Theoretical and Applied Genetics

, Volume 126, Issue 4, pp 985–998 | Cite as

Fine-mapping and molecular marker development for Pi56(t), a NBS-LRR gene conferring broad-spectrum resistance to Magnaporthe oryzae in rice

  • Yan Liu
  • Bin Liu
  • Xiaoyuan Zhu
  • Jianyuan Yang
  • Alicia Bordeos
  • Guoliang Wang
  • Jan E. Leach
  • Hei Leung
Original Paper


The major quantitative trait locus qBR9.1 confers broad-spectrum resistance to rice blast, and was mapped to a ~69.1 kb region on chromosome 9 that was inherited from resistant variety Sanhuangzhan No 2 (SHZ-2). Within this region, only one predicted disease resistance gene with nucleotide binding site and leucine-rich repeat (NBS-LRR) domains was found. Specific markers corresponding to this gene cosegregated with blast resistance in F2 and F3 populations derived from crosses of susceptible variety Texianzhan 13 (TXZ-13) to SHZ-2 and the resistant backcross line BC-10. We tentatively designate the gene as Pi56(t). Sequence analysis revealed that Pi56(t) encodes an NBS-LRR protein composed of 743 amino acids. Pi56(t) was highly induced by blast infection in resistant lines SHZ-2 and BC-10. The corresponding allele of Pi56(t) in the susceptible line TXZ-13 encodes a protein with an NBS domain but without LRR domain, and it was not induced by Magnaporthe oryzae infection. Three new cosegregating gene-specific markers, CRG4-1, CRG4-2 and CRG4-3, were developed. In addition, we evaluated polymorphism of the gene-based markers among popular varieties from national breeding programs in Asia and Africa. The presence of the CRG4-2 SHZ-2 allele cosegregated with a blast-resistant phenotype in two BC2F1 families of SHZ-2 crossed to recurrent parents IR64-Sub1 and Swarna-Sub1. CRG4-1 and CRG4-3 showed clear polymorphism among 19 varieties, suggesting that they can be used in marker-assisted breeding to combine Pi56(t) with other target genes in breeding lines.


Quantitative Trait Locus Rice Blast Blast Resistance Disease Reaction BC2F1 Population 
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), 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_2012_2031_MOESM1_ESM.doc (1.4 mb)
Supplementary material 1 (DOC 1400 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Yan Liu
    • 1
  • Bin Liu
    • 2
  • Xiaoyuan Zhu
    • 3
  • Jianyuan Yang
    • 1
    • 3
  • Alicia Bordeos
    • 1
  • Guoliang Wang
    • 4
  • Jan E. Leach
    • 5
  • Hei Leung
    • 1
  1. 1.International Rice Research InstitutePlant Breeding, Genetics and Biotechnology DivisionMetro ManilaPhilippines
  2. 2.Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
  3. 3.The Plant Protection Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
  4. 4.Department of Plant PathologyOhio State UniversityColumbusUSA
  5. 5.Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsUSA

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