Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.)
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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.
KeywordsAbiotic 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.).
- Andaya VC, Mackill DJ (2003b) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica x indica cross. Theor Appl Genet 106:1084–1090Google Scholar
- Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lu G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320Google Scholar
- IRRI (1979) Report of a rice cold tolerance workshop. In: IRRI Proc. Rice Cold Tolerance Workshop, Office of Rural Development, Suweon, Korea, p.139Google Scholar
- McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207PubMedCrossRefGoogle Scholar
- Misawa S, Mori N, Takumi S, Yoshida S, Nakamura C (2000) Mapping of QTLs for low temperature response in seedlings of rice (Oryza sativa L.). Cereal Res Commun 28:33–40Google Scholar
- Pandey S, Velasco S (1999) Economics of direct seeding in Asia: patterns of adoption and research priorities. Int Rice Res Notes 24:6–11Google Scholar
- Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386Google Scholar
- Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
- Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTLs. J Quant Trait Loci 2: (http://probe.nalusda.gov:8000/otherdocs/jqtl/jqtl1996-8001/ utz.html)Google Scholar
- Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B, Chen Z, Yu S, Zhu J, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu Y, Zhang LS, Liu Y, Yu Z, Fan D, Weng Q, Chen L, Lu T, Liu X, Jia P, Sun T, Wu Y, Zhang Y, Lu Y, Li C, Wang R, Lei H, Li T, Hu H, Wu M, Zhang R, Guan J, Zhu J, Fu G, Gu M, Hong G, Xue Y, Wing R, Jiang J, Han B (2002) A fine physical map of rice chromosome 4. Genome Res 12:817–823Google Scholar