Molecular Breeding

, Volume 20, Issue 4, pp 349–358

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

Article

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 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.

Keywords

Abiotic stress Microsatellite markers QTL mapping Rice 

References

  1. Andaya VC, Mackill DJ (2003a) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Expt Bot 54:2579–2585CrossRefGoogle Scholar
  2. 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
  3. Andaya VC, Tai TH (2006) Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet 113:467–475PubMedCrossRefGoogle Scholar
  4. Blokhina O, Virolainen E, Fagerstedt KV (2003) Antioxidants, oxidative damage and oxygen deprivation stress: a review. Annals Bot 91:179–194CrossRefGoogle Scholar
  5. 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
  6. 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
  7. Jiang L, Liu SJ, Hou MY, Tang JY, Chen LM, Zhai HQ, Wan JM (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crops Res 98:68–75CrossRefGoogle Scholar
  8. Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln SE, Newburg L (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174.181PubMedCrossRefGoogle Scholar
  9. 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
  10. McKenzie KS, Johnson CW, Tseng ST, Oster JJ, Brandon DM (1994) Breeding improved rice cultivars for temperate regions - a case-study. Aust J Exp Agric 34:897–905CrossRefGoogle Scholar
  11. 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
  12. Miura K, Lin SY, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.). Breed Sci 51:293–299CrossRefGoogle Scholar
  13. 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
  14. 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
  15. Sasaki K, Iwai T, Hiraga S, Kuroda K, Seo S, Mitsuhara I, Miyasaka A, Iwano M, Ito H, Matsui H, Ohashi Y (2004) Ten rice peroxidases redundantly respond to multiple stresses including infection with rice blast fungus. Plant Cell Physiol 45:1442–1452PubMedCrossRefGoogle Scholar
  16. Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian LL, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205PubMedCrossRefGoogle Scholar
  17. Sthapit BR, Witcombe JR (1998) Inheritance of tolerance to chilling stress in rice during germination and plumule greening. Crop Sci 38:660–665CrossRefGoogle Scholar
  18. Teixeira FK, Menezes-Benavente L, Margis R, Margis-Pinheiro M (2004) Analysis of the molecular evolutionary history of the ascorbate peroxidase gene family: inferences from the rice genome. J Mol Evol 59:761–770PubMedCrossRefGoogle Scholar
  19. Teixeira FK, Menezes-Benavente L, Galvao VC, Margis R, Margis-Pinheiro M (2006) Rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments. Planta 224:300–314PubMedCrossRefGoogle Scholar
  20. 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
  21. 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
  22. Zhang ZH, Su L, Li W, Chen W, Zhu YG (2005) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci 168:527–534CrossRefGoogle Scholar
  23. 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

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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