Theoretical and Applied Genetics

, Volume 122, Issue 2, pp 341–353 | Cite as

Dissecting quantitative resistance against blast disease using heterogeneous inbred family lines in rice

  • Yan Liu
  • Xiao Yuan Zhu
  • Shaohong Zhang
  • Marichu Bernardo
  • Jeremy Edwards
  • David W. Galbraith
  • Jan Leach
  • Gaisheng Zhang
  • Bin Liu
  • Hei LeungEmail author
Original Paper


SHZ-2 is an indica rice cultivar that exhibits broad-spectrum resistance to rice blast; it is widely used as a resistance donor in breeding programs. To dissect the QTL responsible for broad-spectrum blast resistance, we crossed SHZ-2 to TXZ-13, a blast susceptible indica variety, to produce 244 BC4F3 lines. These lines were evaluated for blast resistance in greenhouse and field conditions. Chromosomal introgressions from SHZ-2 into the TXZ-13 genome were identified using a single feature polymorphism microarray, SSR markers and gene-specific primers. Segregation analysis of the BC4F3 population indicated that three regions on chromosomes 2, 6, and 9, designated as qBR2.1, qBR6.1, and qBR9.1, respectively, was associated with blast resistance and contributed 16.2, 14.9, and 22.3%, respectively, to the phenotypic variance of diseased leaf area (DLA). We further narrowed the three QTL regions using pairs of sister lines extracted from heterogeneous inbred families (HIF). Pairwise comparison of these lines enabled the determination of the relative contributions of individual QTL. The qBR9.1 conferred strong resistance, whereas qBR2.1 or qBR6.1 individually did not reduce disease under field conditions. However, when qBR2.1 and qBR6.1 were combined, they reduced disease by 19.5%, suggesting that small effect QTLs contribute to reduction of epidemics. The qBR6.1 and qBR9.1 regions contain nucleotide-binding sites and leucine rich repeats (NBS-LRR) sequences, whereas the qBR2.1 did not. In the qBR6.1 region, the patterns of expression of adjacent NBS-LRR genes were consistent in backcross generations and correlated with blast resistance, supporting the hypothesis that multiple resistance genes within a QTL region can contribute to non-race-specific quantitative resistance.


Blast Resistance Quantitative Resistance BC4F3 Population Major Resistance Gene BC4F3 Line 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported in part by grants from the Generation Challenge Program (HL), USDA-NRI (DWG, JEL, HL), USAID Linkage Program grants, the MOST Key International Collaboration Project (2006DFB33320, BL, HL), NSFC-IRRI Project (30821140350, BL, HL), and the Guangdong International Collaboration Project (2007A050100037, BL).

Supplementary material

122_2010_1450_MOESM1_ESM.doc (255 kb)
Supplementary material 1 (DOC 255 kb)


  1. Ashikawa I, Hayashi N, Yamane H, Kanamori H, Wu JZ, Matsumoto T, Ono K, Yano M (2008) Two adjacent NBS-LRR class genes are required to confer Pikm-specific rice blast resistance. Genetics 180:2267–2276CrossRefPubMedGoogle Scholar
  2. Bai JF, Pennill LA, Ning JC, Lee SW, Ramalingam J, Webb CA, Zhao BY, Sun Q, Nelson JC, Leach JE, Hulbert SH (2002) Diversity in nucleotide binding site—leucine-rich repeat genes in cereals. Genome Res 12:1871–1884CrossRefPubMedGoogle Scholar
  3. Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant Microbe Interact 21:859–868CrossRefPubMedGoogle Scholar
  4. Ballini E, Vergne E, Tharreau D, Notteghem JL, Morel JB (2009) ARCHIPELAGO: towards bridging the gap between molecular and genetic information in rice blast disease resistance. In: Wang GL, Valent B (eds) Advances in genetics, genomics and control of rice blast disease. Springer, Netherlands, pp 417–425CrossRefGoogle Scholar
  5. Bryan GT, Wu KS, Farrall L, Jia YL, Hershey HP, McAdams SA, Faulk KN, Donaldson GK, Tarchini R, Valent B (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033–2045CrossRefPubMedGoogle Scholar
  6. Carrillo MGC, Goodwin PH, Leach JE, Leung H, Vera Cruz CM (2009) Phylogenomic relationships of rice oxalate oxidases to the cupin superfamily and their association with disease resistance QTL. Rice 2:67–79CrossRefGoogle Scholar
  7. Chen DH, Zeigler RS, Leung H, Nelson RJ (1995) Population structure of Pyricularia grisea at two screening sites in the Philippines. Phytopathology 85:1011–1020CrossRefGoogle Scholar
  8. Edwards JD, Janda J, Sweeney MT, Gaikwad AB, Liu B, Leung H, Galbraith DW (2008) Development and evaluation of a high-through, low-cost genotyping platform based on oligonucleotide microarrays in rice. Plant Methods 4:13CrossRefPubMedGoogle Scholar
  9. Fjellstrom R, Conaway-Bormans CA, McClung AM, Marchetti MA, Shank AR, Park WD (2004) Development of DNA markers suitable for marker assisted selection of three Pi genes conferring resistance to multiple Pyricularia grisea pathotypes. Crop Sci 44:1790–1798CrossRefGoogle Scholar
  10. International Network for Genetic Evaluation of Rice (1996) Standard evaluation system for rice, 4th edn. International Rice Research Institute, Los Banos, Laguna, Philippines, p 52Google Scholar
  11. Jeon JS, Chen D, Yi GH, Wang GL, Ronald PC (2003) Genetic and physical mapping of Pi5 (t), a locus associated with broad-spectrum resistance to rice blast. Mol Genet Genomics 269:280–289PubMedGoogle Scholar
  12. Jia YL, Wang ZH, Singha P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42:2145–2149CrossRefGoogle Scholar
  13. Johnson R (1981) Durable resistance: definition of, genetic control, and attainment in plant breeding. Phytopathology 71:567–568CrossRefGoogle Scholar
  14. Lee SK, Song MY, Seo YS, Kim HK, Ko S, Cao PJ, Suh JP, Yi G, Roh JH, Lee S, An G, Hahn TR, Wang GL, Ronald P, Jeon JS (2009) Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes. Genetics 181:1627–1638CrossRefPubMedGoogle Scholar
  15. Lin F, Liu Y, Wang L, Liu X, Pan QH (2004) A high-resolution map of the rice blast resistance gene Pi15 constructed by sequence-ready markers. Plant Breed 126:287–290CrossRefGoogle Scholar
  16. Liu B, Zhang SH, Zhu XY, Yang QY, ShZh Wu, Mei MT, Mauleon R, Leach JE, Mew T, Leung H (2004) Candidate defense genes as predictors of quantitative blast resistance in rice. Mol Plant Microbe Interact 17:146–152CrossRefGoogle Scholar
  17. Liu B, Zhu XY, Zhang SH, Wu JL, Han SS, Cho YC, Roh JH, Leach JE, Liu Y, Madamba S, Bordeos A, Baraoidan M, Oña I, Vera Cruz CM, Leung H (2009) What it takes to achieve durable resistance to rice blast? In: Wang GL, Valent B (eds) Advances in genetics, genomics and control of rice blast disease. Springer, Netherlands, pp 385–402Google Scholar
  18. Liu J, Wang X, Mitchell T, Hu Y, Liu X, Dai LY, Wang GL (2010) Recent progress and understanding of the molecular mechanisms of the rice-Magnaporth oryzae interaction. Mol Plant Pathol 11:419–427Google Scholar
  19. Manosalva PM, Davidson RM, Liu B, Zhu XY, Hulbert SH, Leung H, Leach JE (2009) A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiol 149:286–296CrossRefPubMedGoogle Scholar
  20. McCouch SR, CGSNL (2008) Gene nomenclature system for rice. Rice 1:72-84Google Scholar
  21. Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:317–332CrossRefPubMedGoogle Scholar
  22. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325CrossRefPubMedGoogle Scholar
  23. Notteghem JL, Chatel M, Dechanet RD (1981) Analyze of two characteristics of rice resistance to Pyricularia oryzae. In: Comptes-rendus du symposium sur la resistance du riz a la pyriculariose. IRAT-GERDAT, Montpellier, France, pp 301–318Google Scholar
  24. Perchepied L, Kroj T, Tronchet M, Loudet O, Roby D (2006) Natural variation in partial resistance to pseudomonas syringae is controlled by two major QTLs in Arabidopsis thaliana. PLoS One 1(123):1–10Google Scholar
  25. Raghavan C, Naredo MEB, Wang HH, Atienza G, Liu B, Qiu FL, McNally KL, Leung H (2007) Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping. Mol Breed 19:87–101CrossRefGoogle Scholar
  26. Richly E, Kurth J, Leister D (2002) Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol Biol Evol 19:76–84PubMedGoogle Scholar
  27. Shang JJ, Tao Y, Chen XW, Zou Y, Lei CL, Wang J, Li XB, Zhao XF, Zhang MJ, Lu ZK, Xu JC, Cheng ZK, Wan JM, Zhu LH (2009) Identification of a new rice blast resistance gene, Pid3, by genome-wide comparison of paired NBS-LRR genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 182:1303–1311Google Scholar
  28. Song FM, Goodman RM (2001) Molecular biology of disease resistance in rice. Physiol Mol Plant Pathol 59:1–11CrossRefGoogle Scholar
  29. Tuinstra MR, Ejeta G, Goldsbrough PB (1997) Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci. Theor Appl Genet 95:1005–1011CrossRefGoogle Scholar
  30. Vergne E, Ballini E, Droc G, Tharreau D, Nottéghem JL, Morel JB (2008) Archipelago: a dedicated resource for exploiting past, present, and future genomic data on disease resistance regulation in rice. Mol Plant Microbe Interact 21:869–878CrossRefPubMedGoogle Scholar
  31. Wang GL, Mackill DJ, Bonman M, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434PubMedGoogle Scholar
  32. Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L, Hayasaka H, Katayose Y, Sasaki T (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19:55–64CrossRefPubMedGoogle Scholar
  33. Wang ZX, Yamanouchi U, Katayose Y, Sasaki T, Yano M (2001) Expression of the Pib gene rice-blast-resistance gene family is up-regulated by environmental conditions favouring infection and chemical signals that trigger secondary plant defense. Plant Mol Biol 47:653–661CrossRefPubMedGoogle Scholar
  34. Yang JY, Chen S, Zeng LX, Li YL, Chuan-ying Li, Zhu XY (2008) Race specificity of major rice blast resistance genes to Magnaporthe grisea isolates collected from indica rice in Guangdong, China. Rice Sci 15:311–318CrossRefGoogle Scholar
  35. Yi G, Lee SK, Hong YK, Cho YC, Nam MH, Kim SC, Han SS, Wang GL, Hahn TR, Ronald PC (2004) Use of Pi5(t) markers in marker-assisted selection to screen for cultivars with resistance to Magnaporthe grisea. Theor Appl Genet 109:978–985CrossRefPubMedGoogle Scholar
  36. Zhu XY, Yang QY, Huo CB, Wu SZ (1996) Studies on the qualitative and quantitative resistance of rice cultivars to blast disease. Chin J Rice Sci 10:181–184Google Scholar
  37. Zhu XY, Yang QY, Liu B, Zhang SH, Wu SZ (2003) The characteristics of resistance to rice blast of SHZ-2 and its derivative varieties. Guangdong Agric Sci 2:37–40Google Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Yan Liu
    • 1
    • 2
  • Xiao Yuan Zhu
    • 3
  • Shaohong Zhang
    • 4
  • Marichu Bernardo
    • 2
  • Jeremy Edwards
    • 5
  • David W. Galbraith
    • 6
  • Jan Leach
    • 7
  • Gaisheng Zhang
    • 1
  • Bin Liu
    • 4
  • Hei Leung
    • 2
    Email author
  1. 1.College of AgronomyNorthwest Agriculture and Forestry UniversityYanglingChina
  2. 2.Plant Breeding, Genetics and Biotechnology DivisionInternational Rice Research InstituteMetro ManilaPhilippines
  3. 3.Plant Protection, Guangdong Academy of Agricultural SciencesGuangzhouChina
  4. 4.Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
  5. 5.University of Florida GCRECWimaumaUSA
  6. 6.School of Plant Sciences and BIO5 InstituteUniversity of ArizonaTucsonUSA
  7. 7.Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsUSA

Personalised recommendations