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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #206441

Title: Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Orysa Sativa L.)

item Andaya, Virgilio
item Tai, Thomas

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2007
Publication Date: 4/11/2007
Citation: Andaya, V.C., Tai, T. 2007. Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Orysa Sativa L.). Molecular Breeding. 20:349-358.

Interpretive Summary: Developing enhanced seedling cold tolerance is an important objective of temperate rice breeding programs. The response of rice seedlings to cold stress is complex and may include wilting, tissue death (necrosis) and yellowing (chlorosis) depending on the intensity and duration of the cold stress. Some rice, such as the California variety M-202, exhibit good levels of tolerance to cold stress at the seedling stage. Earlier studies identified several regions containing genes that contribute to M-202’s tolerance to cold. In this study, we have examined one of those regions, designated qCTS4, which confers tolerance to yellowing and stunting. Using molecular genetic mapping techniques, we have narrowed the region down to 560 kb on chromosome 4. Within this region, there are 49 predicted genes, one of which is a putative cationic peroxidase that is completely linked to the cold tolerance trait. Peroxidases are enzymes known to be involved in stress responses in various biological systems. Although the region is fairly large, this result serves as a foundation for isolating the gene(s) underlying the qCTS4 locus, and the DNA markers developed here should be useful in transferring this locus into cold-sensitive rice varieties for testing and possible development of improved germplasm.

Technical Abstract: 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 560 kb region of chromosome 4, which is highly repressed 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.