Bacterial leaf blight (BLB) disease, which is caused by Xanthomonas oryzae pv oryzae, is one of the devastating biotic stress in rice that results in yield losses. Cultivation of the resistant rice varieties has been proven as an environment-friendly and effective approach to address this problem. As such, this study developed a high quality and tightly linked marker of Xa7 gene, a resistant gene that controls BLB disease in rice. In this study, the mapping population of MR263 X IRBB7 was generated. The F2 population was used for genotyping purpose, while the F2:3 lines were employed for phenotyping purpose. Both genotyping and phenotyping data were used in bulk segregant analysis to narrow down the Xa7 region. A total 87 SNP markers were developed to genotype the mapping population. Out of 87 SNPs, only 65 SNPs exhibited acceptable call rates, and this was followed the Mendelian ration of F2 population (1:2:1). This study had successfully narrowed down the region of Xa7 from 118.5 kb to 58.5 kb, flanked by SNP_Xa7_14 and SNP_Xa7_31 that composed of 13 SNP markers. The developed SNP markers, which were tightly linked to Xa7 gene, emerge to be greatly significant in marker-assisted breeding activity to introgress BLB resistant gene into susceptible rice varieties. The application of the developed SNP marker is bound to enhance both efficiency and accuracy in the selection. The linkage drag phenomenon may be minimised as well as the marker is highly close to the target gene.


  • Busungu C, Taura S, Sakagami JI, Ichitani K (2016) Identification and linkage analysis of a new rice bacterial blight resistance gene from XM14, a mutant line from IR24. Breeding Science 66(4):636-645. http://dx.doi.org/10.1270/jsbbs.16062.
  • Chen S, Huang Z, Zeng L, Yang J, Liu Q, Zhu X (2008) High-resolution mapping and gene prediction of Xanthomonas oryzae pv. oryzae resistance gene Xa7. Molecular Breeding 22(3):433-441. https://doi.org/10.1007/s11032-008-9187-1.
  • Cobb JN, Biswas PS, Platten JD (2019) Back to the future: revisiting MAS as a tool for modern plant breeding. Theoretical and applied genetics 132(3): 647-667. https://doi.org/10.1007/s00122-018-3266-4.
  • Dilla-Ermita CJ, Tandayu E, Juanillas VM, Detras J, Lozada DN, Dwiyanti MS, Cruz CV, Mbanjo EG, Ardales E, Diaz MG, Mendioro M (2017) Genome-wide association analysis tracks bacterial leaf blight resistance loci in rice diverse germplasm. Rice, 10(8):1-17. https://doi.org/10.1186/s12284-017-0147-4.
  • Dubcovsky J (2004) Marker-assisted selection in public breeding programs: the wheat experience. Crop Sci 44:1895–1898.
  • Feng X, Lin K, Zhang W, Nan J, Zhang X, Wang C, Wang R, Jiang G, Yuan Q, Lin S (2019) Improving the blast resistance of the elite rice variety Kongyu-131 by updating the pi21 locus. BMC plant biology, 19(249): 1-12. https://doi.org/10.1186/s12870-019-1868-x.
  • Hospital F (2001) Size of donor chromosome segments around introgressed loci and reduction of linkage drag in marker-assisted backcross programs. Genetics 158(3):1363–1379.
  • Kauffman HE, Reddya PK, Hiesh SPY, Merca SD. 1973. An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Disease Reports 57: 537-541.
  • Kim SM (2018) Identification of novel recessive gene xa44 (t) conferring resistance to bacterial blight races in rice by QTL linkage analysis using an SNP chip. Theoretical and applied genetics 131(12): 2733-2743. https://doi.org/10.1007/s00122-018-3187-2.
  • Kim SM, Suh JP, Qin Y, Noh TH, Reinke RF, Jena KK (2015) Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.). Theoretical and applied genetics 128(10):1933-1943. https://doi.org/10.1007/s00122-015-2557-2.
  • Koebner RM, Summers RW (2003) 21st century wheat breeding: plot selection or plate detection?. Trends in Biotechnology 21(2):59-63. https://doi.org/10.1016/S0167-7799(02)00036-7.
  • Leach JE, Webb KM, Bai J, Ona I, Bruce M, Manosalva P, Lee S, Stephens J, Garrett K, Mew TW, Vera Cruz CM (2007) Understanding Xanthomonas oryzae/rice interactions to guide disease control. In: The 2nd International Conference on Bacterial Blight of Rice, Nanjing, China, October 1–3, pp 2.
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16): 2078-2079. https://doi.org/10.1093/bioinformatics/btp352.
  • Lore, J. S., Vikal, Y., Hunjan, M. S., Goel, R. K., Bharaj, T. S., & Raina, G. L. (2011). Genotypic and pathotypic diversity of Xanthomonas oryzae pv. oryzae, the cause of bacterial blight of rice in Punjab State of India. Journal of Phytopathology, 159(7‐8), 479-487. https://doi.org/10.1111/j.1439-0434.2011.01789.x.
  • Ogawa T, Yamamoto T, Khush GS, Mew TW (1991) Breeding of near-isogenic lines of rice with single genes for resistance to bacterial blight pathogen (Xanthomonas campestris pv. oryzae). Japanese Journal of Breeding 41:523–529. https://doi.org/10.1270/jsbbs1951.41.523.
  • Porter BW, Chittoor JM, Yano M, Sasaki T, White FF (2003) Development and mapping linked to the rice bacterial blight resistance gene Xa7. Crop Science 43:1484–1492. https://doi.org/10.2135/cropsci2003.1484.
  • Sidhu GS, Khush GS, Mew TW (1978) Genetic analysis of bacterial blight resistance in seventy-four cultivars of rice, Oryza sativa L. Theoretical and Applied Genetics 53:105–111. https://doi.org/10.1007/BF00272687.
  • Varshney RK, Graner A, Sorrells ME (2005) Genomics assisted breeding for crop improvement. Trends in plant science 10: 621–630. https://doi.org/10.1016/j.tplants.2005.10.004.
  • Vera Cruz CM, Bai JF, Ona I, Leung H, Nelson RJ, Mew TW, Leach JE (2000) Predicting durability of a disease resistance gene based on an assessment of the fitness loss and epidemiological consequences of a virulence gene mutation. Proceedings of the National Academy of Sciences 97:13500–13505. https://doi.org/10.1073/pnas.250271997.
  • Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research 38(16): e164-e164. https://doi.org/10.1093/nar/gkq603.
  • Yang B, Zhu WG, Johnson LB, White FF (2000) The virulence factor AvrXa7 of Xanthomonas oryzae pv. oryzae is a type III secretion pathway-dependent nuclear-localized double stranded DNA-binding protein. Proceedings of the National Academy of Sciences 97:9807–9812. https://doi.org/10.1073/pnas.170286897.


This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.