Theoretical and Applied Genetics

, Volume 113, Issue 3, pp 467–475 | Cite as

Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice

Original Paper


The temperate japonica rice cultivar M202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M202 and IR50, an indica cultivar that is highly sensitive to cold stress, resulted in the identification of a number of QTL conferring tolerance to cold-induced wilting and necrosis. A major QTL, qCTS12, located on the short arm of chromosome 12, contributes over 40% of the phenotypic variance. To identify the gene(s) underlying qCTS12, we have undertaken the fine mapping of this locus. Saturating the short arm of chromosome 12 with microsatellite markers revealed that qCTS12 is closest to RM7003. Using RM5746 and RM3103, which are immediately outside of RM7003, we screened 1,954 F5-F10 lines to find recombinants in the qCTS12 region. Additional microsatellite markers were identified from publicly available genomic sequence and used to fine map qCTS12 to a region of approximately 87 kb located on the BAC clone OSJNBb0071I17. This region contains ten open reading frames (ORFs) consisting of five hypothetical and expressed proteins of unknown function, a transposon protein, a putative NBS-LRR disease resistance protein, two zeta class glutathione S-transferases (OsGSTZ1 and OsGSTZ2), and a DAHP synthetase. Further fine mapping with markers developed from the ORFs delimited the QTL to a region of about 55 kb. The most likely candidates for the gene(s) underlying qCTS12 are OsGSTZ1 and OsGSTZ2.


Cold Tolerance Marker RM5746 Temperate Japonica Gramene Database Phenotyping Experiment 
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This work was supported by the U.S. Department of Agriculture, Agricultural Research Service, CRIS Project 5306-21000-016D (T.H.T) and by the California Rice Research Board RF-1 and RB-3 Projects (T.H.T.). We extend our thanks to Cynthia Andaya, Peter Colowit, Darryl Aragones and Leslie Snyder for their technical assistance. We are grateful to R.E. Tabien, K.K. Jena, and anonymous reviewers for critical reading of and helpful suggestions on improving our manuscript.


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.Crops Pathology and Genetics Research Unit, Department of Plant SciencesUSDA-ARSDavisUSA

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