Molecular Genetics and Genomics

, Volume 284, Issue 1, pp 45–54 | Cite as

Identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage

  • Maiko Koseki
  • Noriyuki Kitazawa
  • Shoji Yonebayashi
  • Yumiko Maehara
  • Zi-Xuan Wang
  • Yuzo Minobe
Original Paper


Cold tolerance at the seedling stage (CTSS) is an important trait affecting stable rice production in temperate climates and areas of high elevation. In this study, 331 single nucleotide polymorphism (SNP) markers were developed and used along with phenotypic evaluation to identify quantitative trait loci (QTLs) associated with CTSS from a mapping population of 184 F2 plants derived from a cold tolerant wild rice, W1943 (Oryza rufipogon), and a sensitive indica cultivar, Guang-lu-ai 4 (GLA4). Three QTLs were detected on chromosomes 3, 10 and 11. A major locus, qCtss11 (QTL for cold tolerance at seedling stage), was located on the long arm of chromosome 11 explaining about 40% of the phenotypic variation. Introduction of the W1943 allele of qCtss11 to the GLA4 genetic background increased CTSS. Based on the phenotypic and genotypic assessment of advanced backcross progenies, qCtss11 was dissected as a single Mendelian factor. A high-resolution genetic map was constructed using 23 markers across the qCtss11 locus. As a result, qCtss11 was fine mapped to a 60-kb candidate region defined by marker AK24 and GP0030 on chromosome 11, in which six genes were annotated. Expression and resequence analyses of the six candidates supported the hypothesis that Os11g0615600 and/or Os11g0615900 are causal gene(s) of the CTSS.


Rice Cold tolerance Seedling stage QTL mapping 



The authors thank Dr. Noel Cogan and Hiroshi Shinozuka for advice and suggestions regarding to prove the manuscript.

Supplementary material

438_2010_548_MOESM1_ESM.ppt (66 kb)
Supplementary material 1 (PPT 66 kb)
438_2010_548_MOESM2_ESM.xls (22 kb)
Supplementary material 2 (XLS 22 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Maiko Koseki
    • 1
  • Noriyuki Kitazawa
    • 1
  • Shoji Yonebayashi
    • 1
  • Yumiko Maehara
    • 1
  • Zi-Xuan Wang
    • 1
  • Yuzo Minobe
    • 1
  1. 1.Plant Genome CenterTsukubaJapan

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