Molecular Genetics and Genomics

, Volume 289, Issue 3, pp 333–343 | Cite as

QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.)

  • Suk-Man Kim
  • Jung-Pil Suh
  • Chung-Koon Lee
  • Jeong-Heui Lee
  • Yeong-Gyu Kim
  • Kshirod Kumar Jena
Original Paper


Cold stress at the seedling stage is a major threat to rice production. Cold tolerance is controlled by complex genetic factors. We used an F7 recombinant inbred line (RIL) population of 123 individuals derived from a cross of the cold-tolerant japonica cultivar Jinbu and the cold-susceptible indica cultivar BR29 for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8 °C (day/night) cold stress regime revealed continuous variation for cold tolerance. Six QTLs including two on chromosome 1 and one each on chromosomes 2, 4, 10, and 11 for seedling cold tolerance were identified with phenotypic variation (R 2) ranging from 6.1 to 16.5 %. The QTL combinations (qSCT1 and qSCT11) were detected in all stable cold-tolerant RIL groups, which explained the critical threshold of 27.1 % for the R 2 value determining cold tolerance at the seedling stage. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11, respectively, were fine mapped. The markers In1-c3, derived from the open reading frame (ORF) LOC_Os01g69910 encoding calmodulin-binding transcription activator (CAMTA), and In11-d1, derived from ORF LOC_Os11g37720 (Duf6 gene), co-segregated with seedling cold tolerance. The result may provide useful information on seedling cold tolerance mechanism and provide DNA markers for a marker-assisted breeding program to improve seedling cold tolerance in indica rice varieties.


Rice Seedling cold tolerance QTL Candidate genes DNA marker 



Antifreeze glycoprotein


Bacterial artificial chromosome


Calmodulin-binding transcription activator


C-repeat binding factor


Cystathionine β-synthase


Cold damage score


Composite interval mapping


Cold treatment


Glutathione S-transferase


Insertion–deletion polymorphisms


Logarithm of odds


Phenotypic variance




Open reading frame


Quantitative trait loci


Recombinant inbred line


Recovery period


Sum of phenotypic variation


Simple sequence repeat



This research was supported in part by a grant to the Temperate Rice Research Consortium (TRRC) and Agenda Program (Code No. PJ0068272011) of the Rural Development Administration, Republic of Korea. We thank Dr. Benildo De Los Reyes, University of Maine, Orono, Maine, USA for a critical review and suggestions to improve the manuscript. We thank Bill Hardy, senior science editor of IRRI, for editing the manuscript.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Suk-Man Kim
    • 1
    • 2
  • Jung-Pil Suh
    • 3
  • Chung-Koon Lee
    • 3
  • Jeong-Heui Lee
    • 3
  • Yeong-Gyu Kim
    • 3
  • Kshirod Kumar Jena
    • 1
  1. 1.Plant Breeding, Genetics, and Biotechnology DivisionInternational Rice Research InstituteMetro ManilaPhilippines
  2. 2.C/o IRRI-Korea OfficeNational Institute of Crop Science, Rural Development AdministrationSuwonRepublic of Korea
  3. 3.Rice Research DivisionNational Institute of Crop Science, Rural Development AdministrationSuwonRepublic of Korea

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