Molecular Breeding

, Volume 20, Issue 4, pp 349–358 | Cite as

Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.)



Rice seedlings are sensitive to low temperatures (≤15°C) and under prolonged or repeated exposure, yellowing and stunting are commonly observed. Damage to seedlings results in poor stand establishment and delayed maturation, which can cause significant reductions in yield. In general, japonica rice varieties exhibit more cold tolerance than indica varieties. Earlier genetic analysis of the California rice variety M202 revealed several quantitative trait loci (QTL) that contribute to its tolerance to low temperatures in comparison to the indica rice variety IR50. Among these QTL, qCTS4 is associated with tolerance to yellowing and stunting of rice seedlings and accounts for 40% of the phenotypic variation. Here we report on the fine mapping of qCTS4 to a 128 kb region of chromosome 4, which is highly suppressed for recombination in our mapping populations. Our results provide the necessary foundation for identifying the gene(s) underlying qCTS4 and the markers developed here may be used to introgress this region into indica varieties to improve seedling tolerance to low temperatures.


Abiotic stress Microsatellite markers QTL mapping Rice 



We are grateful to David Mackill and Georgia Eizenga for helpful suggestions for improving this manuscript. 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.).


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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.USDA-ARS Crops Pathology and Genetics Research Unit, Department of Plant SciencesUniversity of California DavisDavisUSA

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