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Fine mapping of a gene for low-tiller number, Ltn, in japonica rice (Oryza sativa L.) variety Aikawa 1

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Abstract

Tillering is one of the most important agronomic traits related to grain production in rice (Oryza sativa L.). A japonica-type variety, Aikawa 1, is known to have low-tiller number. The detailed location of a low-tillering gene, Ltn, which has been localized on chromosome 8 in Aikawa 1, was confirmed by molecular mapping. Using BC5F2 individuals derived from a cross between IR64 and Aikawa 1, the low-tillering gene was mapped to an interval defined by SSR markers ssr5816-3 and A4765. This was designated as Ltn because there was no reported gene for tillering in the region of chromosome 8. Through high-resolution linkage analysis, the candidate region of Ltn was located between DNA markers ssr6049-23 and ind6049-1 corresponding to 38.6 kbp on the Nipponbare genome sequence. These DNA markers, which were tightly linked to Ltn, are useful for marker-assisted selection in breeding studies.

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References

  • Araki E, Ebron LA, Cuevas RP, Mercado-Escueta D, Khush GS, Sheehy JE, Kato H, Fukuta Y (2003) Identification of low tiller gene in rice cultivar Aikawa1. Breed Res 5(Suppl 1):95

    Google Scholar 

  • Brondani C, Rangel PHN, Brondani RPV, Ferreira ME (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104:1192–1203

    Article  CAS  PubMed  Google Scholar 

  • Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124:1483–1492

    Article  CAS  PubMed  Google Scholar 

  • Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220

    Article  CAS  PubMed  Google Scholar 

  • Hemamalini GS, Shashidhar HE, Hittalmani S (2000) Molecular marker assisted tagging of morphological and physiological traits under two contrasting moisture regimes at peak vegetative stage in rice (Oryza sativa L.). Euphytica 112:69–78

    Article  CAS  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Ishikawa S, Maekawa M, Arite T, Onishi K, Takamure I, Kyozuka J (2005) Suppression of tiller bud activity in tillering dwarf mutants of rice. Plant Cell Physiol 46:79–86

    Article  CAS  PubMed  Google Scholar 

  • Ishimaru K, Yano M, Aoki N, Ono K, Hirose T, Lin SY, Monna L, Sasaki T, Ohsugi R (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor Appl Genet 102:793–800

    Article  CAS  Google Scholar 

  • Iwata N, Takamure I, Wu HK, Siddiq EA, Rutger JN (1995) List of genes for various traits (with chromosome and main literature). Rice Genet Newsl 12:61–93

    Google Scholar 

  • Jiang H, Guo LB, Xue DW, Zeng DL, Zhang GH, Dong GJ, Gu MH, Qian Q (2006) Genetic analysis and gene-mapping of two reduced-culm-number mutants in rice. J Integr Plant Biol 48:341–347

    Article  CAS  Google Scholar 

  • Khush GS (1987) Rice breeding: past, present and future. J Genet 66:195–216

    Article  Google Scholar 

  • Khush GS (2000) New plant type of rice for increasing the genetic yield potential. In: Nanda JS (ed) Rice breeding and genetics. Science Publishers, Enfield (NH), pp 99–108

    Google Scholar 

  • Khush GS, Virk PS (2005) Selection criteria. In: IR varieties and their impact, International Rice Research Institute, Los Baños, Philippines, pp 6–15

  • Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, Levenson C, Sninsky JJ (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucl Acids Res 18:999–1005

    Article  CAS  PubMed  Google Scholar 

  • Lanceras JC, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:384–399

    Article  CAS  PubMed  Google Scholar 

  • Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Fujimoto H, Yuan M, Luo D, Han B, Li J (2003) Control of tillering in rice. Nature 422:618–621

    Article  CAS  PubMed  Google 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 9:199–207

    Article  CAS  PubMed  Google Scholar 

  • Miyamoto N, Goto Y, Matsui M, Ukai Y, Morita M, Nemoto K (2004) Quantitative trait loci for phyllochron and tillering in rice. Theor Appl Genet 109:700–706

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325

    Article  CAS  PubMed  Google 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, pp 365–386

    Google Scholar 

  • Takamure I (1994) Genetic studies on several mutants related to morphological and physiological characters in rice. Mem Fac Agric Hokkaido Univ 19:151–202

    Google Scholar 

  • Takamure I, Kinoshita T (1993) Genetic analysis of reduced culm number mutants indicated by gamma-ray irradiation in rice. Mem Fac Agric Hokkaido Univ 18:447–454

    Google Scholar 

  • Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257

    Article  CAS  PubMed  Google Scholar 

  • Yan JQ, Zhu J, He CX, Benmoussa M, Wu P (1998) Analysis for the developmental behavior of tiller number in rice (Oryza sativa L.). Theor Appl Genet 97:267–274

    Article  CAS  Google Scholar 

  • Zou J, Chen Z, Zhang S, Zhang W, Jiang G, Zhao X, Zhai W, Pan X, Zhu L (2005) Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.). Planta 222:604–612

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This paper reports the results obtained in the IRRI-Japan Collaborative Research Project phases III, IV, and V supported by the Ministry of Foreign Affairs and the Ministry of Agriculture, Forestry, and Fisheries of Japan. We are grateful to Mr. B. Hardy and Dr. D. J. Mackill of IRRI for English editing to improve manuscript. We would like to thank an editor and anonymous reviewers for critical and constructive comments which have improved the contents of this manuscript.

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Authors and Affiliations

  1. International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

    Daisuke Fujita, Leodegario A. Ebron, Gurdev S. Khush, John E. Sheehy, Tanguy Lafarge & Nobuya Kobayashi

  2. National Agricultural Research Center for Western Region, 6-12-1 Nishi-Fukatsu, Fukuyama, Hiroshima, 721-8514, Japan

    Etsuko Araki

  3. National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan

    Hiroshi Kato

  4. Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UPR AIVA, TA 70/01, Avenue Agropolis, 34398, Montpellier, France

    Tanguy Lafarge

  5. Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan

    Yoshimichi Fukuta & Nobuya Kobayashi

Authors
  1. Daisuke Fujita
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  2. Leodegario A. Ebron
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  3. Etsuko Araki
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  4. Hiroshi Kato
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  5. Gurdev S. Khush
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  6. John E. Sheehy
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  7. Tanguy Lafarge
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  8. Yoshimichi Fukuta
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  9. Nobuya Kobayashi
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Corresponding author

Correspondence to Nobuya Kobayashi.

Additional information

Communicated by M. Wissuwa.

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Fujita, D., Ebron, L.A., Araki, E. et al. Fine mapping of a gene for low-tiller number, Ltn, in japonica rice (Oryza sativa L.) variety Aikawa 1. Theor Appl Genet 120, 1233–1240 (2010). https://doi.org/10.1007/s00122-009-1251-7

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  • DOI: https://doi.org/10.1007/s00122-009-1251-7

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