1 Running Head - Plant Physiology · 55 Institute of Genetics and Developmental Biology, ... 79...

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Running Head: 1

Identification of an Epiallele of RAV6 in rice 2

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Corresponding Author: 4

Xianwei Song 5

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, 6

Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 7

Beijing 100101, China. 8

Tel: 86-10-64869203 9

Fax: 86-10-6487342 10

Email: [email protected] 11

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Research Area: 13

Genes, Development and Evolution (Epigenetics and Gene Regulation) 14

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Plant Physiology Preview. Published on September 8, 2015, as DOI:10.1104/pp.15.00836

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Title 17

Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice 18

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Authors 20

Xiangqian Zhang1,#, Jing Sun2, # , Xiaofeng Cao2,3 and Xianwei Song2, * 21

#These authors contributed equally to this work. 22

* Corresponding author 23

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1 Guangdong Engineering Research Center of Grassland Science, College of Forestry and 25

Landscape Architecture, South China Agricultural University, Guangzhou 510642, China. 26

2 State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute 27

of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. 28

3 Collaborative Innovation Center of Genetics and Development, Shanghai 200433, China. 29

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One-sentence Summary 31

Epigenetic modification of rice RAV6, which encodes a B3 transcription factor, alters 32

rice leaf angle via modulation of brassinosteroid homeostasis. 33

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Footnotes 43

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Financial sources: 45

This work was supported by the National Natural Science Foundation of China (grant 46

nos. 31300987 to X. Song and 30900884 to X. Zhang); by Genetically Modified 47

Breeding Major Projects (grant no. 2014ZX08010-002 to X. Cao); by Natural Science 48

Foundation of Guangdong Province, China (grant no. 2014A030313457), the 49

postdoctoral fellowship to (J. Sun) and the State Key Laboratory of Plant Genomics. 50

51

Corresponding Author: 52

Xianwei Song 53

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, 54

Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 55

Beijing 100101, China. 56

Tel: 86-10-64869203 57

Fax: 86-10-6487342 58

Email: [email protected] 59

60

Author contributions: 61

X.Z designed and performed experiments, J.S analysed data and modified the paper. 62

X.C designed experiments and modified the papers. X.S designed and performed 63

experiments and wrote the paper. 64

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ABSTRACT 71

Heritable epigenetic variants of genes, termed epialleles, can broaden genetic and phenotypic 72

diversity in eukaryotes. Epialleles may also provide a new source of beneficial traits for crop 73

breeding, but very few epialleles related to agricultural traits have been identified in crops. 74

Here, we identified Epi-rav6, a gain-of-function epiallele of rice RELATED TO ABI3 AND 75

VP1 6 (RAV6), which encodes a B3 DNA binding domain-containing protein. The Epi-rav6 76

plants show larger lamina inclination and smaller grain size; these agronomicially important 77

phenotypes are inherited in a semi-dominant manner. We did not find nucleotide sequence 78

variation of RAV6. Instead, we found hypomethylation in the promoter region of RAV6, which 79

caused ectopic expression of RAV6 in Epi-rav6 plants. Bisulfite analysis revealed that 80

cytosine methylation of 4 CG and 2 CNG loci within a continuous 96-bp region plays 81

essential roles in regulating RAV6 expression; this region contains a conserved MITE 82

transposon insertion in cultivated rice genomes. Overexpression of RAV6 in wild type 83

phenocopied the Epi-rav6 phenotype. The brassinosteroid (BR) receptor 84

BRASSINOSTEROID-INSENSITIVE1 (BRI1) and BR biosynthetic genes EBISU DWARF 85

(D2), DWARF11 (D11), and BR-DEFICIENT DWARF1 (BRD1) were ectopically expressed in 86

Epi-rav6 plants. Also, treatment with a BR biosynthesis inhibitor restored the leaf angle 87

defects of Epi-rav6 plants. This indicates that RAV6 affects rice leaf angle by modulating BR 88

homeostasis and demonstrates an essential regulatory role of epigenetic modification on a key 89

gene controlling important agricultural traits. Thus, our work identifies a novel rice epiallele, 90

which may represent a common phenomenon in complex crop genomes. 91

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Keywords: rice, epiallele, DNA methylation, B3 DNA binding protein, brassinosteroid 93

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INTRODUCTION 101

Epigenetic gene variants (epialleles) carry heritable changes in gene expression that do not 102

result from alterations in the underlying DNA sequence (Kakutani, 2002). In eukaryotes, 103

cytosine DNA methylation, a conserved epigenetic mark, plays essential roles in the silencing 104

of transposable elements (TEs) and genes (Law and Jacobsen, 2010). In higher plants, the few 105

known epialleles involve alterations in DNA methylation, indicating that this epigenetic 106

marker makes a large contribution to epigenetic diversity. The Arabidopsis thaliana clark kent 107

(clk) epiallele, which has hypermethylated cytosines at the SUPERMAN locus, causes 108

increased numbers of stamens and carpels (Jacobsen and Meyerowitz, 1997). Also, DNA 109

hypomethylation at two direct repeats in the promoter region of FLOWERING 110

WAGENINGEN (FWA) (Soppe et al., 2000) causes the late-flowering phenotype in 111

Arabidopsis plants carrying the fwa epiallele. Plants carrying the natural epiallele 112

hypermethylated at Linaria cyc-like (Lcyc) show altered floral symmetry, from bilateral to 113

radial, in Linaria vulgaris (Cubas et al., 1999). In tomato, the Colorless non-ripening (Cnr) 114

phenotype results from hypermethylation at the promoter of SQUAMOSA promoter binding 115

protein-like (SBP-box) (Manning et al., 2006). In melon (Cucumis melo L.J), the transition 116

from male to female flowers results from DNA hypermethylation in the promoter of CmWIP1, 117

as mediated by a transposon insertion in gynoecious varieties (Martin et al., 2009). 118

Work in rice has found only two epialleles, Epi-d1 and Epi-df, both of which show a 119

dwarf phenotype (Miura et al., 2009; Zhang et al., 2012). Epi-d1 is a spontaneous epiallele 120

that shows a metastable dwarf phenotype caused by DNA hypermethylation in the promoter 121

region of DWARF 1 (Miura et al., 2009). Epi-df is a gain-of-function epiallele caused by 122

hypomethylation in the 5’ region of FERTILIZATION-INDEPENDENT ENDOSPERM1 123

(FIE1). The ectopic expression of FIE1 in Epi-df results in dwarf and various floral defects 124

that are inherited in a dominant manner (Zhang et al., 2012). 125

In Arabidopsis, DNA methylation occurs in three sequence contexts: CG, CHG, and 126

CHH (where H= A, C, or T) catalyzed by the de novo DNA methyltransferase DRM2 (Cao 127

and Jacobsen, 2002). In the symmetrical contexts, DNA methyltransferases 1 (MET1) and 128



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CHROMOMETHYLASE3 (CMT3) maintain methylation in the CG and CHG contexts, 129

respectively (Law and Jacobsen, 2010; Lindroth et al., 2001). Small interfering RNAs 130

(siRNAs) trigger de novo methylation in all sequence contexts and also trigger the 131

maintenance of CHH methylation, via RNA-directed DNA methylation predominately 132

mediated by DRM2 (Cao and Jacobsen, 2002; Law and Jacobsen, 2010). 133

DNA methylation may be more prevalent and important in rice than in Arabidopsis, 134

owing to the large numbers of TEs in the rice genome. In fact, Arabidopsis mutants of various 135

DNA methyltransferases or DDM1 show few or no developmental defects (Cao and Jacobsen, 136

2002; Lindroth et al., 2001; Saze et al., 2003; Vongs et al., 1993). By contrast, the rice met1a 137

null mutant shows either viviparous germination or early embryonic lethality (Hu et al., 2014; 138

Yamauchi et al., 2014). Moreover, impairment of the RNA-directed DNA methylation 139

pathway proteins DCL3a and DRM2 causes drastic and pleiotropic developmental 140

phenotypes (Moritoh et al., 2012; Wei et al., 2014). 141

Leaf angle is an important agronomic trait that directly affects crop architecture and 142

grain yields (Sinclair and Sheehy, 1999). Crops with erect leaves capture more light for 143

photosynthesis and are suitable for dense planting, all of which increase yields (Sakamoto et 144

al., 2006). In rice, the brassinosteroid (BR) phytohormones participate in the determination of 145

leaf angle (Tong and Chu, 2012; Zhang et al., 2014). BR-deficient or BR-insensitive mutants 146

display erect leaves, while overexpression of BR biosynthesis genes or signaling components 147

results in less-erect leaves with large leaf inclination (Bai et al., 2007; Hong et al., 2005; 148

Yamamuro et al., 2000). For example, loss-of-function mutants of rice OsBRI1 and EBISU 149

DWARF (D2), which encode the rice BR receptor kinase and a BR synthesis enzyme, 150

respectively, show erect leaves (Hong et al., 2003; Yamamuro et al., 2000). In rice, 151

RAV-LIKE 1 (RAVL1), a B3 DNA binding domain-containing protein, maintains BR 152

homeostasis via the coordinated activation of BRI1 and BR biosynthetic genes, D2, 153

DWARF11 (D11), and BR-DEFICIENT DWARF1 (BRD1) (Je et al., 2010). The ravl1 mutant 154

and RAVL1 overexpression lines showed erect leaves and large leaf angles, respectively (Je et 155

al., 2010). 156

Here, we identified a natural epiallele of rice RAV6 and found that plants carrying this 157

epiallele show increased leaf angle and small grains, as well as hypomethylation in the RAV6 158



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promoter region and ectopic expression of RAV6. Our work revealed that epigenetic 159

modification of RAV6 plays an essential role in the regulation of important agricultural traits 160

in rice and found that RAV6 acts via BR homeostasis. 161

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RESULTS 164

A Semi-dominant Mutant Shows Large Lamina Inclination and Small Seed Size 165

A spontaneously occurring rice mutant with large leaf angle and small seeds was isolated 166

from the japonica variety Zhonghua 11 and was named Epi-rav6 based on our subsequent 167

characterization (see below). Compared with the wild type (Zhonghua11), almost all leaf 168

angles throughout all developmental stages were larger in Epi-rav6 plants (Fig. 1A). The 169

mutant had almost the same amount of rachis as wild type but had obviously smaller grains 170

(Supplemental Fig. S1; Fig. 1B-D). Compared with the wild type, the Epi-rav6 seeds were 171

markedly smaller, by 12.8% in length (average 7.8 mm in wild type to 6.8 mm in Epi-rav6) 172

(Fig. 1C and 1D), 25% in width (average 3.6 mm in wild type to 2.7 mm in Epi-rav6) (Fig. 173

1B and 1D) and 20% in thickness (average 2.4 mm in wild type to 1.9 mm in Epi-rav6) (Fig. 174

1E). Thus, the 1,000-grain weight of Epi-rav6 seeds was only 57% of that of wild type (Fig. 175

1E). Together, these findings indicate that Epi-rav6 influences leaf angle and grain size. 176

To determine the inheritance of Epi-rav6, we examined the phenotypes of 260 progeny 177

of self-pollinated Epi-rav6 plants. Three phenotypes segregated in these progeny: 62 were 178

like wild type, 143 were like Epi-rav6, and 55 had severe defects, including fewer tillers, very 179

large leaf angles, and sterility (Fig. 1A). The ratio of wild-type to Epi-rav6-like to severe 180

phenotypes was 1:2.3:0.89 (χ2=2.98, P>0.05). In addition, 27 F1 plants derived from the cross 181

between Epi-rav6 and Zhonghua 11 showed nearly a 1:1 ratio of wild-type progeny and 182

Epi-rav6-like progeny (Supplemental Fig. S2). This genetic evidence demonstrated that the 183

mutant is controlled by a single, semi-dominant locus and the derived allele is heterozygous. 184

Thus, we regarded Epi-rav6-like progeny as heterozygotes and refer to them as Epi-rav6 (+/-); 185

we also regarded the progeny with severe defects as homozygotes and refer to them as 186

Epi-rav6 (-/-). 187

188

Cloning and Characterization of RAV6 189

To explore the molecular mechanism responsible for the Epi-rav6 phenotype, we used 190

map-based cloning to isolate the causal gene. Using an F2 population derived from a cross 191

between the Epi-rav6 mutant and Huajingxian74 (indica), we mapped Epi-rav6 to an 18.5-kb 192



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region on chromosome 2. Based on the MSU7.0 annotation (http://rice.plantbiology.msu.edu/), 193

this region contains only the promoter region of a putative gene, Os02g45850 (Fig. 2A). 194

However, we found no nucleotide sequence difference between the mutant and wild type in 195

this region. We next investigated the expression level of Os02g45850, the only annotated gene 196

in the mapped region. Compared with its low expression level in wild-type leaves, 197

Os02g45850 showed much higher expression in Epi-rav6 (+/-) and Epi-rav6 (-/-) leaves (Fig. 198

2B and 2C). Moreover, the degree of up-regulation was much higher in homozygous than 199

heterozygous lines (Fig. 2B and 2C). 200

To further confirm that the ectopic expression of Os02g45850 is responsible for the 201

developmental defects in Epi-rav6, we over-expressed Os02g45850 in wild type under the 202

control of the maize (Zea mays) Ubiquitin promoter. All the positive transformants with high 203

expression of Os02g45850 displayed large leaf inclination and small grains (Fig. 3). Thus, we 204

concluded that the abnormal phenotype in this mutant results from high expression of 205



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Os02g45850. Os02g45850 encodes a B3 DNA binding domain-containing protein, which 206

belongs to the related to ABI3/VP1 (RAV) family and was named RAV6 (Romanel et al., 207

2009). Therefore, we named the allele Epi-rav6. 208

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RAV6 Regulates Leaf Angle via Mediating Brassinosteroid Homeostasis 210

The plant-specific RAV family belongs to the B3 transcription factor superfamily and consists 211

of 12 members in rice, including RAV6 (Romanel et al., 2009). Phylogenetic analysis showed 212

that the RAV6 (encoded by Os02g45850) is more closely related to RAVL1 (encoded by 213

Os04g49230) than to other members of the RAV family (Fig. 4A). Comparison of deduced 214

amino acid sequences suggested that RAV6 exhibits a high degree of sequence identity with 215

RAVL1, especially in the B3 DNA binding domain (Fig. 4B). These observations indicate that 216

RAV6 and RAVL1 may share similar functions. RAVL1 maintains BR homeostasis via the 217



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coordinated activation of BR synthetic and receptor genes in rice (Je et al., 2010). In addition, 218

plants over-expressing RAVL1 showed increased lamina inclination, like the Epi-rav6 mutants 219

(Je et al., 2010), suggesting that RAV6 may also be involved in the BR pathway via activation 220

of BR biosynthetic and signaling genes. To confirm this, we measured expression of 221

representative genes encoding BR biosynthesis enzymes and the BR receptor, known RAVL1 222

targets, in Epi-rav6 mutants. As expected, expression of BR synthetic genes including D2, 223

D11, and BRD1, was dramatically up-regulated in the Epi-rav6 mutant (Fig. 5A). Similarly, 224

we also observed higher levels of induction for the BR receptor gene BRI1 in Epi-rav6 mutants. 225

These data suggest that RAV6 affects the expression of genes involved in BR signaling and 226

BR biosynthesis. 227

To further confirm that the large lamina inclination of rav6 mutant results from BR 228

overdose, we postulated that treatment with a BR inhibitor would restore, at least partially, the 229

mutant phenotype. As expected, in the presence of Propiconazole (Pcz), a BR biosynthesis 230

inhibitor (Hartwig et al., 2012), the lamina inclination of Epi-rav6 mutant was restored (Fig. 231

5B). Taken together, these results suggest that RAV6 is involved in BR-mediated 232

developmental processes. 233

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Hypomethylation of the Promoter Region of RAV6 in Epi-rav6 plants 235

We found no nucleotide sequence difference between the wild type and Epi-rav6, but we did 236

observe alteration of RAV6 expression levels in the Epi-rav6 plants, suggesting that the 237

mutation may result from an epigenetic modification. We therefore investigated the DNA 238

methylation status of the RAV6 locus. The promoter region of RAV6 contains many TEs 239

including an adh-5-like MITE, a SINE, two unclassified retrotransposons, and a Snabo-like 240

MITE (Fig. 6A; Supplemental Fig. S3A). TEs, especially those proximal to genes, can act as 241

epigenetic mediators to influence nearby gene expression (Hollister and Gaut, 2009; Hollister 242

et al., 2011; Wei et al., 2014). So we performed bisulfite sequencing to analyze methylation in 243

a 2,358-bp genomic region consisting of 573-bp of gene body, 1,321-bp of upstream region 244



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and 464-bp of 5’ distal retrotransposon sequence (Supplemental Fig. S3A). In wild type and 245

homozygous Epi- rav6 mutants, we found no DNA methylation in all three sequence contexts 246

in the 573-bp gene body of RAV6. However, we observed higher CG and CHG but not CHH 247

DNA methylation in proximal and distal upstream regions of RAV6 in wild type compared 248

with the homozygous Epi- rav6 mutant. All the changed methylation sites occurred in a 249

contiguous 96-bp region at -600-bp to -504-bp relative to the transcriptional start site 250

including the closest MITE (adh5-like MITE). This region is hypermethylated in the wild type 251

but hypomethylated in Epi- rav6, containing four CG sites and two CHG sites (Fig. 6B; 252

Supplemental Fig. S3B). To further confirm that the ectopic expression of RAV6 in Epi- rav6 253

results in hypomethylation of the promoter region, we treated the wild-type seeds with 5-aza-2’ 254

deoxycytidine (5-aza-dC), an inhibitor of DNA methylation (Chang and Pikaard, 2005). The 255

expression levels of RAV6 were measured in 7-day-old seedlings with or without 5-aza-dC 256

treatment. Treatment with 5-aza-dC up-regulated RAV6 expression to varying degrees in three 257

cultivated rice strains, including two japonica (Zhonghua11 and Nipponbare) and one indica 258



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(Kasalath) accessions (Figure 6C). These three cultivated accessions also contain the MITE 259

(see below); therefore, these results indicate that the DNA methylation mediated by the TE in 260

the 5’ upstream sequence of RAV6 plays an essential role in the regulation of RAV6 261

expression. 262

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The effect of MITE-mediated DNA methylation on RAV6 expression is conserved in 264

cultivated rice. 265

MITEs are short (less than 600-bp), nonautonomous DNA transposons. As the TEs with the 266

highest copy numbers in the rice genome, MITEs mainly occur in the chromosomal arms, 267

especially in the vicinity of genes (Jiang et al., 2004). According to the Plant Repeat Database, 268

the O. sativa L. spp. japonica cv. Nipponbare genome contains 2984 copies of the adh5-like 269

MITE (Ouyang and Buell, 2004). The adh5-like MITE in the RAV6 promoter region is 100-bp 270

long and located 198-bp upstream of the RAV6 gene body. 271

To further explore the evolutionary significance of the epigenetic regulation of RAV6, we 272

investigated the natural variation of the MITE in the promoter region of the RAV6 locus in 40 273

accessions of cultivated rice, which represent all of the major groups of Asian cultivated rice 274



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(Xu et al., 2012). The results showed that the TE insertion in the promoter region of RAV6 is 275

conserved in all cultivated rice accessions (data not shown). To further confirm this, we 276

aligned the sequences of the MITEs, as well as the 5’ region of RAV6, in four known 277

assembled rice genomes including three cultivated rice strains, Nipponbare, 93-11, Kasalath, 278

and wild rice Oryza brachyantha (Chen et al., 2013; Rice, 2005; Sakai et al., 2014; Yu et al., 279

2002). The MITE insertion was conserved in the cultivated rice genomes but was absent in 280



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Oryza brachyantha (Figure 7A). Consistent with this, the sequence of the 5’ promoter region 281

of RAV6 is also more conserved in cultivated rice, especially the 6 cytosine methylation sites, 282

which are essential for regulation of RAV6 expression (Figure 7A). 283

To further determine the conserved effect of the MITE-mediated DNA methylation on 284

RAV6 expression in cultivated rice accessions, we measured RAV6 transcript levels and DNA 285

methylation patterns in four cultivated rice strains, including three japonica (Nipponbare, 286

Kongyu131, and Koshihikari) and one indica (Kasalath) accessions. Compared with the high 287

expression of RAV6 observed in Epi- rav6, we observed little or no RAV6 expression in leaves 288

at the tillering stage in all cultivated rice strains (Figure 7B). Like the pattern of wild-type 289

Zhonghua11, the other four cultivated rice accessions also showed higher DNA methylation 290

in the contiguous 96-bp region of RAV6 promoter, in contrast with very low DNA 291

methylation in Epi- rav6 (Figure 7C; Supplemental Fig. S4). Thus, it is reasonable to predict 292

that the TE insertion occurred prior to divergence of indica and japonica rice and that the 293

TE-mediated epigenetic regulation of RAV6 expression is evolutionarily conserved in 294

cultivated rice. 295

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DISCUSSION 298

In this work, we identified an epiallele of rice RAV6; this epiallele shows hypomethylation of 299

the RAV6 promoter region, causing ectopic RAV6 expression, larger lamina inclination, and 300

smaller grains. We found that RAV6 expression is associated with extensive methylation of a 301

MITE along with the nearby sequence in the 5’ region of this gene. RAV6 encodes a B3 DNA 302

binding domain-containing protein that has the most sequence similarity to RAVL1, which 303

can maintain BR homeostasis to control rice development (Je et al., 2010). Functional 304

analysis revealed that RAV6 coordinately activates the BR receptor BRI1 and BR 305

biosynthetic genes to control rice leaf angle. This suggests that RAV6 performs a similar 306

function to its homolog, RAVL1. 307

308

The Rice Mutant Epi-rav6 Shows Hypomethylation of DNA at RAV6 309

Ectopic expression of RAV6 in Epi-rav6 mutants indicates that it is a gain-of-function allele 310

of RAV6. Although we found no DNA sequence changes in RAV6, we did find that Epi-rav6 311

shows a loss of cytosine DNA methylation in a MITE along with the nearby sequence located 312

in its 5’ promoter region (Fig. 6A; Supplemental Fig. S3A). Thus, Epi-rav6 has similar 313

features to the Arabidopsis fwa mutant, the first DNA hypomethylated mutant identified in 314

plants, with hypomethylation at two direct repeats in the 5’ region of FWA and ectopic 315

expression of FWA (Soppe et al., 2000). In rice, only two epialleles, Epi-d1 and Epi-df, were 316

identified previously, with hyper- and hypomethylation at the causal genes, respectively 317

(Miura et al., 2009; Zhang et al., 2012). Although both Epi-df and Epi-rav6 are 318

hypomethylated, the methylation sites of the two epi-alleles differ. Epi-df shows 319

hypomethylation mainly in the coding region and not associated with repeated sequences 320

(Zhang et al., 2012). However, the gain of methylation at the D1 locus in Epi-d1 is associated 321

with the upstream repeat sequences (Miura et al., 2009), similar to fwa and Epi-rav6. 322

Therefore, these repeat elements around the causal genes in Epi-d1, fwa, and Epi-rav6 might 323

function as epigenetic mediators to influence nearby gene expression, further confirming 324

previous findings (Hollister et al., 2011; Wei et al., 2014). 325

The phenotypes of epi-alleles generally show metastable inheritance with a low 326



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percentage of revertants, such as in Epi-d1 and Epi-df. Epi-rav6 is a semi-dominant mutant 327

and the homozygous lines are sterile. Therefore, it is impossible to identify authentic 328

revertants between generations (Fig. 1). 329

330

RAV6 Controls Rice Lamina Inclination via Mediating BR Homeostasis 331

The B3 DNA binding domain-containing proteins are plant-specific transcription factors 332

that play important roles in growth, development, flowering time, seed development, and seed 333

maturation (Romanel et al., 2009; Swaminathan et al., 2008). The B3 domain can bind DNA 334

in a sequence-specific or non-specific manner and activate or repress the transcription of 335

specific target genes (Je et al., 2010). Both RAV6 and RAVL1 belong to the RAV (Related to 336

ABI3/VP1) family and have higher sequence similarity to each other than to other members 337

of the RAV family (Figure 4). RAVL1 functions as a transcription factor, directly binding BR 338

biosynthetic and receptor genes and thus maintaining BR homeostasis (Je et al., 2010). In 339

Epi-rav6, the direct targets of RAVL1, including BRI1, D2, D11, and BRD1, showed 340

increased expression (Fig. 5A), indicating that RAV6 might also target these genes. The lines 341

overexpressing RAVL1 showed larger lamina inclination and hypersensitivity to BR (Je et al., 342

2010). Consistent with this, increased leaf angles were observed in Epi-rav6 mutants and 343

RAV6 overexpression lines (Fig. 3A). Moreover, treatment with BR inhibitor fully rescued the 344

larger lamina inclination in Epi-rav6 (Fig. 5B). All these results indicated that both RAV6 and 345

RAVL1 control leaf angles via maintaining BR homeostasis. 346

Besides leaf angle, BRs also influence rice grain size (Zhang et al., 2014). Generally, 347

BR-deficient and BR-insensitive mutants, such as d2, d11, and brd1, showed small grains, 348

while overexpression lines such as Increase Leaf Inclination 1 (OsILI1) and 349

BRI1-SUPPRESSOR 1 (OsBU1) showed large lamina joints and increased grain size (Hong et 350

al., 2002; Hong et al., 2003; Tanabe et al., 2005; Tanaka et al., 2009). The Epi-rav6 plants 351

showed activation of BR signaling and large leaf angles, but small grains, which differs from 352

typical mutants affecting BR. We proposed that decreased grain size in Epi-rav6 may result 353

from an integrated effect of changes in expression of multiple target genes. Since RAV6 354

encodes a B3 DNA binding domain-containing protein, lots of target genes involved multiple 355

developmental processes might be influenced by the gain-of-function change of RAV6 in 356



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Epi-rav6. This also can be confirmed as the Epi-rav6 homozygotes showed pleiotropic 357

developmental defects (Fig. 1A). 358

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MATERIALS AND METHODS 360

Plant Materials and Growth Conditions 361

A spontaneously occurring rice mutant Epi-rav6 was isolated from a Zhonghua 11 (Oryza 362

sativa L. ssp. japonica) population in Guangzhou, China in 2006. Transgenic plants 363

overexpressing RAV6 were produced by introducing the respective genes driven by the maize 364

(Zea mays) Ubiquitin promoter into wild-type plants. Briefly, the 1,239-bp coding sequence 365

of RAV6 was amplified with the primers OsRAV-1BXF and OsRAV-1239RNS 366

(Supplemental Table S1) and the PCR product was inserted into the BamHI/SpeI sites of 367

pCUbi1390, resulting in a plant expression vector driven by the Ubiquitin promoter, which 368

was then transformed into rice. Plants were grown in the field under natural conditions. 369

370

Map-Based Cloning 371

For map-based cloning of OsRAV6, 725 recessive individual plants showing normal leaf 372

inclinations were selected from an F2 population derived from a cross between the Epi-rav6 373

mutant and indica var Huajingxian74. Simple sequence repeat (SSR) markers and 374

insertion/deletion (InDel) markers on chromosome 2 were used for fine mapping. The RAV6 375

gene was selected from an approximately 18-kb region as the candidate gene. To find out the 376

mutation site, we amplified the corresponding fragments from the Epi-rav6 mutant and 377

wild-type plants, respectively. Primers used in the map-based cloning are listed in 378

Supplemental Table S1. 379

380

RT-PCR and Real-Time PCR 381

Real-time PCR analysis was performed using the CFX96 Real-Time PCR System (Bio-Rad) 382

and SYBR Green I (S-7567; Invitrogen). PCR was performed using hot-start Taq DNA 383

polymerase (DR007B; Takara Bio Inc., http://www.takara-bio.com/). For each sample, 384

quantifications were made in triplicate. Melting curves were read at the end of each 385

amplification by steps of 0.3°C from 65°C to 95°C to ensure that the quantifications were 386

derived from real PCR products, and not primer dimers. The primers used for Fig. 5A are 387

listed in Supplemental Table S1. 388



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389

Bisulfite Sequencing 390

Genomic DNAs were isolated from 3-week-old rice seedlings or the leaf at tillering stage. 391

Bisulfite treatment of genomic DNA was conducted using the Methylation-Gold kit according 392

to the manufacturer’s instructions (ZYMO Research Corporation). Treated DNAs were then 393

used for PCR amplification using hot-start Taq DNA polymerase (DR007B; TaKaRa). PCR 394

conditions were as follows: 95°C, 5 min; 35 cycles of (95°C, 30 s; 50°C, 30 s; 72°C, 40 s); 72°C, 395

10 min. The PCR products were cloned into the pEASY-T1 cloning vector (TransGen Biotech 396

Co., Ltd.), and individual clones were sequenced. The analysis of sequencing data was 397

performed using KISMETH (Gruntman et al., 2008). The primers used for bisulfite sequencing 398

are listed in Supplemental Table S1. 399

400

5-Aza-2’Deoxycytidine Treatment 401

Rice seeds were soaked in water at 37°C for 16 h. The seeds were then immersed in 20 mM 402

Tris–HCl, pH 7.5, with or without 0.3 mM 5-aza-2’deoxycytidine (A3656, Sigma) at room 403

temperature for 48 hours in the dark. After washing, seeds were planted in soil. 7-day-old 404

seedlings were sampled for further analysis. 405

406

Phylogenetic Analysis and Alignment 407

Full-length protein sequences were used for phylogenetic analysis. The sequence of OsRAV6 408

was downloaded from TIGR, release 7 (http://rice.plantbiology.msu.edu/) and used to search 409

the proteome database of rice available at TIGR using BLAST. Alignments of protein 410

sequences were performed using MUSCLE (Edgar, 2004) with default parameters (gap 411

opening, -2.9; gap extension, 0; hydrophobicity multiplier, 1.2; max iteration, 8). The 412

maximum likelihood (ML) tree was constructed using MEGA6 (Tamura et al., 2013). 413

Forty-eight different amino acid substitution models were tested and the JTT+G+F model 414

(Jones et al., 1992) was considered as the best model with the lowest BIC (Bayesian 415

Information Criterion) scores. All sites of the alignment were used for model testing. The –Ln 416

likelihood was 10996.08. Nonparametric bootstrap analyses (Sanderson and Wojciechowski, 417

2000) consisted of 1000 replicates. All 4 known genome sequences of Oryza were collected, 418



22

including Oryza. sativa ssp. japonica cv. Nipponbare (Rice, 2005), O. sativa ssp. indica cv. 419

93-11 (Yu et al., 2002), O. sativa ssp. aus cv. Kasalath (Sakai et al., 2014), and O. 420

brachyantha (wild rice) (Chen et al., 2013). The genomic DNA sequence of the OsRAV6 gene 421

body and 230 bp upstream region was used as a query sequence, and homologous regions 422

were searched the in other 3 genomes of Oryza using FASTA (v36.3.5d) (Pearson and 423

Lipman, 1988). Multiple sequence alignment was performed using ClustalW (v2.1) (Larkin et 424

al., 2007; Thompson et al., 1994). 425

426

Propiconazole Treatment 427

In this study, propiconazole (Pcz), a brassinosteroid biosynthesis inhibitor (Hartwig et al., 2012) 428

was used to measure the mutants’ growth and morphological responses to BR by observing 429

inclination of lamina joints after exposure to Pcz. For Pcz treatment, the plants were grown in 430

the fields after incubating seeds for 3 days at 30°C to ensure synchronized germination. The 431

30-d-old seedlings were sprayed with 10 mM Pcz (Banner Maxx, Syngenta) every three days. 432

After 15 days, plants were transplanted into pots and photographed. Control plants were grown 433

and not treated with Pcz. 434

435

Supplemental Data 436

Supplemental Figure S1. The panicle and seeds of WT and Epi-rav6 (+/-) plants. 437

Supplemental Figure S2. The WT, Epi-rav6 (+/-), and hybrid F1 plants at the heading stage. 438

Supplemental Figure S3. Analyses of DNA methylation levels at RAV6 in WT and mutants 439

by bisulfite sequencing. 440

Supplemental Figure S4. Analyses of DNA methylation levels at RAV6 in WT, Epi-rav6 (-/-) 441

and four cultivated rice strains by bisulfite sequencing. 442

Supplemental Table S1. List of primers used in this paper. 443

444

ACKNOWLEDGEMENTS 445

This work was supported by the National Natural Science Foundation of China (grant nos. 446

31300987 to X. Song and 30900884 to X. Zhang); by Genetically Modified Breeding Major 447

Projects (grant no. 2014ZX08010-002 to X. Cao), the postdoctoral fellowship to (J. Sun) and the 448



23

State Key Laboratory of Plant Genomics (2014B0227-01；2015B0129-01). 449

450



24

Figure legends 451

Figure 1. Characterization of a semi-dominant rice mutant with larger leaf angle and smaller 452

seeds. A, The wild-type (WT), heterozygous Epi-rav6 (+/-) and homozygous Epi-rav6 (-/-) 453

plants at tilling stage. Bar = 20cm. B and C, Comparison of grain and seed width (B) and 454

length (C) between WT and Epi-rav6 (+/-). Bar = 1 cm. D, Characterization of seed weight, 455

seed length, seed width, and seed thickness in WT and the Epi-rav6 mutant. Values are means 456

± SD. In each graph, statistically significant differences are indicated by double asterisks 457

(**P<0.01). 458

459

Figure 2. Molecular cloning and expression analysis of RAV6. A, Map-based cloning of 460

RAV6. The RAV6 locus was mapped to the long arm of rice chromosome 2 between markers 461

RM3512 and RM318. The gene was further delimited to an 18-kb genomic region between the 462

markers ID8-26 and ID5-3 within the BAC clones AP004178 and AP004255. The number of 463

recombinants is marked corresponding to the molecular markers. This 18-kb interval contains 464

the candidate gene Os02g45850. Grey and black boxes indicate the untranslated regions and 465

the coding sequence, respectively. B and C, Expression analysis of RAV6 by RT-PCR (B) and 466

real-time RT-PCR (C) in WT, Epi-rav6 (+/-) and Epi-rav6 (-/-). OsEF1a was used as a control. 467

Values are means ±SD of three biological replicates. 468

469

Figure 3. Over-expression of RAV6 phenocopies the Epi-rav6 mutant phenotype. A, The 470

morphologies of WT, Epi-rav6 (+/-), and transgenic plants overexpressing (OV) RAV6 at 471

seedling stages. Bar = 1 cm. B, Relative expression analysis of RAV6 in WT, Epi-rav6 (+/-), 472

and the RAV6-overexpressing (OV) plants at seedling stage. C and D, The grain morphologies 473

of the transformed WT plants. OV-1, 2: transgenic plants overexpressing RAV6. Bars = 2 cm. 474

475

Figure 4. Evolutionary relationship between RAV6 and RAVL1 in rice. A, Phylogenetic 476

relationship of the RAV subfamily of B3 DNA binding domain-containing proteins in rice. 477

The bar indicates substitutions per site. B, Amino acid sequence alignment of rice RAV6 and 478

RAVL1. Identical and similar amino acids are boxed in black and grey, respectively. The 479



25

signature B3 binding domain is underlined. 480

481

Figure 5. RAV6 regulates leaf angle by controlling genes affecting BR homeostasis. A, 482

Real-time RT-PCR analyses of BRD1, D2, D11, and BRI1 in WT, Epi-rav6 (+/-), and 483

Epi-rav6 (-/-) plants. 25S rRNA was used as a control. Values are means ±SD of three 484

biological replicates. B, Lamina inclination of 45-day-old seedlings in WT, Epi-rav6 (+/-), 485

and Epi-rav6 (-/-) plants subjected to propiconazole (Pcz) treatment for 15 days. Bar = 20 cm. 486

487

Figure 6. DNA methylation analysis of the RAV6 locus. A, Schematic representation of RAV6 488

with putative MITE, MITE-adh-5-like DNA transposon. Boxes indicate exon (black), UTR 489

regions (white) and MITE (green). The red line shows the region used for analysis of DNA 490

methylation by bisulfite sequencing (B). B, DNA methylation status of bisulfite-sequenced 491

region (as indicated in A) in WT and Epi-rav6 (-/-) plants. Histograms represent the 492

percentage of CG (red), CNG (blue), and CHH (green). C, Real-time RT-PCR analyses of 493

RAV6 expression in 7-day-old seedlings treated with (+) or without (-) 5-aza-2’ deoxycytidine, 494

an inhibitor of DNA methylation. OsEF1a was used as a control. Values are means ±SD of 495

three biological replicates. 496

497

Figure 7. Genome sequence-, gene expression- and DNA methylation analysis of the RAV6 498

locus in different rice accessions. A, Comparative sequence analysis of the RAV6 locus in 4 499

assembled rice genomes. The synteny of the RAV6 locus in Nipponbare, 93-11, Kasalath, and 500

O. brachyantha is shown in the top panel. The bottom panel shows an alignment of the DNA 501

sequence 258-bp upstream and the 5’ gene body of RAV6 in four assembled rice genomes. 502

The MITE region and 5’ gene body are underlined by green and black lines, respectively. The 503

“*” indicates the cytosine region, whose degree of methylation was reduced in Epi-rav6 (-/-), 504

as shown in Figure 6B. B, Expression analysis of RAV6 by RT-PCR (top) and real-time 505

RT-PCR (bottom) in cultivated rice strains and Epi-rav6 (-/-). Zhonghua11, Nipponbare, 506

Kongyu131 and Koshihikari are japonica cultivars; Kasalath is an indica cultivar. OsEF1a 507

was used as a control. Values are means ± SD of three biological replicates. C, DNA 508

methylation status of the bisulfite-sequenced region (as indicated in Figure 6A) in WT 509



26

(Zhonghua11), Epi-rav6 (-/-) and four cultivated rice strains. Histograms represent the 510

percentage of methylation in the CG (red), CNG (blue), and CHH (green) contexts. 511

512



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http://www.ncbi.nlm.nih.gov/pubmed?term=%28The%5BTitle%5D%29 AND 1%5BVolume%5D AND is rescued by the endogenously accumulated alternative bioactive brassinosteroid%2C dolichosterone%2E Plant Cell 17%2C 2243%5BPagination%5D AND Hong%2C Z%2E%2C Ueguchi%2DTanaka%2C M%2E%2C Fujioka%2C S%2E%2C Takatsuto%2C S%2E%2C Yoshida%2C S%2E%2C Hasegawa%2C Y%2E%2C Ashikari%2C M%2E%2C Kitano%2C H%2E%2C and Matsuoka%2C M%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hong,&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant J%5BTitle%5D%29 AND 32%5BVolume%5D AND 495%5BPagination%5D AND Hong%2C Z%2E%2C Ueguchi%2DTanaka%2C M%2E%2C Shimizu%2DSato%2C S%2E%2C Inukai%2C Y%2E%2C Fujioka%2C S%2E%2C Shimada%2C Y%2E%2C Takatsuto%2C S%2E%2C Agetsuma%2C M%2E%2C Yoshida%2C S%2E%2C Watanabe%2C Y%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hong, Z., Ueguchi-Tanaka, M., Shimizu-Sato, S., Inukai, Y., Fujioka, S., Shimada, Y., Takatsuto, S., Agetsuma, M., Yoshida, S., Watanabe, Y., et al. (2002). Loss-of-function of a rice brassinosteroid biosynthetic enzyme, C-6 oxidase, prevents the organized arrangement and polar elongation of cells in the leaves and stem. Plant J 32, 495-508.


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http://scholar.google.com/scholar?as_q=Loss-of-function of a rice brassinosteroid biosynthetic enzyme, C-6 oxidase, prevents the organized arrangement and polar elongation of cells in the leaves and stem&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hong,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1



Hu, L., Li, N., Xu, C., Zhong, S., Lin, X., Yang, J., Zhou, T., Yuliang, A., Wu, Y., Chen, Y.R., et al. (2014). Mutation of a major CGmethylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl AcadSci U S A 111, 10642-10647.


Jacobsen, S.E., and Meyerowitz, E.M. (1997). Hypermethylated SUPERMAN epigenetic alleles in arabidopsis. Science 277, 1100-1103.


Je, B.I., Piao, H.L., Park, S.J., Park, S.H., Kim, C.M., Xuan, Y.H., Huang, J., Do Choi, Y., An, G., Wong, H.L., et al. (2010). RAV-Like1maintains brassinosteroid homeostasis via the coordinated activation of BRI1 and biosynthetic genes in rice. Plant Cell 22, 1777-1791.


Jiang, N., Feschotte, C., Zhang, X., and Wessler, S.R. (2004). Using rice to understand the origin and amplification of miniatureinverted repeat transposable elements (MITEs). Curr Opin Plant Biol 7, 115-119.


Johannes, F., Porcher, E., Teixeira, F.K., Saliba-Colombani, V., Simon, M., Agier, N., Bulski, A., Albuisson, J., Heredia, F., Audigier,P., et al. (2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5, e1000530.


Jones, D.T., Taylor, W.R., and Thornton, J.M. (1992). The rapid generation of mutation data matrices from protein sequences.Comput Appl Biosci 8, 275-282.


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Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez,R., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.


Law, J.A., and Jacobsen, S.E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. NatRev Genet 11, 204-220.


Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., and Jacobsen, S.E. (2001). Requirement ofCHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077-2080.


Manning, K., Tor, M., Poole, M., Hong, Y., Thompson, A.J., King, G.J., Giovannoni, J.J., and Seymour, G.B. (2006). A naturallyoccurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38, 948-952.


Martin, A., Troadec, C., Boualem, A., Rajab, M., Fernandez, R., Morin, H., Pitrat, M., Dogimont, C., and Bendahmane, A. (2009). Atransposon-induced epigenetic change leads to sex determination in melon. Nature 461, 1135-1138.


Miura, K., Agetsuma, M., Kitano, H., Yoshimura, A., Matsuoka, M., Jacobsen, S.E., and Ashikari, M. (2009). A metastable DWARF1epigenetic mutant affecting plant stature in rice. Proc Natl Acad Sci U S A 106, 11218-11223.


http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 15%5BVolume%5D AND 2900%5BPagination%5D AND Hong%2C Z%2E%2C Ueguchi%2DTanaka%2C M%2E%2C Umemura%2C K%2E%2C Uozu%2C S%2E%2C Fujioka%2C S%2E%2C Takatsuto%2C S%2E%2C Yoshida%2C S%2E%2C Ashikari%2C M%2E%2C Kitano%2C H%2E%2C and Matsuoka%2C M%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hong, Z., Ueguchi-Tanaka, M., Umemura, K., Uozu, S., Fujioka, S., Takatsuto, S., Yoshida, S., Ashikari, M., Kitano, H., and 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.


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http://scholar.google.com/scholar?as_q=A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hong,&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Proc Natl Acad Sci U S A%5BTitle%5D%29 AND 111%5BVolume%5D AND 10642%5BPagination%5D AND Hu%2C L%2E%2C Li%2C N%2E%2C Xu%2C C%2E%2C Zhong%2C S%2E%2C Lin%2C X%2E%2C Yang%2C J%2E%2C Zhou%2C T%2E%2C Yuliang%2C A%2E%2C Wu%2C Y%2E%2C Chen%2C Y%2ER%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hu, L., Li, N., Xu, C., Zhong, S., Lin, X., Yang, J., Zhou, T., Yuliang, A., Wu, Y., Chen, Y.R., et al. (2014). Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl Acad Sci U S A 111, 10642-10647.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hu,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hu,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Science%5BTitle%5D%29 AND 277%5BVolume%5D AND 1100%5BPagination%5D AND Jacobsen%2C S%2EE%2E%2C and Meyerowitz%2C E%2EM%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jacobsen, S.E., and Meyerowitz, E.M. (1997). Hypermethylated SUPERMAN epigenetic alleles in arabidopsis. Science 277, 1100-1103.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jacobsen,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Hypermethylated SUPERMAN epigenetic alleles in arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Hypermethylated SUPERMAN epigenetic alleles in arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jacobsen,&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 22%5BVolume%5D AND 1777%5BPagination%5D AND Je%2C B%2EI%2E%2C Piao%2C H%2EL%2E%2C Park%2C S%2EJ%2E%2C Park%2C S%2EH%2E%2C Kim%2C C%2EM%2E%2C Xuan%2C Y%2EH%2E%2C Huang%2C J%2E%2C Do Choi%2C Y%2E%2C An%2C G%2E%2C Wong%2C H%2EL%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Je, B.I., Piao, H.L., Park, S.J., Park, S.H., Kim, C.M., Xuan, Y.H., Huang, J., Do Choi, Y., An, G., Wong, H.L., et al. (2010). RAV-Like1 maintains brassinosteroid homeostasis via the coordinated activation of BRI1 and biosynthetic genes in rice. Plant Cell 22, 1777-1791.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Je,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=RAV-Like1 maintains brassinosteroid homeostasis via the coordinated activation of BRI1 and biosynthetic genes in rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=RAV-Like1 maintains brassinosteroid homeostasis via the coordinated activation of BRI1 and biosynthetic genes in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Je,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Curr Opin Plant Biol%5BTitle%5D%29 AND 7%5BVolume%5D AND 115%5BPagination%5D AND Jiang%2C N%2E%2C Feschotte%2C C%2E%2C Zhang%2C X%2E%2C and Wessler%2C S%2ER%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jiang, N., Feschotte, C., Zhang, X., and Wessler, S.R. (2004). Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs). Curr Opin Plant Biol 7, 115-119.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jiang,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs)&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs)&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jiang,&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28PLoS Genet%5BTitle%5D%29 AND 5%5BVolume%5D AND 1000530%5BPagination%5D AND Johannes%2C F%2E%2C Porcher%2C E%2E%2C Teixeira%2C F%2EK%2E%2C Saliba%2DColombani%2C V%2E%2C Simon%2C M%2E%2C Agier%2C N%2E%2C Bulski%2C A%2E%2C Albuisson%2C J%2E%2C Heredia%2C F%2E%2C Audigier%2C P%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Johannes, F., Porcher, E., Teixeira, F.K., Saliba-Colombani, V., Simon, M., Agier, N., Bulski, A., Albuisson, J., Heredia, F., Audigier, P., et al. (2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5, e1000530.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Johannes,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Assessing the impact of transgenerational epigenetic variation on complex traits&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Assessing the impact of transgenerational epigenetic variation on complex traits&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Johannes,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Comput Appl Biosci%5BTitle%5D%29 AND 8%5BVolume%5D AND 275%5BPagination%5D AND Jones%2C D%2ET%2E%2C Taylor%2C W%2ER%2E%2C and Thornton%2C J%2EM%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jones, D.T., Taylor, W.R., and Thornton, J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275-282.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jones,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The rapid generation of mutation data matrices from protein sequences&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The rapid generation of mutation data matrices from protein sequences&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jones,&as_ylo=1992&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell Physiol%5BTitle%5D%29 AND 43%5BVolume%5D AND 1106%5BPagination%5D AND Kakutani%2C T%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kakutani, T. (2002). Epi-alleles in plants: inheritance of epigenetic information over generations. Plant Cell Physiol 43, 1106-1111.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kakutani,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Epi-alleles in plants: inheritance of epigenetic information over generations&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Epi-alleles in plants: inheritance of epigenetic information over generations&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kakutani,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%280%2E Bioinformatics%5BTitle%5D%29 AND 23%5BVolume%5D AND 2947%5BPagination%5D AND Larkin%2C M%2EA%2E%2C Blackshields%2C G%2E%2C Brown%2C N%2EP%2E%2C Chenna%2C R%2E%2C McGettigan%2C P%2EA%2E%2C McWilliam%2C H%2E%2C Valentin%2C F%2E%2C Wallace%2C I%2EM%2E%2C Wilm%2C A%2E%2C Lopez%2C R%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Larkin,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Clustal W and Clustal X version 2&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Clustal W and Clustal X version 2&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Larkin,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Rev Genet%5BTitle%5D%29 AND 11%5BVolume%5D AND 204%5BPagination%5D AND Law%2C J%2EA%2E%2C and Jacobsen%2C S%2EE%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Law, J.A., and Jacobsen, S.E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11, 204-220.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Law,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Establishing, maintaining and modifying DNA methylation patterns in plants and animals&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Establishing, maintaining and modifying DNA methylation patterns in plants and animals&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Law,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Science%5BTitle%5D%29 AND 292%5BVolume%5D AND 2077%5BPagination%5D AND Lindroth%2C A%2EM%2E%2C Cao%2C X%2E%2C Jackson%2C J%2EP%2E%2C Zilberman%2C D%2E%2C McCallum%2C C%2EM%2E%2C Henikoff%2C S%2E%2C and Jacobsen%2C S%2EE%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., and Jacobsen, S.E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077-2080.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lindroth,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lindroth,&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Genet%5BTitle%5D%29 AND 38%5BVolume%5D AND 948%5BPagination%5D AND Manning%2C K%2E%2C Tor%2C M%2E%2C Poole%2C M%2E%2C Hong%2C Y%2E%2C Thompson%2C A%2EJ%2E%2C King%2C G%2EJ%2E%2C Giovannoni%2C J%2EJ%2E%2C and Seymour%2C G%2EB%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Manning, K., Tor, M., Poole, M., Hong, Y., Thompson, A.J., King, G.J., Giovannoni, J.J., and Seymour, G.B. (2006). A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38, 948-952.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Manning,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Manning,&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nature%5BTitle%5D%29 AND 461%5BVolume%5D AND 1135%5BPagination%5D AND Martin%2C A%2E%2C Troadec%2C C%2E%2C Boualem%2C A%2E%2C Rajab%2C M%2E%2C Fernandez%2C R%2E%2C Morin%2C H%2E%2C Pitrat%2C M%2E%2C Dogimont%2C C%2E%2C and Bendahmane%2C A%2E%5BAuthor%5D&dopt=abstract

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Saze, H., Mittelsten Scheid, O., and Paszkowski, J. (2003). Maintenance of CpG methylation is essential for epigenetic inheritanceduring plant gametogenesis. Nat Genet 34, 65-69.


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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Proc Natl Acad Sci U S A%5BTitle%5D%29 AND 106%5BVolume%5D AND 11218%5BPagination%5D AND Miura%2C K%2E%2C Agetsuma%2C M%2E%2C Kitano%2C H%2E%2C Yoshimura%2C A%2E%2C Matsuoka%2C M%2E%2C Jacobsen%2C S%2EE%2E%2C and Ashikari%2C M%2E%5BAuthor%5D&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Targeted%5BTitle%5D%29 AND 2%5BVolume%5D AND OsDRM2%2C impairs the growth of rice plants by abnormal DNA methylation%2E Plant J 71%2C 85%5BPagination%5D AND Moritoh%2C S%2E%2C Eun%2C C%2EH%2E%2C Ono%2C A%2E%2C Asao%2C H%2E%2C Okano%2C Y%2E%2C Yamaguchi%2C K%2E%2C Shimatani%2C Z%2E%2C Koizumi%2C A%2E%2C and Terada%2C R%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ouyang,&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Proc Natl Acad Sci U S A%5BTitle%5D%29 AND 85%5BVolume%5D AND 2444%5BPagination%5D AND Pearson%2C W%2ER%2E%2C and Lipman%2C D%2EJ%2E%5BAuthor%5D&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nature%5BTitle%5D%29 AND 436%5BVolume%5D AND 793%5BPagination%5D AND Rice%2C S%2EP%2EI%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28DNA Res%5BTitle%5D%29 AND 21%5BVolume%5D AND 397%5BPagination%5D AND Sakai%2C H%2E%2C Kanamori%2C H%2E%2C Arai%2DKichise%2C Y%2E%2C Shibata%2DHatta%2C M%2E%2C Ebana%2C K%2E%2C Oono%2C Y%2E%2C Kurita%2C K%2E%2C Fujisawa%2C H%2E%2C Katagiri%2C S%2E%2C Mukai%2C Y%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sakai,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Biotechnol%5BTitle%5D%29 AND 24%5BVolume%5D AND 105%5BPagination%5D AND Sakamoto%2C T%2E%2C Morinaka%2C Y%2E%2C Ohnishi%2C T%2E%2C Sunohara%2C H%2E%2C Fujioka%2C S%2E%2C Ueguchi%2DTanaka%2C M%2E%2C Mizutani%2C M%2E%2C Sakata%2C K%2E%2C Takatsuto%2C S%2E%2C Yoshida%2C S%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sakamoto,&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Syst Biol%5BTitle%5D%29 AND 49%5BVolume%5D AND 671%5BPagination%5D AND Sanderson%2C M%2EJ%2E%2C and Wojciechowski%2C M%2EF%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae)&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sanderson,&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Genet%5BTitle%5D%29 AND 34%5BVolume%5D AND 65%5BPagination%5D AND Saze%2C H%2E%2C Mittelsten Scheid%2C O%2E%2C and Paszkowski%2C J%2E%5BAuthor%5D&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Erect leaves and photosynthesis in rice%2E%5BTitle%5D%29 AND Sinclair%2C T%2ER%2E%2C and Sheehy%2C J%2EE%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Roles of DCL4 and DCL3b in rice phased small RNA biogenesis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Roles of DCL4 and DCL3b in rice phased small RNA biogenesis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Song,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Mol Cell%5BTitle%5D%29 AND 6%5BVolume%5D AND 791%5BPagination%5D AND Soppe%2C W%2EJ%2E%2C Jacobsen%2C S%2EE%2E%2C Alonso%2DBlanco%2C C%2E%2C Jackson%2C J%2EP%2E%2C Kakutani%2C T%2E%2C Koornneef%2C M%2E%2C and Peeters%2C A%2EJ%2E%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Soppe,&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

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Vongs, A., Kakutani, T., Martienssen, R.A., and Richards, E.J. (1993). Arabidopsis thaliana DNA methylation mutants. Science 260,1926-1928.


Wei, L., Gu, L., Song, X., Cui, X., Lu, Z., Zhou, M., Wang, L., Hu, F., Zhai, J., Meyers, B.C., et al. (2014). Dicer-like 3 producestransposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A 111, 3877-3882.


Xu, X., Liu, X., Ge, S., Jensen, J.D., Hu, F., Li, X., Dong, Y., Gutenkunst, R.N., Fang, L., Huang, L., et al. (2012). Resequencing 50accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30, 105-111.


Yamamuro, C., Ihara, Y., Wu, X., Noguchi, T., Fujioka, S., Takatsuto, S., Ashikari, M., Kitano, H., and Matsuoka, M. (2000). Loss offunction of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell12, 1591-1606.


Yamauchi, T., Johzuka-Hisatomi, Y., Terada, R., Nakamura, I., and Iida, S. (2014). The MET1b gene encoding a maintenance DNAmethyltransferase is indispensable for normal development in rice. Plant Mol Biol 85, 219-232.


Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. (2002). A draft sequence of the ricegenome (Oryza sativa L. ssp. indica). Science 296, 79-92.


Zhang, C., Bai, M.Y., and Chong, K. (2014). Brassinosteroid-mediated regulation of agronomic traits in rice. Plant Cell Rep 33, 683-696.


Zhang, L., Cheng, Z., Qin, R., Qiu, Y., Wang, J.L., Cui, X., Gu, L., Zhang, X., Guo, X., Wang, D., et al. (2012). Identification andcharacterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Plant Cell 24, 4407-4421.

Pubmed: Author and TitleCrossRef: Author and Title


http://www.ncbi.nlm.nih.gov/pubmed?term=%280%2E Mol Biol Evol%5BTitle%5D%29 AND 30%5BVolume%5D AND 2725%5BPagination%5D AND Tamura%2C K%2E%2C Stecher%2C G%2E%2C Peterson%2C D%2E%2C Filipski%2C A%2E%2C and Kumar%2C S%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30, 2725-2729.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tamura,&hl=en&c2coff=1

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http://scholar.google.com/scholar?as_q=MEGA6: Molecular Evolutionary Genetics Analysis version 6&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tamura,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28A%5BTitle%5D%29 AND 11%5BVolume%5D AND with reduced seed length%2E Plant Cell 17%2C 776%5BPagination%5D AND Tanabe%2C S%2E%2C Ashikari%2C M%2E%2C Fujioka%2C S%2E%2C Takatsuto%2C S%2E%2C Yoshida%2C S%2E%2C Yano%2C M%2E%2C Yoshimura%2C A%2E%2C Kitano%2C H%2E%2C Matsuoka%2C M%2E%2C Fujisawa%2C Y%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=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.

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http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tanabe,&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28BRASSINOSTEROID%5BTitle%5D%29 AND 1%5BVolume%5D AND Tanaka%2C A%2E%2C Nakagawa%2C H%2E%2C Tomita%2C C%2E%2C Shimatani%2C Z%2E%2C Ohtake%2C M%2E%2C Nomura%2C T%2E%2C Jiang%2C C%2EJ%2E%2C Dubouzet%2C J%2EG%2E%2C Kikuchi%2C S%2E%2C Sekimoto%2C H%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tanaka, A., Nakagawa, H., Tomita, C., Shimatani, Z., Ohtake, M., Nomura, T., Jiang, C.J., Dubouzet, J.G., Kikuchi, S., Sekimoto, H., et al. (2009). BRASSINOSTEROID UPREGULATED1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice. Plant Physiol 151, 669-680.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tanaka,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tanaka,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nucleic Acids Res%5BTitle%5D%29 AND 22%5BVolume%5D AND 4673%5BPagination%5D AND Thompson%2C J%2ED%2E%2C Higgins%2C D%2EG%2E%2C and Gibson%2C T%2EJ%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Thompson,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Thompson,&as_ylo=1994&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28J Genet Genomics%5BTitle%5D%29 AND 39%5BVolume%5D AND 3%5BPagination%5D AND Tong%2C H%2E%2C and Chu%2C C%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tong, H., and Chu, C. (2012). Brassinosteroid signaling and application in rice. J Genet Genomics 39, 3-9.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tong,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Brassinosteroid signaling and application in rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Brassinosteroid signaling and application in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tong,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Science%5BTitle%5D%29 AND 260%5BVolume%5D AND 1926%5BPagination%5D AND Vongs%2C A%2E%2C Kakutani%2C T%2E%2C Martienssen%2C R%2EA%2E%2C and Richards%2C E%2EJ%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Vongs, A., Kakutani, T., Martienssen, R.A., and Richards, E.J. (1993). Arabidopsis thaliana DNA methylation mutants. Science 260, 1926-1928.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vongs,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis thaliana DNA methylation mutants&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis thaliana DNA methylation mutants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vongs,&as_ylo=1993&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Proc Natl Acad Sci U S A%5BTitle%5D%29 AND 111%5BVolume%5D AND 3877%5BPagination%5D AND Wei%2C L%2E%2C Gu%2C L%2E%2C Song%2C X%2E%2C Cui%2C X%2E%2C Lu%2C Z%2E%2C Zhou%2C M%2E%2C Wang%2C L%2E%2C Hu%2C F%2E%2C Zhai%2C J%2E%2C Meyers%2C B%2EC%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wei, L., Gu, L., Song, X., Cui, X., Lu, Z., Zhou, M., Wang, L., Hu, F., Zhai, J., Meyers, B.C., et al. (2014). Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A 111, 3877-3882.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wei,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wei,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Biotechnol%5BTitle%5D%29 AND 30%5BVolume%5D AND 105%5BPagination%5D AND Xu%2C X%2E%2C Liu%2C X%2E%2C Ge%2C S%2E%2C Jensen%2C J%2ED%2E%2C Hu%2C F%2E%2C Li%2C X%2E%2C Dong%2C Y%2E%2C Gutenkunst%2C R%2EN%2E%2C Fang%2C L%2E%2C Huang%2C L%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Xu, X., Liu, X., Ge, S., Jensen, J.D., Hu, F., Li, X., Dong, Y., Gutenkunst, R.N., Fang, L., Huang, L., et al. (2012). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30, 105-111.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xu,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Xu,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 12%5BVolume%5D AND 1591%5BPagination%5D AND Yamamuro%2C C%2E%2C Ihara%2C Y%2E%2C Wu%2C X%2E%2C Noguchi%2C T%2E%2C Fujioka%2C S%2E%2C Takatsuto%2C S%2E%2C Ashikari%2C M%2E%2C Kitano%2C H%2E%2C and Matsuoka%2C M%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yamamuro, C., Ihara, Y., Wu, X., Noguchi, T., Fujioka, S., Takatsuto, S., Ashikari, M., Kitano, H., and 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.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yamamuro,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yamamuro,&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Mol Biol%5BTitle%5D%29 AND 85%5BVolume%5D AND 219%5BPagination%5D AND Yamauchi%2C T%2E%2C Johzuka%2DHisatomi%2C Y%2E%2C Terada%2C R%2E%2C Nakamura%2C I%2E%2C and Iida%2C S%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yamauchi, T., Johzuka-Hisatomi, Y., Terada, R., Nakamura, I., and Iida, S. (2014). The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice. Plant Mol Biol 85, 219-232.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yamauchi,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yamauchi,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28ssp%2E indica%2E Science%5BTitle%5D%29 AND 296%5BVolume%5D AND 79%5BPagination%5D AND Yu%2C J%2E%2C Hu%2C S%2E%2C Wang%2C J%2E%2C Wong%2C G%2EK%2E%2C Li%2C S%2E%2C Liu%2C B%2E%2C Deng%2C Y%2E%2C Dai%2C L%2E%2C Zhou%2C Y%2E%2C Zhang%2C X%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yu,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A draft sequence of the rice genome (Oryza sativa L&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A draft sequence of the rice genome (Oryza sativa L&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yu,&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell Rep%5BTitle%5D%29 AND 33%5BVolume%5D AND 683%5BPagination%5D AND Zhang%2C C%2E%2C Bai%2C M%2EY%2E%2C and Chong%2C K%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang, C., Bai, M.Y., and Chong, K. (2014). Brassinosteroid-mediated regulation of agronomic traits in rice. Plant Cell Rep 33, 683-696.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhang,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Brassinosteroid-mediated regulation of agronomic traits in rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Brassinosteroid-mediated regulation of agronomic traits in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 24%5BVolume%5D AND 4407%5BPagination%5D AND Zhang%2C L%2E%2C Cheng%2C Z%2E%2C Qin%2C R%2E%2C Qiu%2C Y%2E%2C Wang%2C J%2EL%2E%2C Cui%2C X%2E%2C Gu%2C L%2E%2C Zhang%2C X%2E%2C Guo%2C X%2E%2C Wang%2C D%2E%2C et al%2E%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang, L., Cheng, Z., Qin, R., Qiu, Y., Wang, J.L., Cui, X., Gu, L., Zhang, X., Guo, X., Wang, D., et al. (2012). Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Plant Cell 24, 4407-4421.


Google Scholar: Author Only Title Only Author and Title


http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhang,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1


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