Euphytica

, Volume 165, Issue 3, pp 459–470

Cold tolerance at the early growth stage in wild and cultivated rice

  • Akhil Ranjan Baruah
  • Noriko Ishigo-Oka
  • Mieko Adachi
  • Yasuyo Oguma
  • Yoshiro Tokizono
  • Kazumitsu Onishi
  • Yoshio Sano
Article

Abstract

The present study was conducted to understand the pattern of variation and the genetic bases for cold tolerance at the early growth stage in Asian rice. The genetic variation was investigated at the germination, plumule and seedling stages among 57 strains including cultivated rice (Oryza sativa ssp. indica and ssp. japonica) and its wild progenitor (Oryza rufipogon). The significant differentiation of cold tolerance was observed among the taxonomically divided groups. At the germination stage, both indica and japonica subspecies tended to be more tolerant than O. rufipogon, whereas at the plumule and seedling stages, ssp. japonica tended to be more tolerant than ssp. indica and O. rufipogon. Furthermore, in cold tolerance at the plumule stage, the clinal variation across the latitude of origins was observed within O. rufipogon and ssp. japonica, suggesting that the current pattern of variation seems to have been shaped by both their phylogenetic histories and on-going adaptation to the local environments. QTL analysis between O. sativa ssp. japonica (tolerant) and O. rufipogon (susceptible) revealed five putative QTLs for cold tolerance at the plumule and seedling stages but not at the germination stage. Substitution mapping was also carried out to precisely locate the two major QTLs for cold tolerance at the plumule stage, which could be used for improvement of tolerance to cold stress in ssp. indica.

Keywords

Cold tolerance Early growth stage Latitudinal cline Oryza rufipogon O. sativa QTL 

References

  1. Andaya VC, Mackill DJ (2003) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot 54:2579–2585. doi:10.1093/jxb/erg243 PubMedCrossRefGoogle Scholar
  2. Andaya VC, Tai TH (2006) Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet 113:467–475. doi:10.1007/s00122-006-0311-5 PubMedCrossRefGoogle Scholar
  3. Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228. doi:10.1007/s00122-001-0819-7 PubMedCrossRefGoogle Scholar
  4. Chuong PV, Omura T (1982) Studies on the chlorosis expressed under low temperature in rice, Oryza sativa L. In: Bulletin of the Institute of Tropical Agriculture, vol 5. Kyushu University, Fukuoka, Japan, pp 1–58Google Scholar
  5. Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y et al (2004) Mapping of quantitative loci controlling low-temperature germinability in rice (Oryza sativa). Theor Appl Genet 108:794–799. doi:10.1007/s00122-003-1509-4 PubMedCrossRefGoogle Scholar
  6. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638. doi:10.1534/genetics.104.035642 PubMedCrossRefGoogle Scholar
  7. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30. doi:10.1007/BF00290078 CrossRefGoogle Scholar
  8. Glaszmann JC, Kaw RN, Khush GS (1990) Genetic divergence among cold tolerant rices (Oryza sativa L.). Euphytica 45:95–104Google Scholar
  9. Gong Z, Lee H, Xiong L, Jagendorf A, Stevenson B, Zhu JK (2002) RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proc Natl Acad Sci USA 99:11507–11512. doi:10.1073/pnas.172399299 PubMedCrossRefGoogle Scholar
  10. Ikehashi H (1973) Studies on the environmental and varietal differences of germination habits in rice seeds with special reference to plant breeding. J Cent Agric Exp Stan 19:1–60 (in Japanese with English summary)Google Scholar
  11. Kwak TS, Vergara BS, Nanda JS, Coffman WR (1984) Inheritance of seedling cold tolerance in rice. SABRAO J 16:83–86Google Scholar
  12. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199PubMedGoogle Scholar
  13. Lee HS, Taguchi K (1969) Studies on the germinability of rice seeds at low temperature. I. The varietal differences and effects of growing conditions of parent plants on the germinability of rice seeds at low temperature. Mem Fac Agric Hokkaido University 7:138–146 (in Japanese with English summary)Google Scholar
  14. Lou Q, Chen L, Sun Z, Xing Y, Li J, Xu X et al (2007) A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica 158:87–94. doi:10.1007/s10681-007-9431-5 CrossRefGoogle Scholar
  15. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410. doi:10.1073/pnas.0403715101 PubMedCrossRefGoogle Scholar
  16. Mackill DJ, Lei X (1997) Genetic variation for traits related to temperate adaptation of rice cultivars. Crop Sci 37:1340–1346Google Scholar
  17. 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
  18. Mitchell-Olds T, Willis JH, Goldstein DB (2007) Which evolutionary processes influence natural genetic variation for phenotypic traits? Nat Rev Genet 8:845–856. doi:10.1038/nrg2207 PubMedCrossRefGoogle Scholar
  19. Miura K, Lin SY, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Breed Sci 51:293–299. doi:10.1270/jsbbs.51.293 CrossRefGoogle Scholar
  20. Monna L, Lin HX, Kojima S, Sasaki T, Yano M (2002) Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice. Theor Appl Genet 104:772–778. doi:10.1007/s00122-001-0813-0 PubMedCrossRefGoogle Scholar
  21. Morishima H, Oka HI (1981) Phylogenetic differentiation of cultivated rice, XXII. Numerical evaluation of the indica-japonica differentiation. Jpn J Breed 31:402–413Google Scholar
  22. Murray MG, Thomson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325. doi:10.1093/nar/8.19.4321 PubMedCrossRefGoogle Scholar
  23. Nagamine T (1991) Genic control of tolerance to chilling injury at seedling stage in rice. Jpn J Breed 41:35–40Google Scholar
  24. Nagamine T, Nakagahra M (1990) Genetic variation of chilling injury at seedling stage in rice, Oryza sativa L. Jpn J Breed 40:449–455Google Scholar
  25. Oka HI (1954) Phylogenetic differentiation of the cultivated rice plant. V. Variation of minimum germination temperature and temperature constant among rice varieties. Jpn J Breed 4:6–10 (in Japanese)Google Scholar
  26. Oka HI (1958) Intervarietal variation and classification of cultivated rice. Indian J Genet Plant Breed 18:79–89Google Scholar
  27. Oka HI (1988) Origin of cultivated rice. Elsevier, TokyoGoogle Scholar
  28. Oka HI, Chang WT (1960) Survey of variations in photoperiodic response in wild Oryza species. Bot Bull Acad Sinica (Taiwan) 1:1–14Google Scholar
  29. Onishi K, Horiuchi Y, Ishigoh-Oka N, Takagi K, Ichikawa N, Maruoka M et al (2007) A QTL cluster for plant architecture and its ecological significance in Asian wild rice. Breed Sci 57:7–16. doi:10.1270/jsbbs.57.7 CrossRefGoogle Scholar
  30. Rozen S, Skaletsky HJ (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, TotowaGoogle Scholar
  31. Satake T (1976) Sterility-type cool injury in paddy rice plants. In: Institute International Rice Research (ed) Climate and rice. International Rice Research Institute, Los Baños, PhilippinessGoogle Scholar
  32. Schaal BA, Gaskin JF, Caicedo AL (2003) Phylogeography, hpaplotype trees, and invasive plant species. J Hered 94:197–204. doi:10.1093/jhered/esg060 PubMedCrossRefGoogle Scholar
  33. Skøt L, Sackville Hamilton NR, Mizen S, Chorlton KH, Thomas ID (2002) Molecular genecology of temperature response in Lolium perenne: 2. Association of AFLP markers with ecogeography. Mol Ecol 11:1865–1876. doi:10.1046/j.1365-294X.2002.01568.x PubMedCrossRefGoogle Scholar
  34. 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 11:1441–1452. doi:10.1101/gr.184001 PubMedCrossRefGoogle Scholar
  35. Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol 50:571–599. doi:10.1146/annurev.arplant.50.1.571 PubMedCrossRefGoogle Scholar
  36. Van Ooijen JW, Boer MP, Jansen C, Maliepaard C (2002) Map QTL 4.0: software for the calculation of QTL position on genetic maps. Plant research international, Wageningen (Netherlands)Google Scholar
  37. Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139–146. doi:10.1016/S1369-5266(03)00009-8 PubMedCrossRefGoogle Scholar
  38. Vergara BS (1976) Physiological and morphological adaptability of rice varieties to climate. In: Institute International Rice Research (ed) Climate and rice. International Rice Research Institute, Los Baños, PhilippinesGoogle Scholar
  39. Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genomics 272:504–511. doi:10.1007/s00438-004-1069-6 PubMedCrossRefGoogle Scholar
  40. Zhang ZH, Su L, Li W, Chen W, Zhu YG (2004) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci 168:527–534. doi:10.1016/j.plantsci.2004.09.021 CrossRefGoogle Scholar
  41. Zhen T, Ungerer MC (2008) Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana. New Phytol 177:419–427PubMedGoogle Scholar
  42. Zhu Q, Ge S (2005) Phylogenetic relationship among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167:249–265. doi:10.1111/j.1469-8137.2005.01406.x PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Akhil Ranjan Baruah
    • 1
  • Noriko Ishigo-Oka
    • 1
  • Mieko Adachi
    • 1
  • Yasuyo Oguma
    • 1
  • Yoshiro Tokizono
    • 1
  • Kazumitsu Onishi
    • 1
  • Yoshio Sano
    • 1
  1. 1.Laboratory of Plant Breeding, Department of Applied Science, Research Faculty of AgricultureHokkaido UniversitySapporoJapan

Personalised recommendations