Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Fine mapping of qSB-11 LE, the QTL that confers partial resistance to rice sheath blight

  • 1067 Accesses

  • 31 Citations


Sheath blight (SB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. No major resistance genes to SB have been identified so far. All discovered loci are quantitative resistance to rice SB. The qSB-11LE resistance quantitative trait locus (QTL) has been previously reported on chromosome 11 of Lemont (LE). In this study, we report the precise location of qSB-11 LE. We developed a near isogenic line, NIL-qSB11TQ, by marker-assisted selection that contains susceptible allele(s) from Teqing (TQ) at the qSB-11 locus in the LE genetic background. NIL-qSB11TQ shows higher susceptibility to SB than LE in both field and greenhouse tests, suggesting that this region of LE contains a QTL contributing to SB resistance. In order to eliminate the genetic background effects and increase the accuracy of phenotypic evaluation, a total of 112 chromosome segment substitution lines (CSSLs) with the substituted segment specific to the qSB-11 LE region were produced as the fine mapping population. The genetic backgrounds and morphological characteristics of these CSSLs are similar to those of the recurrent parent LE. The donor TQ chromosomal segments in these CSSL lines contiguously overlap to bridge the qSB-11 LE region. Through artificial inoculation, all CSSLs were evaluated for resistance to SB in the field in 2005. For the recombinant lines, their phenotypes were evaluated in the field for another 3 years and during the final year were also evaluated in a controlled greenhouse environment, showing a consistent phenotype in SB resistance across years and conditions. After comparing the genotypic profile of each CSSL with its phenotype, we are able to localize qSB-11 LE to the region defined by two cleaved-amplified polymorphic sequence markers, Z22-27C and Z23-33C covering 78.871 kb, based on the rice reference genome. Eleven putative genes were annotated within this region and three of them were considered the most likely candidates. The results of this study will greatly facilitate the cloning of the genes responsible for qSB-11 LE and marker-assisted breeding to incorporate qSB-11 LE into other rice cultivars.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6


  1. Abiola O, Angel JM, Avner P, Bachumanov AA, Belknap JK, Bennett B, Blankenhorn EP, Blizard DA, Bolivar V, Brockmann GA, Buck KJ, Bureau JF, Casley WL, Chesler EJ, Cheverud JM, Churchill GA, Cook M, Crabbe JC, Crusio WE, Darvasi A, Haan G, Dermant P, Doerge RW, Elliot RW, Farber CR, Flaherty L, Flint J, Gershenfeld H, Gibson JP, Gu J, Gu W, Himmelbauer H, Hitzemann R, Hsu HC, Hunter K, Iraqi FF, Jansen RC, Johnson TE, Jones BC, Kempermann G, Lammert F, Lu L, Manly KF, Matthews DB, Medrano JF, Mehrabian M, Mittlemann G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Mountz JD, Nagase H, Nowakowski RS, O’Hara BF, Osadchuk AV, Paigen B, Palmer AA, Peirce JL, Pomp D, Rosemann M, Rosen GD, Schalkwyk LC, Seltzer Z, Settle S, Shimomura K, Shou S, Sikela JM, Siracusa LD, Spearow JL, Teuscher C, Threadgill DW, Toth LA, Toye AA, Vadasz C, Zant GV, Wakeland E, Williams RW, Zhang HG, Zou F, Complex Trait Consortium (2003) The nature and identification of quantitative trait loci: a community’s view. Nat Rev (genetics) 4:911–991

  2. Al-Chaarani GR, Roustaee A, Gentzbittel L, Mokrani LG, Dechamp-Guillaume G, Sarrafi A (2002) A QTL analysis of sunflower partial resistance to downy mildew (Plasmopara hal-stedii) and black stem (Phoma macdonaldii) by the use of recombinant inbred lines (RILs). Theor Appl Genet 104:490–496

  3. Ando T, Yamamoto T, Shimizu T, Ma XF, Shomura A, Takeuchi Y, Lin SY, Yano M (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116:881–890

  4. Channamallikarjuna V, Sonah H, Prasad M, Rao GJN, Chand S, Upreti HC, Singh NK, Sharma TR (2010) Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice. Mol Breed 25:155–166

  5. Chen XW, Ronald PC (2011) Innate immunity in rice. Trends Plant Sci 16(8):451–459

  6. Chen H, Wang S, Xing Y, Xu C, Hayes PM, Zhang Q (2003) Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley. Proc Natl Acad Sci USA 100:2544–2549

  7. Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of Yield-Associated QTL. Genetics 141:1147–1162

  8. Fu D, Chen L, Yu GH, Liu Y, Lou QJ, Mei HW, Xiong L, Li M-S, Xu XY, Luo LJ (2011) QTL mapping of sheath blight resistance in a deep-water rice cultivar. Euphytica 180(2):209–218

  9. Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298:2345–2349

  10. Groth DE, Nowick EM (1992) Selection for resistance to rice sheath blight through number of infection cushions and lesion type. Plant Dis 76:721–723

  11. Han YP, Xing YZ, Chen ZX, Gu SL, Pan XB, Chen XL, Zhang QF (2002) Mapping QTLs for horizontal resistance to sheath blight in an elite rice restorer line, Minghui63. Acta Genetica Sinica 29:565–570 (In Chinese with English abstract)

  12. Han YP, Xing YY, Gu SL, Chen ZX, Pan XB, Chen XL (2003) Effect of morphological traits on sheath blight resistance in rice. Acta Botanica Sinica 45:825–831

  13. Hu KM, Qiu DY, Shen XL, Li XH, Wang SP (2008) Isolation and manipulation of quantitative trait loci for disease resistance in rice using a candidate gene approach. Mol Plant 1(5):786–793

  14. Ishimaru K, Kiyomi O, Kashiwagi T (2004) Identification of a new gene controlling plant height in rice using the candidate-gene strategy. Planta 218:388–395

  15. Ji Q, Lu JF, Chao Q, Gu MH, Xu ML (2005) Delimiting a rice wide-compatibility gene s 5 n to a 50 Kb region. Theor Appl Genet 111:1495–1503

  16. Jia YL, Correa-Victoria F, McClung A, Zhu L, Liu GJ, Wamishe Y, Xie J, Marchetti MA, Pinson SRM, Rutger JN, Correll JC (2007) Rapid determination of rice cultivar responses to the sheath blight pathogen Rhizoctonia solani using a micro-chamber screening method. Plant Dis 91:485–489

  17. Jia YL, Liu GJ, Costanzo S, Lee SH, Dai YT (2009) Current progress on genetic interactions of rice with rice blast and sheath blight fungi. Front Agric China 3(3):231–239

  18. Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168

  19. Lecomte L, Duffe P, Buret M, Servin B, Hospital F, Causse M (2004) Marker-assisted introgression of five QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds. Theor Appl Genet 109:658–668

  20. Lee FN, Rush MC (1983) Rice sheath blight: a major rice disease. Plant Dis 67:829–832

  21. Li ZK, Pinson SRM, Marshetti MA, Stansel JW, Park WD (1995) Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistance to sheath blight (Rhizoctonia solani). Theor Appl Genet 91:374–381

  22. Li ZK, Luo LJ, Mei HW, Paterson AH, Zhao XH, Zhong DB, Wang YP, Yu XQ, Zhu L, Tabien R, Stansel JW, Ying CS (1999) A “defeated” rice resistance gene acted as a QTL against a virulent strain of Xanthomonas pryzae pv. oryzae. Mol Gen Genet 261:58–63

  23. Liu GJ, Jia YL, Correa-Victoria FJ, Prado GA, Yeater KM, McClung AM, Correll JC (2009) Mapping quantitative trait loci responsible for resistance to rice sheath blight disease using greenhouse assays. Phytopathology 99(9):1078–1084

  24. McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Konok I, Yano M, Fjellstrom R, Declerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

  25. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

  26. Ng G, Seabolt S, Zhang C, Salimian S, Watkins TA, Lu H (2011) Genetic dissection of salicylic acid-mediated defense signaling networks in Arabidopsis. Genetics. doi:10.1534/genetics.111.132332

  27. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:883–887

  28. Pan XB, Zhang YF, Zuo SM, Chen ZX (2005) Discussion on QTLs identification and application of important quantitative traits in crops, agricultural and life science edition. J Yangzhou Univ 26(2):50–55 (In Chinese with English abstract)

  29. Perchepied L, Dogimont C, Pitrat M (2005) Strain-specific and recessive QTLs involved in the control of partial resistance to Fusarium oxysporum f. sp. melonis race 1.2 in a recombinant inbred line population of melon. Theor Appl Genet 111:65–74

  30. Pinson SRM, Capdevielle FM, Oard JH (2005) Confirming QTLs and finding additional loci conditioning sheath blight resistance in rice using recombinant inbred lines. Crop Sci 45:503–510

  31. Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14(1):21–29

  32. Price AH (2006) Believe it or not, QTLs are accurate. Trends Plant Sci 11(5):213–216

  33. Rush MC, Hoff BJ, Mcllrath WO (1976) A uniform disease rating system for rice disease in the United States. Proceedings of the 16th Rice Tech Working Group. Lake Charles, Louisana, p 64

  34. Sato H, Ideta O, Audo I, Kunihiro Y, Hirabayashi H, Iwano M, Miyasaka A, Nemoto H, Imbe T (2004) Mapping QTLs for sheath blight resistance in the rice line WSS2. Breed Sci 54:265–271

  35. Silva J, ScheZer B, Sanabria Y, Guzman DC, Galam D, Farmer A, Woodward J, May G, Oard J (2012) IdentiWcation of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing. Theor Appl Genet 124(1):63–74

  36. Talukder ZI, Tharreau D, Price AH (2004) Quantitative trait loci analysis suggests that partial resistance to rice blast is mostly determined by race-specific interactions. New Phytol 162:197–209

  37. Tan CX, Ji XM, Yang Y, Pan XB, Zuo SM, Zhang YF, Zou JH, Chen ZX, Zhu LH, Pan XB (2005) Identification and marker assisted selection of two major quantitative genes controlling rice sheath blight resistance in backcross generations. Acta Genetica Sinica 32:399–405 (In Chinese with English abstract)

  38. Venu RC, Jia YL, Gowda M, Jia MH, Jantasuriyarat C, Stahlberg E, Li HM, Rhineheart A, Boddhireddy P, Singh P, Rutger N, Kudrna D, Wing R, Nelson JC, Wang GL (2007) RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Mol Genet Genomics 278:421–431

  39. Wamishe YA, Jia YL, Singh P, Cartwright RD (2007) Identification of field isolates of Rhizoctonia solani to detect quantitative resistance in rice under greenhouse conditions. Front Agric China 1:361–367

  40. Wang Z, Taraminoet G, Yang D, Liu G, Tingey SV, Miao GH, Wang GL (2001) Rcie ESTs with disease-resistance gene or defense-response gene-like sequences mapped to regions containing major resistance genes or QTLs. Mol Genet Genomics 265:302–310

  41. Wang Y, Pinson SRM, Fjellstrom RG, Tabien RE (2012) Phenotypic gain from introgression of two QTL, qSB9-2 and qSB12-1, for rice sheath blight resistance. Mol Breed 30:293–303

  42. Wu XJ, Zuo SM, Chen ZX, Zhang YF, Zhu JK, Ma N, Tang JY, Chu CC, Pan XB (2011) Fine mapping of qSTV11TQ, a major gene conferring resistance to rice stripe disease. Theor Appl Genet 122:915–923

  43. Xu Q, Yuan XP, Yu HY, Wang YP, Tang SX, Wei XH (2011) Mapping quantitative trait loci for sheath blight resistance in rice using double haploid population. Plant Breed 130:404–406

  44. Young ND (1996) QTL mapping and quantitative disease resistance in plants. Annu Rev Phytopathol 34:479–501

  45. Zhao CJ, Wang AR, Shi YJ, Wang LQ, Liu WD, Wang ZH, Lu GD (2008) Identification of defense-related genes in rice responding to challenge by Rhizoctonia solani. Theor Appl Genet 116:501–516

  46. Zou JH, Pan XB, Chen ZX, Xu JY, Lu JF, Zhai WX, Zhu LH (2000) Mapping quantitative trait loci controlling sheath blight resistance in two rice cultivars (Oryza sativa L.). Theor Appl Genet 101:569–575

  47. Zuo SM, Zhang YF, Yin YJ, Chen ZX, Pan XB (2006) Establishment and improvement of inoculation technique and rating system in researching rice sheath blight resistance in field, agriculture and life sciences edition. J Yangzhou Univ 27(4):57–61 (In Chinese with English abstract)

  48. Zuo SM, Yin YJ, Zhang L, Zhang YF, Chen ZX, Pan XB (2007) Breeding value and further mapping of a QTLqSB-11 conferring the rice sheath blight resistance. Chin J Rice Sci 21(2):136–142 (In Chinese with English abstract)

  49. Zuo SM, Zhang L, Wang H, Yin YJ, Zhang YF, Chen ZX, Ma YY, Pan XB (2008) Prospect of the QTL-qSB-9Tq utilized in molecular breeding program of japonica rice against sheath blight. J Genet Genomics 35:499–505

  50. Zuo SM, Zhang YF, Chen ZX, Chen XJ, Pan XB (2010) Current progress on genetics and breeding in resistance to rice sheath blight. Scientia Sinica Vitae 40(11):1014–1023

  51. Zuo SM, Yin YJ, Zhang L, Zhang YF, Chen ZX, Gu SL, Zhu LH, Pan XB (2011) Effect and breeding potential of qSB-11LE, a sheath blight resistance quantitative trait loci from a susceptible rice cultivar. Can J Plant Sci 91:191–198

Download references


We thank Prof. Chenwu Xu, Dr. Xijun Chen, Dr. Zhiqiu Hu, Dr. Jing Xiao, and Dr. Zaixiang Tang for their great assistance in SB inoculation and disease evaluation, and in statistical analysis. We also thank Prof. Mingliang Xu, Dr. Mawsheng Chern, and Mr. Daniel Caddell for their helpful suggestions in language correction and manuscript preparation. This work was partially supported by the grants from the National Natural Science Foundation of China (30671283, 30900883), the ‘863’ High Technology Project of China (2006AA10Z165), and the Ministry of Agriculture of China (2009ZX08001-014B), and a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Author information

Correspondence to Shimin Zuo or Xuebiao Pan.

Additional information

Communicated by T. Sasaki.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 161 kb)

Supplementary material 2 (DOC 53 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zuo, S., Yin, Y., Pan, C. et al. Fine mapping of qSB-11 LE, the QTL that confers partial resistance to rice sheath blight. Theor Appl Genet 126, 1257–1272 (2013).

Download citation


  • Quantitative Trait Locus
  • Sheath Blight
  • Head Date
  • BC4F2 Population
  • Chromosome Segment Substitution Line