, Sheikh MA, Kousar S, Arif A, Zafar Y. Identification of bacterial blight resistance genes Xa4 in Pakistani rice germplasm using PCR. AJB. 2008;7:541-545.
Muhammad S, Tahira B, Hafiz UF, Zulqarnain H, Imad N, Abid M, Muhammad A. Molecular screening of rice (Oryza sativa L.) germplasm for Xa4, xa5 and Xa21 bacterial leaf blight (BLB) resistant genes using linked marker approach AJB. 2016;15(41):2317-2324.
Loko YLE, Ewedje E, Orobiyi A, Djedatin G, Toffa J, Gbemavo CDSJ, Tchakpa C, Gavoedo D, Sedah P, Sabot F. On-farm management of rice diversity, varietal preference criteria, and farmers' perceptions of the African (Oryza glaberrima Steud.) versus Asian rice (Oryza sativa L.) in the Republic of Benin (West Africa): implications for breeding and conservation. Economic Botany. 2021; 75(1):1-29.
Available:www.fao.org com.
Accessed on 05/12/2021
USAID. Global Food Security Response: West Africa Rice Value Chain Analysis; 2009.
Available:https://www.fao.org/sustainable-food-value-chain
Agrimonde. World agriculture and food in 2050: scenarios and challenges for sustainable development. Briefing note, 2nd ed. INRA/CIRAD 2009 Montpellier: Cirad.
Available:www.cirad.fr/publications-ressources/edition/etudes-et-documents/agrimonde.
Adhikari TB, Vera Cruz CM, Zhang Q, Nelson RJ, Skinner DZ, Mew TW, Leach JE. Genetic Diversity of Xanthomonas oryzae pv. oryzae in Asia. Applied and environmental microbiology. 1995;61:6.
Djedatin G, Ndjiondjop MN, Mathieu T, Vera Cruz CM, Sanni A, Ghesquière A, Verdier V. Evaluation of African cultivated rice Oryza glaberrima for resistance to bacterial blight. Plant Disease. 2011;95:441-447
Onasanya A, Ekperigin MM, Nwilene FE, Séré Y, Onasanya RO. Two pathotypes of Xanthomonas oryzae pv. oryzae virulence identified in West Africa. Current Research in Bacteriology. 2009;2:22-35.
Sere Y, Onasanya A, Verdier V, Akator K, Ouedraogo LS, Segda Z, Mbare MM, Sido AY, 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. 2005;4:577-579.
Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Hasan MM, Oladosu YA, et al. Bacterial leaf blight resistance in rice: A review of conventional breeding to molecular approach. Mol. Biol. Rep. 2019;(46):1519–1532.
Afolabi O, Amoussa R, Bilé M, Oludare A, Gbogbo V, Poulin L, Koebnik R, Szurek B, Silué D. First report of bacterial leaf blight in Benin; 2015.
Available:https: //doi.org/10.1094/PDIS-07-15-0821-PDN
Pandey MK, Rani NS, Sundaram RM, Laha GS, Madhav MS, Rao KS. Improvement of two traditional basmati rice varieties for bacterial blight resistance and plant stature through morphological and marker-assisted selection. Molecular Breeding. 2013;(31):239–246.
DOI: 978-3-319-45021-6_20/s11032-012-9779-7
Priya LB, Ujjal KN, Sharmistha G, Gayatri G, Shalim U, Omar MA, Arafat AH, Alison ML, Yong-Ming G and Akbar H. Introgression of bacterial blight resistance genes in the rice cultivar ciherang: Response against Xanthomonas oryzae pv. oryzae in the F6 generation. Plants. 2021;10:2048.
Available:https://doi.org/10.3390/plants10102048
Neelam K, Mahajan R, Gupta V, Bhatia D, Gill BK, Komal, R. High-resolution genetic mapping of a novel bacterial blight resistance gene xa45(t) identified from Oryza glaberrima and transferred to Oryza sativa. Theor. Appl. Broom. 2020;133:689–705.
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. 2016;9:18.
Available:https://doi.org/10.1186/s12284-016-0090-9.
Song W, Wang G, Chen L, Kim H, Pi L, Holsten T, et al. A Receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science. 1995;270:1804.
Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang Z, Kono I, et al. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc. Natl. Acad. Sci. 1998;95:1663.
Iyer AS, McCouch SR. The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol. Plant-Microbe Interact. 2004;17:1348–1354
Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, et al. Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J. 2004;37:517–527.
Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, et al. R gene expression induced by a type-III effector triggers disease resistance in rice. Nature. 2005;435:1122–1125.
Chu Z, Fu B, Yang H, Xu C, Li Z, Sanchez A, et al. Targeting xa13, a recessive gene for bacterial blight resistance in rice. Theor. Appl. Genet. 2006;112:455–461.
Liu Q, Yuan M, Zhou YAN, Li X, Xiao J and Wang S. A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice. Plant Cell Environ. 2011;34:1958–1969.
Tian D, Wang J, Zeng X, Gu K, Qiu C, Yang X, et al. The Rice TAL effector–dependent resistance protein XA10 Triggers cell death and calcium depletion in the endoplasmic reticulum. Plant Cell. 2014;26:497.
Hutin M, Sabot F, Ghesquière A, Koebnik R, Boris S. A knowledge-based molecular screen uncovers a broad spectrum OsSWEET14 resistance allele to bacterial blight from wild rice. Plant J. 2015;84:694–703
Wan C, Zhang X, Fan Y, Gao Y, Zhu Q, Zheng C, et al. XA23 is an executor r protein and confers broad-spectrum disease resistance in rice. Mol. Plant. 2015;8:290–302.
Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H et al. Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nat. Plants. 2017; 3:17009.
Bhupendra SP, Ruchi T, Rallapalli R, Chet R and Subhash N. Molecular marker-based screening for bacterial leaf blight resistance genes in landraces and cultivars of rice in Gujarat. Indian J. Plant Genet. Resour. 2018;31(1):51-56.
DOI: 10.5958/0976-1926.2018.00008.6
Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H, Xie W, Liu H, Cui Y, Cao Y, Sun X, Xiao J, Li X, Zhang Q and Wang S. Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nature Plants. 2017;3:17009.
DOI: 10.1038/nplants.2017.9 |
Kam H, Ndjiondjop MN, Laing MD and Ahmadi N. Molecular characterisation and diversity analysis of burkina faso rice landraces using 23microsatellite markers and establishment of a core collection. Int. J. Curr. Res. 2017;9(8):56222-56232.
Gawel NJ and Jarret RL. A modified CTAB DNA extraction procedure for Musa and Ipomoea. Plant Molecular Biology Reporter. 1991;9:262–266
Adje C, Achigan-Dako E and Agbangla C. Optimizing genomic DNA isolation in Pineapple (Ananas Comosus L.) J. Plant Breed. Genet. 2016;1:11-18.
Ma B, Wang W, Zhao B, Zhou Y, Zhu L, and Zhai W. Studies of PCR marker for the rice bacterial blight resistance gene Xa-4. Hereditas. 1999;21(3):9-12.
Santoni S, Faivre-Rampant P, Prado E and Prat D. Marqueurs moléculaires pour l'analyse des ressources génétiques et l'amélioration des plantes. Cahiers Agricultures. 2000;9:311-27.
Vishnu VN, Raveendran M, Sudhakar D, Rajeswari S, Balaji AP, Govinthraj P, Karthika G, Manonmani S, Suji K K and Robin S. Analysis of population structure and genetic diversity in rice germplasm using SSR markers: An initiative towards association mapping of agronomic traits in Oryza sativa. Rice. 2015;8:30.
Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK. Highly variable SSR markers suitable for rice genotyping using agarose gels. Molecular Breeding. 2010;25:359–364.
Kumar R, Singh AK, Kumar A and Radha. Evaluation of genetic diversity in rice using simple sequence repeats (SSR) markers. AJB. 2012;11(84):14956-14995.
Wang S, Liu W, Lu D, Lu Z, Wang X, Xue J and He X. Distribution of bacterial blight resistance genes in the main cultivars and application of Xa23 in rice breeding. Frontiers in Plant Science. 2020;11:555228.
DOI: 10.3389/fpls.2020.555228
Arif M, Jaffar M, Babar M, Sheikh MA, Kousar S, Arif A, Zafar Y. Identification of bacterial blight resistance genes Xa4 in Pakistani rice germplasm using PCR. AJB. 2008;7:541-545.
Muhammad S, Tahira B, Hafiz UF, Zulqarnain H, Imad N, Abid M, Muhammad A. Molecular screening of rice (Oryza sativa L.) germplasm for Xa4, xa5 and Xa21 bacterial leaf blight (BLB) resistant genes using linked marker approach AJB. 2016;15(41):2317-2324.
Loko YLE, Ewedje E, Orobiyi A, Djedatin G, Toffa J, Gbemavo CDSJ, Tchakpa C, Gavoedo D, Sedah P, Sabot F. On-farm management of rice diversity, varietal preference criteria, and farmers' perceptions of the African (Oryza glaberrima Steud.) versus Asian rice (Oryza sativa L.) in the Republic of Benin (West Africa): implications for breeding and conservation. Economic Botany. 2021; 75(1):1-29.
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