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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #192334
Title: FINE MAPPING OF THE QCTS12 LOCUS, A MAJOR QTL FOR SEEDLING COLD TOLERANCE IN RICE

Author
item Andaya, Virgilio
item Tai, Thomas

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2006
Publication Date: 8/1/2006
Citation: Andaya, V.C., Tai, T. 2006. Fine mapping of the qcts12 locus, a major qtl for seedling cold tolerance in rice. Theoretical and Applied Genetics. vol. 113, no. 3, pp. 467-475

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 qCTS12, which confers tolerance to wilting and necrosis. Using molecular genetic mapping techniques, we have narrowed the region down to 22 kb on chromosome 12. Within this region, there are 4 genes, 2 of which are members of the glutathione S-transferase (GST) gene family. GSTs are enzymes known to be involved in stress responses in various biological systems and it is likely that the basis for M-202’s seedling cold tolerance is one or both of these GST genes.

Technical Abstract: The temperate japonica rice cultivar M-202 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 M-202 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 the 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 10 open reading frames (ORFs) consisting of five hypothetical and expressed proteins with 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 22 kb region. The most likely candidates for the gene(s) underlying qCTS12 are OsGSTZ1 and OsGSTZ2.