Global gene expression analysis of a rice high-tillering dwarf mutant

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 Arite T, Umehara M, Ishikawa S, Hanada A, Maekawa M, Yamaguchi S, Kyozuka J (2009) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant Cell Physiol 50:1416–1624 Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C (2013) Plant protein interactomes. Annu Rev Plant Biol 64:161–187 Cao P, Jung K, Choi D, Hwang D, Zhu J, Ronald P (2012) The rice oligonucleotide array database: an atlas of rice gene expression. Rice 5:17 Hayward A, Stirnberg P, Beveridge C, Leyser O (2009) Interactions between auxin and strigolactone in shoot branching control. Plant Physiol 151:400–412 Hedden P (2003) The genes of the green revolution. Trends Genet 19:5–9 Ho C, Wu Y, Shen H, Provart N, Geisler M (2012) A predicted protein interactome for rice. Rice 5:15. doi:10.1186/1939-8433-5-15 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 Ishikawa S, Maekawa M, Arite T, Onish K, Takamure I, Kyozuka J (2005) Suppression of tiller bud activity in tillering dwarf mutants of rice. Plant Cell Physiol 46:79–86 Itoh H, Ueguchi-Tanaka M, Sentoku N, Kitano H, Matsuoka M, Kobayashi M (2001) Cloning and functional analysis of two gibberellins 3b-hydroxylase genes that are differently expressed during the growth of rice. Proc Natl Acad Sci USA 98:8909–8914 Itoh H, Tatsumi T, Sakamoto T, Otomo K, Toyomasu T, Kitano H, Ashikari M, Ichihara S, Matsuoka M (2004) A rice semi-dwarf gene, Tan-ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase. Plant Mol Biol 54:533–547 Kawahara Y, de la Bastide M, Hamilton J, Kanamori H, McCombie W, Ouyang S, Schwartz D, Tanaka T, Wu J, Zhou S et al (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4 Khush G (2001) Green revolution: the way forward. Nat Rev Genet 2:815–822 Leyser O (2003) Regulation of shoot branching by auxin. Trends Plant Sci 8:541–545 Lin H, Wang R, Qian Q, Yan M, Meng X, Fu Z, Yan C, Jiang B, Su Z, Li J et al (2009) DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth. Plant Cell 21:1512–1525 Mori M, Nomura T, Ooka H, Ishizaka M, Yokota T, Sugimoto K, Okabe K, Kajiwara H, Satoh K, Yamamoto K et al (2002) Isolation and characterization of a rice dwarf mutant with defect in brassinosteroid biosynthesis. Plant Physiol 130:1152–1161 Sasaki A, Ashikari M, Ueguchi-tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush G et al (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702 Sato Y, Antonio B, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y (2011) RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res 39:D1141–D1148 Supek F, Bosnjak M, Skunca N, Smuc T (2011) REVIGO summarizes and visualizes long lists of Gene Ontology terms. PLoS ONE. doi:10.1371/journal.pone.0021800 Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, Matsuoka M, Ueguchi C (2003) The OsTB1gene negatively regulates lateral branching in rice. Plant J 33:513–520 Tanabe S, Ashikari M, Fujioka S, Takatsuto S, Yoshida S, Yano M, Yoshimura A, Kitano H, Matsuoka M, Fujisawa Y et al (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 Tian F, Li D, Fu Q, Zhu Z, Fu Y, Wang X, Sun C (2005) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580 Wang Y, Li J (2011) Branching in rice. Curr Opin Plant Biol 14:94–99 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 Yan J, Zhu J, He C, Benmoussa M, Wu P (1998) Quantitative trait loci analysis for the developmental behavior of tiller number in rice (Oryza sativa. L). Theor Appl Genet 97:267–274 Zhang B, Tian F, Tan L, Xie D, Sun C (2011a) Characterization of a novel high-tillering dwarf 3 mutant in rice. J Genet Genomics 38:411–418 Zhang F, Wang P, Sun C, Wang B, Li X, Zhu J, Gao X, Deng X (2011b) Fine mapping and candidate gene analysis of the dwarf gene d162 (t) in rice (Oryza sativa L.). Genes Genomics 33:25–30 Zheng Q, Wang X (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36:W358–W363 Zou J, Zhang S, Zhang W, Li G, Chen Z, Zhai W, Zhao X, Pan X, Xie Q, Zhu L (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