Theoretical and Applied Genetics

, Volume 109, Issue 3, pp 515–522 | Cite as

Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice

  • K. SaitoEmail author
  • Y. Hayano-Saito
  • W. Maruyama-Funatsuki
  • Y. Sato
  • A. Kato
Original Paper


Norin-PL8 is a cold-tolerant variety of rice (Oryza sativa L.) that was developed by introgressing chromosomal segments from a cold-tolerant tropical japonica variety, Silewah, into a template japonica variety, Hokkai241. We previously identified two closely linked quantitative trait loci, Ctb1 and Ctb2, for cold tolerance at the booting stage of Norin-PL8 in the long arm of chromosome 4. We report here the physical mapping of Ctb1 and the identification of the candidate genes. A total of 2,008 segregating individuals were screened for recombination in the Ctb1 region by a PCR-based screening, and a series of near-isogenic lines (NILs) were developed from progenies of recombinants. A comparison of the degrees of cold tolerance of the NILs indicated that Ctb1 is located in the 56-kb region covered by a bacterial artificial chromosome clone, OSJNBa0058 K23, that had been sequenced by the International Rice Genome Sequence Project. We found seven open reading frames (ORFs) in the 56-kb region. Two ORFs encoded receptor-like protein kinases that are possibly involved in signal transduction pathways. Proteins that may be associated with a ubiquitin-proteasome pathway were encoded by three ORFs, two of which encoded F-box proteins and one of which encoded a protein with a BAG domain. The other two ORFs encoded a protein with an OTU domain and an unknown protein. We were also able to show that Ctb1 is likely to be associated with anther length, which is one of major factors in cold tolerance at the booting stage.


Quantitative Trait Locus Bacterial Artificial Chromosome Cold Tolerance Spikelet Fertility Japonica Variety 
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.



We thank the Rice Genome Research Program, Japan for providing RFLP probes and Eriko Fujii for her technical assistance. This work was supported by the Rice Genome Project sponsored by the Ministry of Agriculture, Forestry and Fisheries of Japan.


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • K. Saito
    • 1
    Email author
  • Y. Hayano-Saito
    • 1
  • W. Maruyama-Funatsuki
    • 1
  • Y. Sato
    • 1
  • A. Kato
    • 1
  1. 1.National Agricultural Research Center for Hokkaido RegionSapporoJapan

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