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Fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice (Oryza rufipogon Griff.)

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Abstract

Identification of genes in rice that affect production and quality is necessary for improving the critical global food source. CSSL58, a chromosome segment substitution line (CSSL) containing a chromosome segment of Oryza rufipogon in the genetic background of the indica cultivar Teqing showed significantly smaller panicles, fewer grains per panicle, smaller grains and dwarfness compared with the recurrent parent Teqing. Genetic analysis of the BC4F1 and BC4F2 generations, derived from a cross between CSSL58 and Teqing, showed that these traits are controlled by the recessive gene spd6, which mapped to the short arm of chromosome 6. Fine mapping and high-resolution linkage analysis using 24,120 BC4F3 plants and markers flanking spd6 were carried out, and the gene was localized to a 22.4 kb region that contains four annotated genes according to the genome sequence of japonica Nipponbare. Phenotypic evaluation of the nearly isogenic line NIL(spd6) revealed that spd6 from wild rice has pleiotropic effects on panicle number per plant, grain size, grain weight, grain number per panicle and plant height, suggesting that this gene might play an important role in the domestication of rice. The discovery of spd6 may ultimately be useful for the design and breeding of crops with high grain yield and quality.

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References

  • Arite T, Iwata H, Ohshima K, Maekawa M, Nakajima M, Kojima M, Sakakibara H, Kyozuka J (2007) DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice. Plant J 51:1019–1029

    Article  PubMed  CAS  Google Scholar 

  • Ashikari M, Sakakibara H, Lin SY, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745

    Article  PubMed  CAS  Google Scholar 

  • De Baere I, Derua R, Janssens V, Van Hoof C, Waelkens E, Merlevede W, Goris J (1999) Purification of porcine brain protein phosphatase 2A leucine carboxyl methyltransferase and cloning of the human homologue. Biochemistry 38:16539–16547

    Article  PubMed  Google Scholar 

  • Fan CH, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang QF (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Rustgi S, Kumar N (2006) Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants. Genome 49:565–571

    Article  PubMed  Google Scholar 

  • Hao W, Jin J, Sun SY, Zhu MZ, Lin HX (2006) Construction of chromosome segment substitution lines carrying overlapping chromosome segments of the whole wild rice genome and identification of quantitative trait loci for rice quality. J Plant Physiol Mol Biol 32:354–362 (in Chinese with an English abstract)

    CAS  Google Scholar 

  • Hong Z, Ueguchi-Tanaka M, Umemura K, Uozu S, Fujioka S, Takatsuto S, Yoshida S, Ashikari M, Kitano H, Matsuoka M (2003) A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450. Plant Cell 15:2900–2910

    Article  PubMed  CAS  Google Scholar 

  • Hong Z, Ueguchi-Tanaka M, Fujioka S, Takatsuto S, Yoshida S, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M (2005) The rice brassinosteroid-deficient dwarf2 mutant, defective in the rice homolog of Arabidopsis DIMINUTO/DWARF1, is rescued by the endogenously accumulated alternative bioactive brassinosteroid, dolichosterone. Plant Cell 17:2243–2254

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Itoh H, Ueguchi-Tanaka M, Sakamoto T, Kayano T, Tanaka H, Ashikari M, Matsuoka M (2002) Modification of rice plant height by suppressing the height-controlling gene, D18, in rice. Breed Sci 52:215–218

    Article  CAS  Google Scholar 

  • Janssens V, Goris J (2001) Protein phosphatase 2A: a highly regulated family of serine/threonine phosphatases implicated in cell growth and signalling. Biochem J 353:417–439

    Article  PubMed  CAS  Google Scholar 

  • Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365–1369

    Article  PubMed  CAS  Google Scholar 

  • Komatsu M, Maekawa M, Shimamoto K, Kyozuka J (2001) The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development. Dev Biol 231:364–373

    Article  PubMed  CAS  Google Scholar 

  • Komatsu K, Maekawa M, Ujiie S, Satake Y, Furutani I, Okamoto H, Shimamoto K, Kyozuka J (2003a) LAX and SPA: Major regulators of shoot branching in rice. Proc Natl Acad Sci USA 100:11765–11770

    Article  PubMed  CAS  Google Scholar 

  • Komatsu M, Chujo A, Nagato Y, Shimamoto K, Kyozuka J (2003b) FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. Development 130:3841–3850

    Article  PubMed  CAS  Google Scholar 

  • Komorisono M, Ueguchi-Tanaka M, Aichi I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M, Sazuka T (2005) Analysis of the rice mutant dwarf and gladius leaf 1 aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling. Plant Physiol 138:1982–1993

    Article  PubMed  CAS  Google Scholar 

  • Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trends Genet 23:578–587

    Article  PubMed  CAS  Google Scholar 

  • Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, Sakakibara H, Kyozuka J (2007) Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature 445:652–655

    Article  PubMed  CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Lee JA, Pallas DC (2007) Leucine carboxyl methyltransferase-1 is necessary for normal progression through mitosis in mammalian cells. J Biol Chem 282:30974–30984

    Article  PubMed  CAS  Google Scholar 

  • Li XY, Qian Q, Fu ZM, Wang YH, Xiong GS, Zeng DL, Wang XQ, Liu XF, Teng S, Hiroshi F, Yuan M, Luo D, Han B, Li JY (2003) Control of tillering in rice. Nature 422:618–621

    Article  PubMed  CAS  Google Scholar 

  • Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002) Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breed Sci 52:35–41

    Article  CAS  Google Scholar 

  • Mase K, Sato K, Nakano Y, Nishikubo N, Tsuboi Y, Zhou JM, Kitano H, Katayama Y (2005) The ectopic expression of phenylalanine ammonia lyase with ectopic accumulation of polysaccharide-linked hydroxycinnamoyl esters in internode parenchyma of rice mutant Fukei 71. Plant Cell Rep 24:487–493

    Article  PubMed  CAS  Google Scholar 

  • McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, 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  PubMed  CAS  Google Scholar 

  • Mori M, Nomura T, Ooka H, Ishizaka M, Yokota T, Sugimoto K, Okabe K, Kajiwara H, Satoh K, Yamamoto K, Hirochika H, Kikuchi S (2002) Isolation and characterization of a rice dwarf mutant with a defect in brassinosteroid biosynthesis. Plant Physiol 130:1152–1161

    Article  PubMed  CAS  Google Scholar 

  • Ogawa S, Toyomasu T, Yamane H, Murofushi N, Ikeda R, Morimoto Y, Nishimura Y, Omori T (1996) A step in the biosynthesis of gibberellins that is controlled by the mutation in the semi-dwarf rice cultivar Tan-ginbozu. Plant Cell Physiol 37:363–368

    CAS  Google Scholar 

  • Sakamoto T, Morinaka Y, Ohnishi T, Sunohara H, Fujioka S, Ueguchi-Tanaka M, Mizutani M, Sakata K, Takatsuto S, Yoshida S, Tanaka H, Kitano H, Matsuoka M (2006) Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nat Biotechnol 24:105–109

    Article  PubMed  CAS  Google Scholar 

  • Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702

    Article  PubMed  CAS  Google Scholar 

  • Sasaki A, Itoh H, Gomi K, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Jeong DH, An G, Kitano H, Ashikari M, Matsuoka M (2003) Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299:1896–1898

    Article  PubMed  CAS  Google Scholar 

  • Sato Y, Sentoku N, Miura Y, Hirochika H, Kitano H, Matsuoka M (1999) Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. EMBO J 18:992–1002

    Article  PubMed  CAS  Google Scholar 

  • Sazuka T, Aichi I, Kawai T, Matsuo N, Kitano H, Matsuoka M (2005) The rice mutant dwarf bamboo shoot 1: a leaky mutant of the NACK-type kinesin-like gene can initiate organ primordia but not organ development. Plant Cell Physiol 46:1934–1943

    Article  PubMed  CAS  Google Scholar 

  • Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028

    Article  PubMed  CAS  Google Scholar 

  • Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630

    Article  PubMed  CAS  Google Scholar 

  • Sweeney M, McCouch S (2007) The complex history of the domestication of rice. Ann Bot (Lond) 100:951–957

    Article  Google Scholar 

  • Takeda K (1977) Internode elongation and dwarfism in some gramineous plants. Gamma Field Sym 16:1–18

    Google Scholar 

  • Tanabe S, Ashikari M, Fujioka S, Takatsuto S, Yoshida S, Yano M, Yoshimura A, Kitano H, Matsuoka M, Fujisawa Y, Kato H, Iwasaki Y (2005) A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length. Plant Cell 17:776–790

    Article  PubMed  CAS  Google Scholar 

  • Tian F, Zhu ZF, Zhang BS, Tan LB, Fu YC, Wang XK, Sun CQ (2006) Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.). Theor Appl Genet 113:619–629

    Article  PubMed  CAS  Google Scholar 

  • Ueguchi-Tanaka M, Fujisawa Y, Kobayashi M, Ashikari M, Iwasaki Y, Kitano H, Matsuoka M (2000) Rice dwarf mutant d1, which is defective in the alpha subunit of the heterotrimeric G protein, affects gibberellin signal transduction. Proc Natl Acad Sci USA 97:11638–11643

    Article  PubMed  CAS  Google Scholar 

  • Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow TY, Hsing YIC, Kitano H, Yamaguchi I, Matsuoka M (2005) GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437:693–698

    Article  PubMed  CAS  Google Scholar 

  • Vaughan DA, Lu BR, Tomooka N (2008) The evolving story of rice evolution. Plant Sci 174:394–408

    CAS  Google Scholar 

  • Vinatzer BA, Zhang HB, Sansavini S (1998) Construction and characterization of a bacterial artificial chromosome library of apple. Theor Appl Genet 97:1183–1190

    Article  CAS  Google Scholar 

  • Wang E, Wang J, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374

    Article  PubMed  CAS  Google Scholar 

  • Weng JF, Gu SH, Wan XY, Gao H, Guo T, Su N, Lei CL, Zhang X, Cheng ZJ, Guo XP, Wang JL, Jiang L, Zhai HQ, Wan JM (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209

    Article  PubMed  CAS  Google Scholar 

  • Xing YZ, Tang WJ, Xue WY, Xu CG, Zhang QF (2008) Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice. Theor Appl Genet 116:789–796

    Article  PubMed  CAS  Google Scholar 

  • Xiong GS, Hu XM, Jiao YQ, Yu YC, Chu CC, Li JY, Qian Q, Wang YH (2006) LEAFY HEAD2, which encodes a putative RNA-binding protein, regulates shoot development of rice. Cell Res 16:267–276

    Article  PubMed  CAS  Google Scholar 

  • Xue WY, Xing YZ, Weng XY, Zhao Y, Tang WJ, Wang L, Zhou HJ, Yu SB, Xu CG, Li XH, Zhang QF (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

    Article  PubMed  CAS  Google Scholar 

  • Yamagishi M, Takeuchi Y, Kono I, Yano M (2002) QTL analysis for panicle characteristics in temperate japonica rice. Euphytica 128:219–224

    Article  CAS  Google Scholar 

  • Yamamuro C, Ihara Y, Wu X, Noguchi T, Fujioka S, Takatsuto S, Ashikari M, Kitano H, Matsuoka M (2000) Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell 12:1591–1606

    Article  PubMed  CAS  Google Scholar 

  • Zhou HF, Xie ZW, Ge S (2003) Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theor Appl Genet 107:332–339

    Article  PubMed  CAS  Google Scholar 

  • Zou JH, Zhang SY, Zhang WP, Li G, Chen ZX, Zhai WX, Zhao XF, Pan XB, Xie Q, Zhu LH (2006) The rice HIGH-TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds. Plant J 48:687–696

    Article  PubMed  CAS  Google Scholar 

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Acknowldgments

This work was supported by grants from the Ministry of Science and Technology of China (2007AA10Z187, 2006AA10Z1F7), the Ministry of Agriculture of China, the Chinese Academy of Sciences (KSCX1-YW-03) and Shanghai Institutes for Biological Sciences (SIBS2008004).

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Authors and Affiliations

  1. National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Science, 300 Fenglin Road, 200032, Shanghai, China

    Jun-Xiang Shan, Mei-Zhen Zhu, Min Shi, Ji-Ping Gao & Hong-Xuan Lin

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  1. Jun-Xiang Shan
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  2. Mei-Zhen Zhu
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  3. Min Shi
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  4. Ji-Ping Gao
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Correspondence to Hong-Xuan Lin.

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Communicated by M. Xu.

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Shan, JX., Zhu, MZ., Shi, M. et al. Fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice (Oryza rufipogon Griff.). Theor Appl Genet 119, 827–836 (2009). https://doi.org/10.1007/s00122-009-1092-4

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