References
- Alexandrov, N., S. Tai, W. Wang, L. Mansueto, K. Palis, R. R. Fuentes, V. J. Ulat, D. Chebotarov, G. Zhang, Z. Li, R. Mauleon, R. S. Hamilton, and K. L. McNally. 2014. “SNP-Seek Database of SNPs Derived from 3000 Rice Genomes.” Nucleic Acids Research 43: D1023–D1027. doi: https://doi.org/10.1093/nar/gku1039.
- Andaya, C. B., and P. C. Ronald. 2003. “A Catalytically Impaired Mutant of the Rice Xa21 Receptor Kinase Confers Partial Resistance to Xanthomonas Oryzae Pv Oryzae.” Physiological and Molecular Plant Pathology 62: 203–208. doi: https://doi.org/10.1016/S0885-5765(03)00060-2.
- Benson, D. A., M. Cavanaugh, K. Clark, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E.W. Sayers. 2017. “GenBank.” Nucleic Acids Research 45: D37–D42. doi: https://doi.org/10.1093/nar/gkw1070.
- Brutus, A., F. Sicilia, A. Macone, F. Cervone, and G. De Lorenzo. 2010. “A Domain Swap Approach Reveals A Role of the Plant Wall-Associated Kinase 1 (WAK1) as A Receptor of Oligogalacturonides.” Proceedings of the National Academy of Sciences 107 (20): 9452–9457. doi: https://doi.org/10.1073/pnas.1000675107.
- Caddell, D. F., C. J. Park, N. C. Thomas, P. E. Canlas, and P. C. Ronald. 2017. “Silencing of the Rice Gene LRR1 Compromises Rice Xa21 Transcript Accumulation and XA21-mediated Immunity.” Rice 10: 23. doi: https://doi.org/10.1186/s12284-017-0162-5.
- Century, K. S., R. A. Lagman, M. Adkisson, J. Morlan, R. Tobias, K. Schwartz, A. Smith, J. Love, P. C. Ronald, and M. C. Whalen. 1999. “Developmental Control of Xa21-mediated Disease Resistance in Rice.” Plant Journal 20: 231–236. doi: https://doi.org/10.1046/j.1365-313X.1999.00589.x.
- Chen, X., S. Zuo, M. Chern, P. Canalas, R. Ruan, B. Schwessinger, and P. C. Ronald. 2014. “The XA21-associated Kinase 1 (XAK1) Regulates Immunity Mediated by the Pattern-recognition Receptors XA21 and XA3.” Molecular Plant 7: 874–892. doi: https://doi.org/10.1093/mp/ssu003.
- Collard, B. C. Y., and D. J. Mackill. 2008. “Marker-assisted Selection: An Approach for Precision Plant Breeding in the Twenty-first Century.” Philosophical Transactions of the Royal Society B: Biological Sciences 363: 557–572. doi: https://doi.org/10.1098/rstb.2007.2170.
- da Silva, F. G., Y. Shen, C. Dardick, S. Burdman, R. C. Yadav, A. L. de Leon, and P. C. Ronald. 2007. “Bacterial Genes Involved in Type I Secretion and Sulfation are Required to Elicit the Rice Xa21-mediated Innate Immune Response.” Molecular Plant-Microbe Interactions 17: 593–601. doi: https://doi.org/10.1094/mpmi.2004.17.6.593.
- Deshmukh, U. C., R. K. Verma, R. R. Saxena, P. Mohan, and S. B. Verulkar. 2017. “Marker-assisted Selection for Bacterial Leaf Blight Resistance in Segregating Populations of Karma Mahsuri.” Vegetos 30: 55–58. doi: doi.https://doi.org/10.5958/2229-4473.2017.00010.6.
- Dong, C., K. Vincent, and P. Sharp. 2009. “Simultaneous Mutation Detection of Three Homoeologous Genes in Wheat by High Resolution Melting Analysis and Mutation Surveyor®.” BMC Plant Biology 9: 143. doi: https://doi.org/10.1186/1471-2229-9-143.
- Doyle, J., and J. Doyle. 1987. “Genomic Plant DNA Preparation from Fresh Tissue-CTAB Method.” Phytochemical Bulletin 19: 11–15.
- Ganopoulos, I., A. Argiriou, and A. Tsaftaris. 2011. “Adulterations in Basmati Rice Detected Quantitatively by Combined Use of Microsatellite and Fragrance Typing with High Resolution Melting (HRM) Analysis.” Food Chemistry 19: 11–15. doi: doi: https://doi.org/10.1016/j.foodchem.2011.04.109.
- Gautam, R. K., P. K. Singh, K. Sakthivel, M. Srikumar, N. Kumar, K. Kumar, A. K. Singh, and S. D. Roy. 2015. “Analysis of Pathogenic Diversity of the Rice Bacterial Blight Pathogen (Xanthomonas Oryzae Pv. Oryzae) in the Andaman Islands and Identification of Effective Resistance Genes.” Journal of Phytopathology 163: 423–432. doi:https://doi.org/10.1111/jph.12338.
- Hajira, S. K., R. M. Sundaram, G. S. Laha, A. Yugander, S. M. Balachandran, B. C. Viraktamath, K. Sujatha, C. H. Balachiranjeevi, K. Pranathi, M. Anila, S. Bhaskar, V. Abhilash, H. K. Mahadevaswamy, M. Kousik, T. D. Kumar, G. Harika, and G. Rekha. 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. doi: https://doi.org/10.1016/j.rsci.2015.11.004.
- Hall, T. A., A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth, M. Remm, and S. G. Rozen. 2012. “Primer3-new Capabilities and Interfaces.” Nucleic Acids Research 40: 1–12. doi: https://doi.org/10.1093/nar/gks596.
- Hasan, M. M., S. I. Ismail, I. Akos, U. G. Magaji, M. Y. Rafii, S. C. Chukwu, S. I. Ramlee, K. K. Olalekan, and Y. A. Oladosu. 2019. “Bacterial Leaf Blight Resistance in Rice: A Review of Conventional Breeding to Molecular Approach.” Molecular Biology Reports 46: 1519–1532. doi: https://doi.org/10.1007/s11033-019-04584-2.
- Hayden, M. J., T. M. Nguyen, A. Waterman, and K. J. Chalmers. 2008. “Multiplex-Ready PCR: A New Method for Multiplexed SSR and SNP Genotyping.” BMC Genomics 9: 80. doi: https://doi.org/10.1186/1471-2164-9-80.
- He, Z., Z-Y. Wang, J. Li, Q. Zhu, C. Lamb, P. Ronald, and J. Chory. 2000. “Perception of Brassinosteroids by the Extracellular Domain of the Receptor Kinase BRI1.” Science 288: 2360–2363. doi: https://doi.org/10.1126/science.288.5475.2360.
- Ikeda, R., G. S. Khush, and R. E. Tabien. 1990. “A New Resistance Gene to Bacterial Blight Derived from O. Longistaminata.” Japanese Journal of Breeding 40: 280–281.
- Jayatilake, D. V., E. J. Tucker, J. Brueggemann, J. Lewis, M. Garcia, S. Dreisigacker, M. J. Hayden, K. Chalmers, and D. E. Mather. 2015. “Genetic Mapping of the Cre8 Locus for Resistance against Cereal Cyst Nematode (Heterodera Avenae Woll.) In Wheat.” Molecular Breeding 35: 66. doi: https://doi.org/10.1007/s11032-015-0235-3.
- Kearse, M., R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, and C. Duran. 2012. “Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data.” Bioinformatics 28: 1647–1649. doi: https://doi.org/10.1093/bioinformatics/bts199.
- Khoshkdaman, M., A. A. Ebadi, F. Majidi-Shilsar, and S. Dariush. 2014. “Preliminary Evaluation of Resistance Genes in Rice against Bacterial Leaf Blight in Guilan Province—Iran.” Agricultural Sciences 5: 94–98. doi: https://doi.org/10.4236/as.2014.52012.
- Khush, G. S. 1984. “Breeding Rice for Resistance to Insects.” Protection Ecology 7: 147–165. doi: https://doi.org/10.1146/annurev.py.30.090192.002451.
- Koch, M. 1989. “Methods for Assessing Resistance to Bacterial Blight.” In Bacterial Blight of Rice: Proceedings of the International Workshop on Bacterial Blight of Rice, 111–1223. International Rice Research Institute, Manila, Philippines.
- Lehmensiek, A., M. W. Sutherland, and R. B. McNamara. 2008. “The Use of High-resolution Melting (HRM) to Map Single Nucleotide Polymorphism Markers Linked to a Covered Smut Resistance Gene in Barley.” Theoretical and Applied Genetics 117: 721–728. doi: https://doi.org/10.1007/s00122-008-0813-4.
- Li, J. Y., J. Wang, and R. S. Zeigler. 2014a. “The 3,000 Rice Genomes Project: New Opportunities and Challenges for Future Rice Research.” Gigascience 3: 8. doi: https://doi.org/10.1186/2047-217X-3-8.
- Li, Z., B. Y. Fu, Y. M. Gao, W. S. Wang, J. L. Xu, F. Zhang, X. Q. Zhao, T. Q. Zheng, Y. L. Zhou, G. Zhang, S. Tai, J. Xu, W. Hu, M. Yang, Y. Niu, M. Wang, Y. Li, L. Bian, X. Han, J. Li, X. Liu, B. Wang, K. L. McNally, M. E. B. Naredo, S. M. Q. Mercado, M. C. Rellosa, R. A. Reaño, G. L. S. Capilit, F. C. de Guzman, J. Ali, N. R. S. Hamilton, R. P. Mauleon, N. N. Alexandrov, and H. Leung. 2014b. “The 3,000 Rice Genomes Project.” Gigascience 3: 1–6. doi: https://doi.org/10.1186/2047-217X-3-7.
- Monaco, M. K., J. Stein, S. Naithani, S. Wei, P. Dharmawardhana, S. Kumari, V. Amarasinghe, K. Youens-Clark, J. Thomason, J. Preece, S. Pasternak, A. Olson, Y. Jiao, Z. Lu, D. Bolser, A. Kerhornou, D. Staines, B. Walts, G. Wu, P. D’Eustachio, R. Haw, D. Croft, P. J. Kersey, L. Stein, P. Jaiswal, and D. Ware. 2014. “Gramene 2013: Comparative Plant Genomics Resources.” Nucleic Acids Research 42: 1–7. doi: https://doi.org/10.1093/nar/gkt1110.
- Muhammad, S., B. Tahira, U. F. Hafiz, H. Zulqarnain, N. Imad, M. Abid, and A. Muhammad. 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. doi: https://doi.org/10.5897/ajb2016.15612.
- Nanayakkara, N. H. L. D. L. D., V. Herath, and D. V. Jayatilake. 2018. “Haplotype Diversity Analysis of Bacterial Leaf Blight Resistance Gene Xa21 in Rice.” Tropical Agricultural Research 30: 56–68. doi: https://doi.org/10.4038/tar.v30i1.8278
- Neelam, K., R. Mahajan, V. Gupta, D. Bhatia, B. K. Gill, R. Komal, J. S. Lore, G. S. Mangat, and K. Singh. 2020. “High-resolution Genetic Mapping of a Novel Bacterial Blight Resistance Gene Xa-45(t) Identified from Oryza Glaberrima and Transferred to Oryza Sativa.” Theoretical and Applied Genetics 133: 689–705. doi: doi.https://doi.org/10.1007/s00122-019-03501-2.
- Nguyen, H. T., Q. H. Vu, T. V. Mai, T. T. Nguyen, L. D. Vu, L. V. Nguyen, H. T. T. Vu, et al. 2018. “Marker-assisted Selection of Xa21 Conferring Resistance to Bacterial Leaf Blight in Indica Rice Cultivar LT2.” Rice Science 25: 52–56. doi: https://doi.org/10.1016/j.rsci.2017.08.004.
- Park, C. J., S. W. Han, X. Chen, and P. C. Ronald. 2010. “Elucidation of XA21-mediated Innate Immunity.” Cellular Microbiology 12: 1017–1025. doi: https://doi.org/10.1111/j.1462-5822.2010.01489.x.
- Park, C. J. and P. C. Ronald. 2012. “Cleavage and Nuclear Localization of the Rice XA21 Immune Receptor.” Nature Communication 3: 1–6. doi: https://doi.org/10.1038/ncomms1932.
- Peng, H., Z. Chen, Z. Fang, J. Zhou, Z. Xia, L. Gao, L. Chen, L. Li, T. Li, W. Zhai, and W. Zhang. 2015. “Rice Xa21 Primed Genes and Pathways that are Critical for Combating Bacterial Blight Infection.” Scientific Reports 5: 1–12. doi: https://doi.org/10.1038/srep12165.
- Peng, Y., L. E. Bartley, X. Chen, C. Dardick, M. Chern, R. Ruan, P. E. Canlas, and P. C. Ronald. 2008. “Oswrky62 Is a Negative Regulator of Basal and Xa21-mediated Defense against Xanthomonas Oryzae Pv. Oryzae in Rice.” Molecular Plant 1: 446–458. doi: https://doi.org/10.1093/mp/ssn024.
- Perumalsamy, S. M., M. S. Bharani, P. Nagarajan, L. Arul, R. Saraswathi, P. Balasubramanian, and J. Ramalingam. 2010. “Functional Marker-assisted Selection for Bacterial Leaf Blight Resistance Genes in Rice (Oryza Sativa L.).” Plant Breeding 129: 400–406. doi:https://doi.org/10.1111/j.1439-0523.2009.01705.x.
- Pradhan, S. K., D. K. Nayak, S. Mohanty, L. Behera, S. R. Barik, E. Pandit, S. Lenka, and A. Anandan. 2015. “Pyramiding of Three Bacterial Blight Resistance Genes for Broad-spectrum Resistance in Deepwater Rice Variety, Jalmagna.” Rice 8: 19. doi: https://doi.org/10.1186/s12284-015-0051-8.
- Pruitt, R. N., B. Schwessinger, A. Joe, N. Thomas, F. Liu, M. Albert, M. R. Robinson, L. J. G Chan, D. D. Luu, H. Chen, O. Bahar, A. Daudi, D. De Vleesschauwer, D. Caddell, W. Zhang, X. Zhao, X. Li, J. L. Heazlewood, D. Ruan, D. Majumder, M. Chern, H. Kalbacher, S. Midha, P. B. Patil, R. V. Sonti, C. J. Petzold, C. C. Liu, J. S. Brodbelt, G. Felix, and P. C. Ronald. 2015. “The Rice Immune Receptor XA21 Recognizes a Tyrosine-Sulfated Protein from a Gram-negative Bacterium.” Science Advances 1: 1–13. doi: https://doi.org/10.1126/sciadv.1500245.
- Ronald, P. C., B. Albano, R. Tabien, L. Abenes, K. S. Wu, S. McCouch, and S. D. Tanksley. 1992. “Genetic and Physical Analysis of the Rice Bacterial Blight Disease Resistance Locus, Xa21.” Molecular and General Genetics 236: 113–120. doi: https://doi.org/10.1007/BF00279649.
- Rosenberg, M. S. 2004. “Minitab for Windows. Release 11.” The Quarterly Review of Biology 72: 240–242. doi: https://doi.org/10.1086/419856.
- Sabar, M., T. Bibi, H. U. Farooq, Z. Haider, I. Naseem, A. Mahmood, and M. Akhter. 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. doi: https://doi.org/10.5897/AJB2016.15612.
- Sanchez, A. C., D. S. Brar, N. Huang, Z. Li, and G. S. Khush. 2000. “Sequence Tagged Site Marker-assisted Selection for Three Bacterial Blight Resistance Genes in Rice.” Crop Science 40: 792–797. doi: https://doi.org/10.2135/cropsci2000.403792x.
- Sharma, P., L. C. Bora, K. C. Puzari, A. M. Baruah, R. Baruah, K. Talukdar, L. Kataky, and A. Phukan. 2017. “Review on Bacterial Blight of Rice Caused by Xanthomonas Oryzae Pv. Oryzae: Different Management Approaches and Role of Pseudomonas Fluorescens; as a Potential Biocontrol Agent.” International Journal of Current Microbiology and Applied Science 6: 982–1005. doi: https://doi.org/10.20546/ijcmas.2017.603.117.
- Singh, R. J., G. S. Khush, and T. W. Mew. 2010. “A New Gene for Resistance to Bacterial Blight in Rice.” Crop Science 23: 558. doi: https://doi.org/10.2135/cropsci1983.0011183x002300030026x.
- Singh, S., J. S. Sidhu, N. Huang, Y. Vikal, Z. Li, D. S. Brar, H. S. Dhaliwal, and G. S. Khush. 2001. “Pyramiding Three Bacterial Blight Resistance Genes into Indica Rice Cultivar PR106.” Theoretical and Applied Genetics 102: 1011–1015. doi: doi.https://doi.org/10.1007/s001220000.
- Suh, J-P., T-H. Noh, K-Y. Kim, J-J. Kim, Y-G. Kim, and K. K. Jena. 2009. “Expression Levels of Three Bacterial Blight Resistance Genes against K3a Race of Korea by Molecular and Phenotype Analysis in Japonica Rice (O. Sativa L.).” Journal of Crop Science and Biotechnology 12: 103–108. doi: https://doi.org/10.1007/s12892-009-0103-y.
- Sundaram, R. M., S. K. Biradar, G. S. Laha, G. A. Reddy, N. S. Rani, N. P. Sarma, M. R. Vishnupriya, and R. V. Sonti. 2008. “Marker-assisted Introgression of Bacterial Blight Resistance in Samba Mahsuri, an Elite Indica Rice Variety.” Euphytica 160: 411–422. doi: https://doi.org/10.1007/s10681-007-9564-6.
- Tan, Y. Y., H. W. Fu, H. J. Zhao, S. Lu, J. J. Fu, Y. F. Li, H. R. Cui, and Q. Y. Shu. 2013. “Functional Molecular Markers and High-resolution Melting Curve Analysis of Low Phytic Acid Mutations for Marker-assisted Selection in Rice.” Molecular Breeding 31: 517–528. doi: https://doi.org/10.1007/s11032-012-9809-5.
- Thomas, N. C., N. Oksenberg, F. Liu, D. Caddell, A. Nalyvayko, Y. Nguyen, B. Schwessinger, and P. C. Ronald. 2018. “The Rice XA21 Ectodomain Fused to the Arabidopsis EFR Cytoplasmic Domain Confers Resistance to Xanthomonas Oryzae Pv. Oryzae.” PeerJ 6: e4456. doi: https://doi.org/10.7717/peerj.4456.
- Tucker, E. J., and B. L. Huynh. 2014. “Genotyping by High-resolution Melting Analysis.” Methods in Molecular Biology 1145: 59–66. doi: https://doi.org/10.1007/978-1-4939-0446-4_5.
- The UniProt Consortium. 2019. “UniProt: A Worldwide Hub of Protein Knowledge.” Nucleic Acids Research 47: D506–515. doi: https://doi.org/10.1093/nar/gky1049.
- Wang, G-L. 1998. “Xa21D Encodes a Receptor-like Molecule with a Leucine-rich Repeat Domain that Determines Race-specific Recognition and Is Subject to Adaptive Evolution.” The Plant Cell 10: 765–780. doi: https://doi.org/10.1105/tpc.10.5.765.
- Weerasinghe, W. D. P., K. S. Udawela, U. Heiyantuduwa, and H. A. M. Wickramasinghe. 2017. “Molecular Marker Validation for Bacterial Leaf Blight Resistant Genes Xa21 and Xa4 in Ld 99-12-38/IRBB 60 Genetic Background.” Tropical Agricultural Research 28: 402. doi: https://doi.org/10.4038/tar.v28i4.8241.
- Williams, C. E., B. Wang, T. E. Holsten, J. Scambray, F. De Assis Goes Da Silva, and P. C. Ronald. 1996. “Markers for Selection of the Rice Xa21 Disease Resistance Gene.” Theoretical and Applied Genetics 93: 1119–1122. doi: https://doi.org/10.1007/BF00230134.
- Yap, R., Y. C. Hsu, Y. P. Wu, Y. R. Lin, and C. W. Kuo. 2016. “Multiplex PCR Genotyping for Five Bacterial Blight Resistance Genes Applied to Marker-assisted Selection in Rice (Oryza Sativa).” Plant Breeding 135: 309–317. doi: https://doi.org/10.1111/pbr.12368.