Molecular Breeding

, 37:106 | Cite as

Marker-assisted breeding of Chinese elite rice cultivar 9311 for disease resistance to rice blast and bacterial blight and tolerance to submergence

  • Yanchang Luo
  • Tingchen Ma
  • Aifang Zhang
  • Kar Hui Ong
  • Zhixiang Luo
  • Zefu Li
  • Jianbo Yang
  • Zhongchao YinEmail author


Rice (Oryza sativa L.) is the staple food crop for more than half of the world’s population. The development of hybrid rice is a practical approach to increase rice production. However, rice production was frequently affected by biotic and abiotic stresses. Rice blast and bacterial blight are two major diseases in rice growing regions. Rice plantation is also frequently affected by short-term submergence or seasonal floods in wet seasons and drought in dry seasons. The utilization of natural disease resistance (R) genes and stress tolerance genes in rice breeding is the most economic and efficient way to combat or adapt to these biotic and abiotic stresses. Rice cultivar 9311 is widely planted rice variety, either as inbred rice or the paternal line of two-line hybrid rice. Here, we report the pyramiding of rice blast R gene Pi9, bacterial blight R genes Xa21 and Xa27, and submergence tolerance gene Sub1A in 9311 genetic background through backcrossing and marker-assisted selection. The improved rice line, designated as 49311, theoretically possesses 99.2% genetic background of 9311. 49311 and its hybrid rice, GZ63S/49311, conferred disease resistance to rice blast and bacterial blight and showed tolerance to submergence for over 18 days without significant loss of viability. 49311 and its hybrids had similar agronomic traits and grain quality to 9311 and the control hybrid rice, respectively. The development of 49311 provides an improved paternal line for two-line hybrid rice production with disease resistance to rice blast and bacterial blight and tolerance to submergence.


Rice Marker-assisted selection Gene pyramiding Rice blast Rice bacterial blight Submergence tolerance 



We wish to thank G. Liu for 75-1-127, D. J. Mackill for IR64 (Sub1ASub1A), and Y. Zhou for field trial. This research is sponsored by Temasek Foundation and Temasek Life Sciences Laboratory Innovation Fund. Y. Luo conducted the experiments with the help from T. Ma, A. Zhang, K.Ong, Z. Luo, Z. Li and J. Yang. Y. Luo and Z. Yin designed the experiments and wrote the manuscript.

Supplementary material

11032_2017_695_MOESM1_ESM.pdf (424 kb)
ESM 1 (PDF 424 kb)


  1. 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. Breed Sci 66(4):636–645. doi: 10.1270/jsbbs.16062 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Cao Y, Ding X, Cai M, Zhao J, Lin Y, Li X, Xu C, Wang S (2007) The expression pattern of a rice disease resistance gene xa3/xa26 is differentially regulated by the genetic backgrounds and developmental stages that influence its function. Genetics 177(1):523–533. doi: 10.1534/genetics.107.075176 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Chen S, Lin X, Xu C, Zhang Q (2000) Improvement of bacterial blight resistance of ‘Minghui 63’, an elite restorer line of hybrid rice, by molecular marker-assisted selection. Crop Sci 40(1):239–244CrossRefGoogle Scholar
  4. Cruz ND, Khush GS (2000) Rice grain quality evaluation procedures. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford and IBH Publishing Co. Pvt. Ltd, New Delhi, pp 24–36Google Scholar
  5. Duncan DB (1955) Multiple range and multiple F tests. Biometrics 11:1–42CrossRefGoogle Scholar
  6. Fukao T, Xu K, Ronald PC, Bailey-Serres J (2006) A variable cluster of ethylene response factor–like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18(8):2021–2034CrossRefPubMedPubMedCentralGoogle Scholar
  7. Fukao T, Yeung E, Bailey-Serres J (2011) The submergence tolerance regulator SUB1A mediates crosstalk between submergence and drought tolerance in rice. Plant Cell 23(1):412–427CrossRefPubMedGoogle Scholar
  8. Gnanamanickam S, Priyadarisini VB, Narayanan N, Vasudevan P, Kavitha S (1999) An overview of bacterial blight disease of rice and strategies for its management. Curr Sci 77(11):1435–1444Google Scholar
  9. Gu K, Tian D, Yang F, Wu L, Sreekala C, Wang D, Wang GL, Yin Z (2004) High-resolution genetic mapping of Xa27 (t), a new bacterial blight resistance gene in rice, Oryza sativa L. Theor Appl Genet 108(5):800–807CrossRefPubMedGoogle Scholar
  10. Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, Yang F, Chu Z, Wang G-L, White FF (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435(7045):1122–1125CrossRefPubMedGoogle Scholar
  11. Ikeda R, Khush G, Tabien R (1990) A new resistance gene to bacterial blight derived from O. longistaminata. Jpn J Breed 40(suppl 1):280–281Google Scholar
  12. Kauffman H, Reddy A, Hsieh S, Merca S (1973) An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Disease Reporter 57(6):537–541Google Scholar
  13. Khanna A, Sharma V, Ellur RK, Shikari AB, Gopala Krishnan S, Singh UD, Prakash G, Sharma TR, Rathour R, Variar M, Prashanthi SK, Nagarajan M, Vinod KK, Bhowmick PK, Singh NK, Prabhu KV, Singh BD, Singh AK (2015) Development and evaluation of near-isogenic lines for major blast resistance gene(s) in basmati rice. Theor Appl Genet 128(7):1243–1259. doi: 10.1007/s00122-015-2502-4 CrossRefPubMedGoogle Scholar
  14. 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.) Theor Appl Genet 128(10):1933–1943CrossRefPubMedGoogle Scholar
  15. Koide Y, Ebron LA, Kato H, Tsunematsu H, Telebanco-Yanoria MJ, Kobayashi N, Yokoo M, Maruyama S, Imbe T, Fukuta Y (2011) A set of near-isogenic lines for blast resistance genes with an Indica-type rainfed lowland elite rice (Oryza sativa L.) genetic background. Field Crop Res 123(1):19–27. doi: 10.1016/j.fcr.2011.04.005 CrossRefGoogle Scholar
  16. Li JB, Xia MY, Qi HX (2015) Development and evaluation of disease resistance of pyramided lines with blast resistance genes Pi1 and Pi2 in Rice. J Anhui Agri Sci 43(5):12–14 31 Google Scholar
  17. Liu G, Lu G, Zeng L, Wang GL (2002) Two broad-spectrum blast resistance genes, Pi9( t) and Pi2( t), are physically linked on rice chromosome 6. Mol Gen Genomics 267(4):472–480. doi: 10.1007/s00438-002-0677-2 CrossRefGoogle Scholar
  18. Liu J, Wang X, Mitchell T, Hu Y, Liu X, Dai L, Wang GL (2010) Recent progress and understanding of the molecular mechanisms of the rice-Magnaporthe oryzae interaction. Mol Plant Pathol 11(3):419–427. doi: 10.1111/j.1364-3703.2009.00607.x CrossRefPubMedGoogle Scholar
  19. Luo Y, Yin Z (2013) Marker-assisted breeding of Thai fragrance rice for semi-dwarf phenotype, submergence tolerance and disease resistance to rice blast and bacterial blight. Mol Breed 32:709–721. doi: 10.1007/s11032-013-9904-2 CrossRefGoogle Scholar
  20. Luo Y, Sangha J, Wang S, Li Z, Yang J, Yin Z (2012) Marker-assisted breeding of Xa4, Xa21 and Xa27 in the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight. Mol Breed 30:1601–1610. doi: 10.1007/s11032-012-9742-7 CrossRefGoogle Scholar
  21. Luo Y, Ma T, Zhang A, Ong KH, Li Z, Yang J, Yin Z (2016) Marker-assisted breeding of the rice restorer line Wanhui 6725 for disease resistance, submergence tolerance and aromatic fragrance. Rice (N Y) 9(1):66. doi: 10.1186/s12284-016-0139-9 Google Scholar
  22. Mew T, Alvarez A, Leach J, Swings J (1993) Focus on bacterial blight of rice. Plant Dis 77(1):5–12CrossRefGoogle Scholar
  23. Moffat AS (1994) Plant genetics. Mapping the sequence of disease resistance. Science 265(5180):1804–1805CrossRefPubMedGoogle Scholar
  24. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BC, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115(6):767–776. doi: 10.1007/s00122-007-0607-0 CrossRefPubMedGoogle Scholar
  25. Ni D, Song F, Ni J, Zhang A, Wang C, Zhao K, Yang Y, Wei P, Yang J, Li L (2015) Marker-assisted selection of two-line hybrid rice for disease resistance to rice blast and bacterial blight. Field Crop Res 184:1–8CrossRefGoogle Scholar
  26. Pruitt RN, Schwessinger B, Joe A, Thomas N, Liu F, Albert M, Robinson MR, Chan LJG, Luu DD, Chen H (2015) The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a gram-negative bacterium. Sci Adv 1(6):e1500245CrossRefPubMedPubMedCentralGoogle Scholar
  27. Si H, Liu W, Fu Y, Sun ZX, Hu G (2011) Current situation and suggestions for development of two-line hybrid rice in China. Chin J Rice Sci 25(5):544–522Google Scholar
  28. Song W-Y, Wang G-L, Chen L-L, Kim H-S (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270(5243):1804CrossRefPubMedGoogle Scholar
  29. Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99(13):9043–9048. doi: 10.1073/pnas.132266399 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Wu L, Goh ML, Sreekala C, Yin Z (2008) XA27 depends on an amino-terminal signal-anchor-like sequence to localize to the apoplast for resistance to Xanthomonas oryzae pv oryzae. Plant Physiol 148(3):1497–1509CrossRefPubMedPubMedCentralGoogle Scholar
  31. Xu KN, Mackill DJ (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Mol Breed 2(3):219–224CrossRefGoogle Scholar
  32. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442(7103):705–708CrossRefPubMedGoogle Scholar
  33. Yuan L (1997) Breeding for superior high yielding of hybrid rice. Hybrid Rice 12:1–3Google Scholar
  34. Yuan L, Yang Z, Yang J (1994) Hybrid rice in China. In: Virmani S (ed) Hybrid Rice technology: new developments and future prospects. International Rice Research Institute, Manila, pp 143–147Google Scholar
  35. Zhang Q (2007) Strategies for developing green super Rice. Proc Natl Acad Sci U S A 104(42):16402–16409. doi: 10.1073/pnas.0708013104 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Zheng W, Wang Y, Wang L, Ma Z, Zhao J, Wang P, Zhang L, Liu Z, Lu X (2016) Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. Theor Appl Genet 129(5):1035–1044. doi: 10.1007/s00122-016-2681-7 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.Temasek Life Sciences Laboratory, 1 Research LinkNational University of SingaporeSingaporeRepublic of Singapore
  2. 2.Key Laboratory of Rice Genetics and Breeding, Rice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
  3. 3.Plant Protection Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
  4. 4.Department of Biological SciencesNational University of SingaporeSingaporeRepublic of Singapore

Personalised recommendations