1 Running Head - Plant Physiology3 44 ABSTRACT 45 46 In rice (Oryza sativa L.), hybrids between indica and japonica subspecies are usually 47 highly sterile, which provides a model

1

Running Head: 1

Transcriptomic basis of a rice reproductive barrier 2

3

Corresponding Author: 4

Qifa Zhang 5

National Key Laboratory of Crop Genetic Improvement and National Center of Plant 6

Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 7

Phone: 86-27-87282429 8

Fax: 86-27-87287092 9

E-mail: [email protected] 10

11

Research Area: 12

Genes, Development and Evolution 13

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Plant Physiology Preview. Published on May 8, 2017, as DOI:10.1104/pp.17.00093

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Title of article: 15

Reproductive barriers in indica-japonica rice hybrids are uncovered by transcriptome 16

analysis 17

All authors’ full names: 18

Yanfen Zhu, Yiming Yu, Ke Cheng, Yidan Ouyang, Jia Wang, Liang Gong, Qinghua 19

Zhang, Xianghua Li, Jinghua Xiao and Qifa Zhang* 20

*For correspondence (Fax: 86-27-87287092; Phone: 86-27-87282429; e-mail: 21

[email protected]) 22

23

Author contributions: 24

Y.Z. and Qifa Zhang designed the research; Y.Z., Y.Y., K.C., Y.O., J.W., L.G. and 25

Qinghua Zhang performed the research; X.L. and J.X. contributed reagents; Y.Z. and 26

Qifa Zhang analyzed data and wrote the paper. 27

The authors declare no conflict of interests. 28

29

Affiliations: 30

National Key Laboratory of Crop Genetic Improvement and National Center of Plant 31

Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 32

33

One Sentence Summary: 34

A reproductive barrier causes female gamete abortion of indica-japonica rice hybrids 35

by damaging cell wall integrity inducing massive biotic and abiotic stresses resulting 36

in ER stress leading to premature PCD. 37

38

Footnotes: 39

Financial source: This work was supported by grants from the National Key Research 40

and Development Program (2016YFD0100903) and National Natural Science 41

Foundation (31130032) of China. 42

43



3

ABSTRACT 44

45

In rice (Oryza sativa L.), hybrids between indica and japonica subspecies are usually 46

highly sterile, which provides a model system for studying postzygotic reproductive 47

isolation. A killer-protector system S5 composed of three adjacent genes, ORF3, 48

ORF4 and ORF5, regulates female gamete fertility of indica-japonica hybrids. To 49

characterize the processes underlying this system, we performed transcriptomic 50

analyses of pistils from rice variety Balilla (BL), Balilla with transformed ORF5+ 51

(BL5+) producing sterile female gametes, and Balilla with transformed ORF3+ and 52

ORF5+ (BL3+5+) producing fertile gametes. RNA sequencing of tissues collected 53

before (MMC), during (MEI), and after (AME) meiosis of the megaspore mother cell 54

detected 19,269 to 20,928 genes as expressed. Comparison between BL5+ and BL 55

showed that ORF5+ induced differential expression of 8,339, 6,278 and 530 genes at 56

MMC, MEI, and AME. At MMC, large-scale differential expression of cell wall 57

modifying genes and biotic and abiotic response genes indicated that cell wall 58

integrity damage induced severe biotic and abiotic stresses. The processes continued 59

to MEI and induced ER stress as indicated by differential expression of ER stress 60

responsive genes, leading to PCD at MEI and AME, resulting in abortive female 61

gametes. In the BL3+5+/BL comparison, 3,986, 749 and 370 genes were 62

differentially expressed at MMC, MEI and AME. Large numbers of cell wall 63

modification and biotic and abiotic response genes were also induced at MMC but 64

largely suppressed at MEI without inducing ER stress and PCD, producing fertile 65

gametes. These results have general implications for the understanding of biological 66

processes underlying reproductive barriers. 67

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4

INTRODUCTION 69

Reproductive isolation, a phenomenon widely existing in natural organisms, 70

promotes speciation and maintains the integrity of species over time (Coyne and Orr, 71

2004). It is divided into two general categories depending on whether it occurs before 72

or after fertilization: prezygotic reproductive isolation and postzygotic reproductive 73

isolation (Seehausen et al., 2014). The former prevents the formation of hybrid 74

zygotes, while the latter results in hybrid incompatibility including hybrid necrosis, 75

weakness, sterility, and lethality in F1 or later generations (Ouyang and Zhang, 2013). 76

The Dobzhansky-Muller model suggests that hybrid incompatibility is caused by the 77

negative interactions between functionally divergent genes in the parental species 78

(Dobzhansky, 1937; Muller, 1942). 79

Rice, a major food crop and model plant for genomic study of monocotyledon 80

species, also provides a model system for studying reproductive isolation. The Asian 81

cultivated rice is composed of two subspecies, indica and japonica. Their hybrids are 82

usually highly sterile, which is a barrier for utilization of the strong vigor in 83

indica-japonica hybrids. A number of loci responsible for hybrid sterility have been 84

identified, including ones that cause embryo-sac sterility, pollen sterility and spikelet 85

sterility (Ouyang et al., 2009). So far, six loci responsible for hybrid incompatibility 86

have been cloned. Among them, DPL1/DPL2 (Mizuta et al., 2010), S27/S28 87

(Yamagata et al., 2010) and Sa (Long et al., 2008) are responsible for pollen fertility, 88

while hsa1 (Kubo et al., 2016), S7 (Yu et al., 2016), and S5 (Chen et al., 2008; Yang et 89

al., 2012) control female fertility, all of them cause spikelet sterility. Three 90

evolutionary genetic models have been proposed to summarize the findings: parallel 91

divergence model, sequential divergence model and parallel-sequential divergence 92

model (Ouyang and Zhang, 2013). DPL1/DPL2 and S27/S28 in rice, HPA1/HPA2 in 93

Arabidopsis, and JYAlpha in Drosophila conform to the parallel divergence model. Sa, 94

hsa1 and many loci in other species can be explained by the sequential divergence 95

model. However, S5 in rice is the only case identified so far to follow the 96

parallel-sequential divergence model. 97

S5 is a major locus controlling indica-japonica hybrid sterility identified in many 98



5

studies (Ikehashi and Araki, 1986; Liu et al., 1992; Liu et al., 1997; Wang et al., 1998; 99

Qiu et al., 2005; Song et al., 2005; Wang et al., 2005; Chen et al., 2008), and is also 100

associated with the divergence and domestication of rice (Du et al., 2011; Ouyang et 101

al., 2016). In a typical indica-japonica hybrid, the preferential abortion of female 102

gametes with japonica allele is regulated cooperatively by three adjacent genes, ORF3, 103

ORF4, and ORF5 at the S5 locus (Yang et al., 2012). Typical japonica and indica 104

varieties carry ORF3-ORF4+ORF5- and ORF3+ORF4-ORF5+, respectively, where 105

the functional allele of each gene is indicated with “+” while the non-functional allele 106

as “-”. ORF5 encodes an aspartic protease with cell wall localization. The indica 107

allele ORF5+ differs from the japonica allele ORF5- by two nucleotides, both of 108

which cause amino acid changes (Chen et al., 2008). The japonica allele ORF4+ 109

encodes an unknown transmembrane protein while the indica allele ORF4- has an 110

11-bp deletion resulting in an endoplasmic reticulum (ER)-localization. ORF3 is 111

predicted to encode a heat shock protein (HSP) resident in ER functioning to resolve 112

ER stress. The japonica allele ORF3- has a frameshift in the C terminus relative to the 113

indica ORF3+ due to a 13-bp deletion. In this system, extracellular ORF5+ 114

presumably catalyzes its substrate producing a substance that is sensed by the 115

transmembrane protein ORF4+, which induces ER stress and subsequently leading to 116

premature programed cell death (PCD). It is speculated that ORF3+, but not ORF3-, 117

can prevent/resolve the ER stress caused by ORF5+/ORF4+. Based on the results of 118

genetic and cytological analyses, Yang et al (2012) proposed a killer-protector model 119

for the roles of these three genes in this system: ORF5+, together with ORF4+, kills 120

the gametes by inducing ER stress that causes premature PCD. ORF3+ protects the 121

gametes from being killed thus restores the hybrids fertility by preventing/resolving 122

ER stress. 123

In recent years, transcriptomic analysis based on RNA-sequencing technology 124

has become a powerful tool to characterize regulatory networks and pathways to 125

enhance understanding of biological processes (Vogel et al., 2005; Digel et al., 2015; 126

Groszmann et al., 2015; Coolen et al., 2016). In this study, we performed a 127

comparative transcriptomic analysis of pistils from Balilla (a typical japonica variety), 128



6

BalillaORF5+ (Balilla with a transformed ORF5+) and BalillaORF3+ORF5+ 129

(Balilla with transformed ORF3+ and ORF5+) before, during, and after the 130

megaspore meiosis. The comparisons detected thousands of genes that were 131

differentially regulated in these three genotypes at various stages. Functional 132

classification of the differentially regulated genes identified major patterns of 133

differential expression, which suggested the biological processes underlying the 134

killer-protector system of the S5 locus. These results provide insights into the 135

functional roles of ORF3+, ORF4+ and ORF5+ genes as well as the cellular and 136

biochemical nature of their interactions in regulating indica-japonica hybrid sterility. 137

138

139



7

RESULTS 140

Ovule abortion process of BL5+ 141

Previous study (Yang et al., 2012) showed that the S5 reproductive barrier is 142

composed of three tightly-linked genes, ORF3, ORF4 and ORF5, in which ORF5+ 143

and ORF4+ together function as the killer of the female gametes and ORF3+ protects 144

the gametes from killing. A typical indica variety has the haplotype of ORF3+, 145

ORF4-, ORF5+ and japonica variety is of ORF3-, ORF4+, ORF5-. Balilla 146

(abbreviated BL) is a typical japonica variety. Transgenic plants BalillaORF5+ 147

(abbreviated BL5+) carrying a transformed ORF5+ under its native promoter showed 148

extremely low spikelet fertility (6.50%) compared with wild type BL (75.52%). In 149

contrast, BalillaORF3+ORF5+ (abbreviated BL3+5+), carrying both transformed 150

ORF5+ and transformed ORF3+ (also under its native promoter), had normal spikelet 151

fertility (77.35%) due to the protective role of ORF3+ (Supplemental Fig. S1A-C). 152

Paraffin section results showed that the ovule development process in both BL and 153

BL3+5+ was normal. In brief, the archesporial cell enlarged initially and developed 154

into a megaspore mother cell (Fig. 1A, K). The megaspore mother cell then 155

underwent meiotic division forming four megaspores in a line (Fig. 1B, C, L, and M). 156

The three megaspores near the micropyle degenerated, while the megaspore nearest 157

the chalaza enlarged and developed into a functional megaspore (FM) (Fig. 1D, N). 158

The FM underwent three rounds of mitotic division to produce an eight-nucleate 159

embryo-sac (Fig. 1E, O). In the aborted ovule of BL5+, the megaspore mother cell, 160

dyad and tetrad could be produced as in BL (Fig. 1F-H). However, the nucellus cells 161

showed vacuolization and even degeneration at the meiosis stage (Fig. 1G-H). After 162

meiosis, morphological abnormalities of both nucellus cells and FM were observed 163

(Fig. 1I). The abnormal FM did not enlarge and failed to develop into a mature 164

embryo-sac. The aborted embryo-sac accumulated unknown substances that were 165

deeply stained (Fig. 1J). Thus, the megaspore meiosis process in BL5+ was normal 166

but the nucellus cells around the megaspores showed serious defects at the megaspore 167

meiosis stage. The nucellus cells degradation and FM abortion caused the sterility of 168

BL5+. 169



8

ORF5 and ORF4 were neighboring genes overlapping in their promoter region 170

(Yang et al., 2012). This kind of gene pairs are frequently co-expressed (Wang et al., 171

2009; Kourmpetli et al., 2013). ORF5 and ORF4 had similar expression profile and 172

relative high expression in reproductive organs (Yang et al., 2012). The in situ 173

hybridization showed that ORF5+ had localized expression in developing ovules 174

(Chen et al., 2008). Similarly, ORF4+ also displayed high and specific expression in 175

ovule tissues (Supplemental Fig. S2G-K). The specific expression of ORF5+ and 176

ORF4+ in ovules was in accordance with the specific abortion of ovules in BL5+. 177

However, the protector ORF3+ showed a wide range of expression in many tissues 178

including ovules, indicating its possible function in many processes (Supplemental 179

Fig. S2A-F). 180

Based on the ovule development process, we divided the ovule abortion process 181

into three stages (Fig. 1). The first was the megaspore mother cell (MMC) stage when 182

the ovule had megasporocyte and no obvious abnormalities were observed in BL5+. 183



9

The second was the meiosis (MEI) stage when meiosis was in progress and the 184

nucellus cells of BL5+ were vacuolated. The third was after meiosis (AME) when 185

some unknown substances accumulated in embryo-sac (Fig. 1). 186

187

Processes underlying gamete abortion in BL5+ 188

We collected the pistils of wild type BL, sterile BL5+ and fertility-restored 189

BL3+5+ at MMC, MEI and AME, and performed transcriptomic analysis. A data 190

matrix of three stages from three genotypes was generated. Totally 19,269 to 20,928 191

genes were detected as expressed in these tissues at different stages representing 192

34.53% to 37.50% of total annotated genes of the Nipponbare reference genome 193

(Supplemental Table S1) (Kawahara et al., 2013). A total of 8,339, 6,278 and 530 194

genes were differentially expressed in BL5+ compared with BL at MMC, MEI and 195

AME, respectively, including 4,234, 2,430 and 410 genes that were up-regulated at 196

the three stages and 4,105, 3,848 and 120 genes that were down-regulated 197

(Supplemental Table S2; Supplemental Dataset 1). Among the differentially expressed 198

genes (DEGs), 2,067 were up-regulated and 3,325 were down-regulated at both MMC 199

and MEI (Fig. 2A). These 5,392 common DEGs accounted for 64.66% and 85.89% of 200

total DEGs at MMC and MEI, respectively, indicating that MMC and MEI involved 201

substantially overlapping cellular and molecular responses. 202

An overview of the differentially induced processes in BL5+ revealed by the 203

transcriptomes. We performed MapMan and Gene Ontology (GO) enrichment 204

analyses to classify the DEGs. MapMan is an effective tool to analyze metabolic 205

pathways and other biological processes of the transcriptome systematically (Thimm 206

et al., 2004; Ramsak et al., 2014). To get a global view of the 8,339 DEGs in BL5+ at 207

MMC, we used the “Metabolism overview” and “Cellular response” of MapMan to 208

outline the transcriptional changes of genes with putative functions in metabolism and 209

cellular response (Fig. 2B-C). 210

In “Metabolism overview”, primary metabolic processes, including cell wall (354 211

genes), amino acid (226 genes), lipids (316 genes), nucleotide (81 genes) and major 212

carbohydrate (128 genes) metabolism, accounted for 13.25% of total DEGs. The cell 213



10

wall localization of ORF5+, which was previously hypothesized to initiate the 214

premature PCD (Yang et al., 2012), led us to focus our attention to the cell wall 215

metabolic genes. We found that 187 (128 up-regulated and 59 down-regulated) of the 216

354 genes were involved in cell wall degradation and modification, which may affect 217

the cell wall structures in one way or another. The secondary metabolism processes 218

including terpenes (64 genes), flavonoids (105 genes), and phenylpropanoids (120 219

genes) metabolism, which are important in plant stress response (Dixon and Paiva, 220

1995; Winkelshirley, 2002; Tholl, 2006), constituted 3.47% of all DEGs. In the term 221



11

of “Cellular response”, 8.65% (721 genes) of DEGs were responsive to biotic and 222

abiotic stress; 1.94% (162 genes) of DEGs were related to redox, a phenomenon 223

usually triggered by stress; 6.67% (667 genes) of DEGs functioned in developmental 224

processes. 225

GO analysis for up-regulated genes revealed that three GO terms related to cell 226

wall metabolism, seven GO terms involved in stress or stimulus response, and eleven 227

GO terms associated with gene expression, protein synthesis and translation were 228

significantly enriched (FDR < 0.005) (Fig. 3). 229

The change in cell wall structure by cell wall modification genes may cause cell 230

wall integrity damage, which was similar to the situation of pathogen or pest attack. 231

We thus explored the “Biotic stress” in BL5+ at MMC and found that DEGs in 232

various functional categories of biotic stress were enriched including R genes, 233

pathogen-related proteins, signaling, hormone signaling, proteolysis, ROS-regulation 234

and biotic stress-responsive transcription factors (Supplemental Fig. S3A). 235

Thus, both of the MapMan and GO results indicated that a severe stress response 236

including both biotic and abiotic stresses were induced in BL5+ at MMC, which may 237

be caused by the damage in cell wall integrity, even though no abnormalities were 238

observed at this stage (Fig. 1F). 239

At MEI, 163 of the 300 DEGs in “cell wall” were related to the cell wall 240

degradation and modification including 102 up-regulated and 61 down-regulated ones 241

(Fig. 2B-C). Cell wall-related GO terms such as “glucan metabolic process”, 242

“polysaccharide metabolic process” and “polysaccharide biosynthetic process” were 243

enriched (Fig. 3). The continuous up-regulation of cell wall degrading and modifying 244

genes at MMC and MEI might be related to the observed cell wall abnormalities such 245

as vacuolization and degradation at MEI (Fig. 1G-H). In addition, 599 DEGs (9.54% 246

of total DEGs) in “biotic stress” and “abiotic stress” and genes in various functional 247

categories of biotic stress were identified (Fig. 2B, Supplemental Fig. S3B), 248

suggesting that the stress response also continued at MEI. 249

By the AME stage, DEG numbers in all the metabolic processes and cellular 250

responses were largely reduced compared to those at MMC and MEI (Fig. 2B). The 251



12

ovule had aborted with the accumulation of unknown substances. In contrast, however, 252

a GO term “cellulose biosynthetic process” was significantly enriched (Fig. 3), 253

indicating misregulation of cellulose biosynthesis in BL5+. 254



13

Large-scale transcriptional changes of cell wall modifying and degrading 255

genes in BL5+ at MMC and MEI. The MapMan and GO results showed that cell 256

wall metabolism especially cell wall modification and degradation were active in 257

BL5+ (Fig. 2). Cell wall modifying and degrading genes, also called cell wall 258

remodeling genes, affect cell growth by changing the extensibility and 259

physiochemical properties of the cell wall (Cosgrove, 1999; Yu et al., 2011; Gou et al., 260

2012; Hepler et al., 2013; Xiao et al., 2014). We analyzed the expression of genes 261

from seven main enriched families: expansins (EXPs), xyloglucan 262

endotransglucosylase/hydrolases (XTHs), pectin methyl esterases (PMEs), pectin 263

acetylesterases (PAEs), polygalacturonases (PGases), glycoside hydrolase family 9 264

(GH9) and arabinogalactan proteins (AGPs), which affect cell wall structure and 265

extension by enzymatic or non-enzymatic ways (Bosch et al., 2005; Coimbra et al., 266

2008; Maris et al., 2009; Gou et al., 2012; Che et al., 2016). We found that 95, 85 and 267

23 genes from these families were differentially expressed at MMC, MEI, and AME, 268

respectively, of which 73 genes were differentially expressed at both MMC and MEI, 269

including 59 up-regulated and 14 down-regulated (Fig. 4A-B). The 59 up-regulated 270

genes consisted of 13 EXPs, 7 XTHs, 5 PMEs, 4 PAEs, 8 PGases, 7 GH9s and 15 271

AGPs. OsEXP4 was elevated in BL5+ at MMC and MEI. In rice, overexpression of 272

OsEXP4 results in increased cell length, while repression of OsEXP4 reduces cell 273

length (Choi et al., 2003). Three up-regulated XTHs (Os06g48160, Os03g01800 and 274

Os10g39840) have been characterized to utilize xyloglucan, one of the cell wall 275

components, as substrate (Hara et al., 2014). OsGLU1, a GH9 member, which 276

regulates cell elongation in rice (Zhou et al., 2006; Zhang et al., 2012), was found 277

up-regulated as well. The up-regulation of genes involved in cell wall degradation and 278

cell size regulation was in accordance with cell wall abnormalities in BL5+ (Fig. 279

1G-H). Thus, we inferred that the up-regulation of the cell wall remodeling genes 280

induced by ORF5+ in BL5+ led to cell structure change, damaging the cell wall 281

integrity. 282

Cellulose deposition in BL5+. In BL5+, unknown substances were accumulated 283

in the aborted ovule at AME (Fig. 1I-J). The enrichment of GO term “cellulose 284



14

biosynthetic process” suggested a misregulation of cellulose biosynthesis and that the 285

deposited substances in the aborted ovule might over-accumulate cellulose. To 286

validate this, we used Pontamine fast scarlet 4B (S4B) and calcofluor white to stain 287

cellulose (Anderson et al., 2010; Thomas et al., 2012), and observed strong 288

fluorescence signals in BL5+ at the site where the substances accumulated, indicating 289

that cellulose was indeed in large quantity (Fig. 5B, E), which was also supported by 290

the much higher cellulose content in panicles of BL5+ than in BL (Fig. 5G). In 291

contrast, normal mature embryo-sac structures were easily identified in the ovule of 292

BL and BL3+5+, where low fluorescence intensity was detected (Fig. 5A, C, D, and 293

F). 294

Cellulose is a major cell wall polysaccharide composed of unbranched β-1, 295

4-linked glucan chains. In rice, OsMYB46 and OsSWNs are secondary cell wall 296



15

biosynthetic regulators. OsSWN1 acts on the upstream of OsMYB46 by binding to the 297

SNBE element in its promoter region. Overexpression of OsSWN1 or OsMYB46 in 298

Arabidopsis results in the ectopic deposition of cellulose, xylan and lignin (Zhong et 299

al., 2011). In BL5+, OsSWN1, OsSWN4, OsSWN6 and OsMYB46 were up-regulated 300

at MMC and MEI. Three cellulose synthases, OsCESA4, OsCESA7 and OsCESA9, 301

which are regarded as subunits of cellulose synthase complex (Tanaka, 2003), were 302

continuously up-regulated from MMC to AME. In addition, expression of five 303

cellulose synthase-like genes (OsCslA1, OsCslA3, OsCslA5, OsCslA9 and OsCslF6) 304

and two brittle culm genes (BC1 and BC3) were also elevated at MMC or MEI (Fig. 305

4C). Upstream transcription factors such as OsSWN1, OsSWN6 and OsMYB46 had 306

peak expression at MEI while their downstream genes such as OsCESAs and two 307

brittle culm genes had highest expression at AME (Supplemental Fig. S4), in 308

agreement with the over-accumulation of cellulose at AME (Fig. 5B, E). These results 309

showed that the cellulose biosynthetic pathway was highly activated in BL5+ 310

resulting in the accumulation of cellulose in the aborted embryo-sac. 311

Callose deposition in BL5+. Callose is a dynamic component of plant cell wall, 312

which plays important roles in megasporogenesis. The uneven distribution of the 313

callose wall around the megaspores decides the polarization of megaspores, the 314



16

formation of a functional megaspore and the abortion of the other three non-functional 315

megaspores (Ünal et al., 2013). Since many genes encoding β-1,3-glucanases, which 316

have putative functions in callose metabolism, were differentially expressed in BL5+ 317

at MMC and MEI (Supplemental Fig. S5), we investigated the dynamic callose 318

distributions in ovule of BL, BL5+ and BL3+5+. During meiosis, callose 319

preferentially accumulated at the micropylar end of megaspores. Two callose bands 320

were observed in all three genotypes at the dyad stage (Fig. 6A-F), and at tetrad stage 321

at least three callose bands could be recognized also in all three genotypes although 322

slightly different in distribution patterns (Fig. 6G-L). This apparent normal callose 323

distribution in megaspores of BL5+ indicated likely normal meiosis. Unlike BL and 324

BL3+5+, however, weak callose deposition was detected in nucellus cells at the 325

tetrad stage in BL5+ (Fig. 6I). At the functional megaspore (FM) stage, callose 326

accumulated in the three degenerated gametes but not in the FM (Fig. 6M-R). The 327

survived FM subsequently developed to embryo-sac (Fig. 6S, T, W, X). However, the 328



17

ovule of BL5+ displayed irregular callose deposition around the FM and in nucellus 329

cells (Fig. 6O, P), and finally, the aborted embryo-sac was stuffed with large amount 330

of callose (Fig. 6U, V). Thus, ORF5+ resulted in a misregulation of callose deposition 331

during megasporogenesis such that callose began to accumulate abnormally from MEI 332

and was deposited in large quantity at AME in the ovule of BL5+. 333

ER stress and premature PCD induced in BL5+. Under stress conditions, the 334

number of misfolded proteins will increase and may exceed the capacity of the ER 335

quality-control system, thus inducing ER stress (Howell, 2013; Wan and Jiang, 2016). 336

In BL5+, 78.95% genes in “RNA transcription”, 66.23% genes in “RNA processing”, 337

57.69% genes in “protein synthesis initiation”, 58.33% genes in “protein synthesis 338

elongation”, 82.46% genes in “ribosomal protein synthesis” and 60.91% genes in 339

“ribosome biogenesis” were up-regulated at MMC (Supplemental Fig. S6), suggesting 340

a greatly increased level of protein synthesis, which may increase the protein folding 341

burden on ER. To detect whether ER stress occurred in BL5+ at MMC, we examined 342

the expression of ER stress responsive genes in BL5+ and found that 10 such genes 343

were significantly up-regulated including OsbZIP50, which is a key ER stress 344

regulator in rice (Fig. 7A). The mRNA of OsbZIP50 was spliced when ER stress 345

occurred (Hayashi et al., 2012). We then detected the unconventional splicing of 346

OsbZIP50 mRNA in different materials and found that OsbZIP50 mRNA was spliced 347

in BL5+ at MMC, but not in BL or BL3+5+ (Fig. 7B). The spliced OsbZIP50 mRNA 348

encodes a transcription factor OsbZIP50-S, which binds to the pUPRE-II cis-element 349

in the promoter regions of OsBIP4, ORF3, OsEBS and OsPDIL2-3 (Hayashi et al., 350

2013; Takahashi et al., 2014; Wakasa et al., 2014). Accordingly, expression of these 351

four genes was elevated (Fig. 7A). Some other genes including Fes1-like, CRT2-2, 352

CRT1 and SAR1B-like, which were induced in ER stress, were also up-regulated. 353

These results showed that ER stress occurred in BL5+ at MMC relative to BL and 354

BL3+5+. In response to ER stress, genes involved in protein modification (303 355

up-regulated and 358 down-regulated) and targeting (70 up-regulated and 53 356

down-regulated) were differentially expressed presumably to help protein processing 357

and transportation. In addition, 793 DEGs (339 up-regulated and 454 down-regulated) 358



18

involved in “protein degradation” were found, likely as remedy to degrade the 359

misfolded or unfolded proteins (Supplemental Fig. S6). The splicing of OsbZIP50 360

mRNA and up-regulation of ER stress responsive genes were also detected at MEI 361

and AME (Fig. 7A-B), indicating that ER stress proceeded continuously in BL5+. 362

The unresolved ER stress could induce premature programmed cell death (PCD) 363

(Cai et al., 2014). In BL5+, PCD signals were detected from the meiosis stage (Yang 364

et al., 2012), corresponding to the MEI stage in this study. At MEI, we detected 365

up-regulation of two aspartic protease-encoding genes, OsAP25 and OsAP37 (Fig. 7A, 366

C), both of which participate in the tapetal PCD process and induce PCD in yeast and 367

plants (Niu et al., 2013). Overexpression of OsAP25 or OsAP37 in plants results in 368

cell death, which is suppressed by aspartic protease-specific inhibitor pepstatin A. 369

Transformation of OsAP25 or OsAP37 into a PCD-deficient yeast strain restores the 370

PCD ability of the strain. OsAP25 showed the highest expression at MEI (Fig. 7C), 371



19

consistent with the observation of PCD signals at this stage. In tapetal PCD process, 372

transcription factor EAT1 directly regulates the expression of OsAP25 and OsAP37 373

(Niu et al., 2013). However, EAT1 was down-regulated at MEI, indicating that some 374

other regulators might have replaced EAT1 to activate OsAP25 and OsAP37. TDR and 375

TIP2, which work upstream of OsAP25 and OsAP37 in pollen development (Niu et al., 376

2013), were up-regulated in BL5+ at MMC and MEI (Fig. 7A, D). The coordinated 377

up-regulation of TDR, TIP2, OsAP25 and OsAP37 suggested that the ovule and 378

tapetum may share some common genes/pathways in PCD. Taken together, an 379

OsbZIP50-dependent ER stress pathway and a premature PCD pathway involving the 380

tapetal PCD genes were activated in BL5+. 381

These results suggested that the ORF5+-induced up-regulation of cell wall 382

degradation and modification genes in BL5+ caused cell wall damage, which induced 383

both biotic and abiotic stresses. Lasting stress responses induced ER stress and 384

unresolved ER stress led to premature PCD eventually resulting in the ovule abortion. 385

Processes detected in the BL3+5+ /BL comparison. 386

BL3+5+ carrying both the killer ORF5+ and the protector ORF3+ showed no 387

phenotypic difference from the wild type BL with respect to fertility (Supplemental 388

Fig. S1). However, 3,986 DEGs were still identified between BL3+5+ and BL at 389

MMC (Supplemental Table S2; Supplemental Dataset 2), of which 3,843 DEGs were 390

shared with the BL5+/BL comparison at this stage, indicating that ORF5+ induced 391

similar processes in BL3+5+ (Fig. 8A). As expected, the process of “cell wall” was 392

enriched with 217 DEGs (Fig. 8B), of which 64 (55 up-regulated and 9 393

down-regulated) were cell wall modifying and degrading genes from the seven main 394

families (Fig. 4A-B). GO terms “glucan metabolic process” and “polysaccharide 395

metabolic process” were significantly enriched in up-regulated genes (Fig. 8C). Terms 396

“biotic stress” and “abiotic stress” were also enriched involving 339 DEGs. However, 397

the number of DEGs in each of the enriched functional categories was smaller than 398

that in the BL5+/BL comparison (Fig. 4A-B). Moreover, the splicing of OsbZIP50 399

mRNA and the up-regulation of its downstream genes were not detected (Fig. 7A-B). 400

These results suggested that ORF5+ induced similar processes in BL3+5+ at MMC 401



20

especially with respect to cell wall integrity damage, but to a much lesser extent, 402

which did not trigger ER stress. 403

At MEI, the difference between BL3+5+ and BL was greatly narrowed that only 404

749 DEGs were identified, compared with 6,278 genes in the BL5+/BL comparison 405

(Supplemental Table S2; Supplemental Dataset 2). Thus numbers of DEGs especially 406

those in cell wall, biotic stress and abiotic stress were greatly reduced (Fig. 8B). Only 407

7 DEGs from the seven cell wall families were found (Fig. 4A-B), suggesting that cell 408

wall integrity damage was suppressed. The cell wall compensation pathways such as 409

cellulose biosynthesis and callose deposition were not activated (Fig 4C; Fig. 6K, Q), 410

and ER stress and PCD did not occur (Fig. 7). As a result, the cell wall maintained 411



21

integrity and the ovule meiosis was undisturbed (Fig. 1L-M). 412

At AME, the number of DEGs was further reduced to 370 in BL3+5+ compared 413

with BL (Supplemental Table S2; Supplemental Dataset 2). These results indicated 414

that ORF5+ induced similar but weaker damage processes in BL3+5+ as in BL5+ at 415

MMC, but these processes were soon suppressed by ORF3+. Consequently, the 416

embryo-sac developed normally producing fertile female gametes (Fig. 1O). 417

418

419



22

DISCUSSION 420

The killer-protector system of S5 is composed of three proteins, cell wall protein 421

ORF5+, transmembrane protein ORF4+, and ER resident protein ORF3+. Based on 422

the comparative transcriptome results of BL5+ and BL3+5+, we proposed a model to 423

summarize the processes underlying the S5 system (Fig. 9). 424

In BL5+, many cell wall modifying and degrading genes in the families EXPs, 425

XTHs, PMEs, PAEs, PGases, GH9, and AGPs were up-regulated at MMC and MEI, 426

and many genes of these families play important roles in cell elongation or cell 427

expansion (Zhou et al., 2006; Chen and Ye, 2007; Yang et al., 2007; Coimbra et al., 428

2008; Maris et al., 2009; Zhang et al., 2010; Yu et al., 2011; Gou et al., 2012; Zhang et 429

al., 2012; Ma et al., 2013; Miedes et al., 2013; Hara et al., 2014; Xiao et al., 2014; 430

Che et al., 2016). It has been suggested that post-synthetic modifications of the cell 431

wall by cell wall modifying genes may affect cell wall integrity (CWI) (Pogorelko et 432

al., 2013). Thus, large-scale up-regulation of cell wall remodeling genes induced by 433

ORF5+ may lead to changes of cell wall structures, which affect CWI thus inducing 434

stress response. 435

ORF5+ encodes an extracellular aspartic protease. In yeast, extracellular aspartic 436

proteases yapsins are required for the CWI maintenance (Krysan et al., 2005; Guan et 437

al., 2012). Two plant aspartic proteases A36 and A39 participate in cell wall 438

remodeling in pollen tube (Gao et al., 2017). The study in Candida albicans shows 439

that secreted aspartic proteinases use a set of cell wall proteins as substrates (Schild et 440

al., 2011). We speculated that one or more substrates of ORF5+ existed in the rice cell 441

wall, which induced cell wall damage after activated by ORF5+. In yeast, CWI 442

damage triggers unfolded protein response (UPR), a homeostatic response to alleviate 443

ER stress, which in turn affects the CWI (Krysan, 2009; Scrimale et al., 2009). In 444

plants, pathogen invasion or pest attack can induce CWI damage and subsequent 445

stress response (Bellincampi et al., 2014; Pogorelko et al., 2013). CWI damage 446

eventually leads to PCD (Paparella et al., 2015). In BL5+, the functional categories 447

responsive to pathogen invasion or pest attack were enriched, and ER stress was 448

accordingly induced presumably by CWI impairment, which in turn exacerbated the 449



23

cell wall damage and its subsequent stress responses, thus finally leading to PCD. To 450

alleviate the adverse effects caused by CWI damage, cells usually trigger a cell wall 451

compensatory pathway to strengthen the cell wall (Hamann, 2012). For example, 452

disruption by aspartic protease Yps7p in Pichia pastoris reduces chitin content in the 453

lateral cell wall, but the cell thickens the inner cell wall for compensation (Guan et al., 454

2012). Similarly in BL5+, key genes in secondary cell wall biosynthesis were 455

significantly up-regulated resulting in the cellulose accumulation to repair cell wall. 456

Callose, a polysaccharide usually accumulated under stress conditions to provide 457



24

physical barrier to the adverse environments (Pirselova and Matusikova, 2012), was 458

deposited in large quantity. Despite other roles of callose in ovule development, the 459

large amount deposition of callose in BL5+ was most likely to strengthen cell wall. 460

ORF4+ acted as a partner of ORF5+ with a transmembrane localization. We 461

speculated that ORF4+ functioned as a sensor of CWI damage. In plants, a 462

well-studied cell wall sensor is AtWAK1, a wall-associated kinase, which resides in 463

the plasma membrane and responds to oligogalacturonides derived from the 464

hydrolysis of cell wall component (Brutus et al., 2010). Xa4, a wall-associated kinase 465

in rice, contributes to disease resistance by strengthening the cell wall via promoting 466

cellulose synthesis and suppressing cell wall loosening (Hu et al., 2017). Unlike 467

wall-associated kinase, no extracellular binding domain or inner kinase domain was 468

found in ORF4+, thus there may exist a co-receptor that interacts with ORF4+ in the 469

plasma membrane and/or a downstream signal protein that interacts with plasma 470

membrane receptor to transmit signals. 471

Based on these analyses, it was deduced that ORF5+ damaged CWI by cleaving 472

its substrates leading to up-regulation of the cell wall modifying and degrading genes. 473

ORF4+ sensed the CWI impairment and induced biotic and abiotic stress responses, 474

consequently induced ER stress due to the accumulation of drastically increased 475

misfolded proteins in ER. The occurrence of ER stress in turn deteriorated the CWI 476

damage and led to a more serious stress response. Finally, the unresolved cell wall 477

damage, stress response and ER stress triggered PCD. Meanwhile, the cellulose and 478

callose accumulated in ovule as the cells’ unsuccessful remedy to repair the damaged 479

cell wall. 480

BL3+5+ showed no difference with BL with respect to ovule development and 481

fertility, but a number of cell wall modifying and degrading genes were still 482

up-regulated in BL3+5+ at MMC, which may induce CWI damage. However, 483

transcriptional change of these genes was suppressed at MEI and AME. Thus, the 484

subsequent negative effects caused by CWI damage including ER stress, PCD, 485

cellulose and callose deposition were prevented in BL3+5+. ORF3+ encodes a heat 486

shock protein 70 chaperone, which is a downstream target of OsbZIP50s and induced 487



25

by ER stress. ORF3+ is believed to help protein folding in ER to resolve ER stress 488

like OsBIP1-OsBIP5 in the HSP70 gene family (Yang et al., 2012; Hayashi et al., 489

2013; Wakasa et al., 2014). BIP protein alleviates Cd2+ stress-induced PCD (Xu et al., 490

2013). The tobacco plants with overexpression of BIP show delayed leaf senescence 491

(Carvalho et al., 2014). In BL3+5+, ORF3+ suppressed the ORF5+-induced ER 492

stress and PCD. It was speculated that one role of ORF3+ was alleviating ER stress 493

thus not to induce premature PCD. The chaperone activity of ORF3+ may also help 494

the folding of the signal proteins downstream of ORF5+ and ORF4+ so that the stress 495

response may be suppressed at MEI. 496

In conclusion, we revealed the processes underlying a reproductive barrier 497

composed of ORF3, ORF4, and ORF5 at the transcriptomic level and proposed a 498

mechanistic model based on the results. Nevertheless, further studies are needed to 499

support and enrich the model. 500

501

MATERIALS AND METHODS 502

Sample preparation and library construction 503

Balilla was a typical japonica rice variety. The transgenic plant BalillaORF5+ 504

was generated by introducing ORF5+ from an indica variety Nanjing 11 into Balilla 505

under its native promoter (Chen et al., 2008). The plant BalillaORF3+ORF5+ was 506

isolated from the hybrid offspring between BalillaORF5+ and BalillaORF3+, which 507

contained a transformed ORF3+ from Nanjing 11 under its native promoter (Yang et 508

al., 2012). All the rice plants were grown in the fields of the experimental station of 509

Huazhong Agricultural University, Wuhan, China. We determined the relationship 510

between the floret length and stage of ovule development by the paraffin section 511

observation of florets from the variety Balilla. The pistils from florets of Balilla, 512

BalillaORF5+ and BalillaORF3+ORF5+ in length ranges of 3.8-4.2 mm, 5.5-6.0 mm, 513

and 7.0-7.5 mm were collected as MMC, MEI and AME stage samples with two 514

biological replicates. RNA was extracted using TRIzol reagent (Invitrogen) according 515

to the manufacture’s manual. RNA yields and quality were measured using Nanodrop 516

2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer 517



26

(Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits 518

(Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library 519

was constructed using 3 μg total RNA using the TruSeq RNA Library Preparation Kit 520

v2 (Illumina). The libraries were sequenced using Illumina HiSeq 2000 sequencing 521

platform at National Key Laboratory for Crop Genetic Improvement in Huazhong 522

Agricultural University, Wuhan, China. 523

Data processing and DEGs identification 524

The data of the two replicates of all samples were collected, and analyzed 525

following the workflow described previously (Trapnell et al., 2012). In brief, the raw 526

sequencing reads were mapped to the rice reference genome (MSU7.0, 527

http://rice.plantbiology.msu.edu/index.shtml) using TopHat, then the transcripts were 528

assembled and quantified using Cufflinks, and finally, differentially expressed genes 529

were analyzed using Cuffdiff. The raw data files can be found in the NCBI database 530

under the accession numbers GSE95200. Genes with ≥ 2-fold expression 531

up-regulation or down-regulation and adjusted p-value ≤ 0.05 (counted using Cuffdiff) 532

were regarded as up-regulated or down-regulated genes. 533

GO and MapMan analysis 534

Gene ontology (GO) enrichment was performed in AgriGO, a web-based tool for 535

gene ontology analysis (Du et al., 2010) (http://bioinfo.cau.edu.cn/agriGO/index.php). 536

The species “Oryza sativa” were chosen. GO terms in biological process groups with 537

FDR < 0.005 were identified and analyzed further. The MapMan software version 538

3.5.1.R2 and pathways were downloaded from MapMen Site of analysis 539

(http://mapman.gabipd.org/web/guest/mapmanstore). The mapping information of 540

rice genes (osa_MSU_v7_2015-09-08_mapping.txt.tar.gz) that can be imported to the 541

MapMan software was downloaded from GoMapMan 542

(http://www.gomapman.org/export/current/mapman) (Ramsak et al., 2014). 543

In situ hybridization 544

The methods for preparation of paraffin embedded sections followed the 545

previously described protocol (Weng et al., 2014). Primer pairs (listed in 546

Supplemental Table S4) ORF3insituF and ORF3insituR, ORF4insituF and 547



27

ORF4insituR were used to prepare probes for ORF3 and ORF4, respectively. Products 548

amplified from ORF3+ or ORF4+ cDNA were ligated to pGEM-T vector (Promega). 549

The sense probe was transcribed with T7 RNA polymerase, and the antisense probe 550

was transcribed with SP6 RNA polymerase. The probes were labeled with 551

digoxigenin (Roche). Hybridization and detection were performed as described 552

previously (De Block and Debrouwer, 1993). 553

PCR and RT-qPCR 554

Total RNA of pistils were isolated with TRIzol reagent (Invitrogen) and treated 555

with RNase-free DNaseI (Invitrogen) for 20 min at room temperature to digest the 556

contaminating DNA. The first-strand cDNA was synthesized using SSIII reverse 557

transcriptase (Invitrogen) with Oligo(dT)15 Primer (Promega) following the 558

manufacturers’ instruction. For amplification of OsbZIP50s, specific primers around 559

the splice site were used. PCR conditions and PCR products detection were performed 560

as described before (Yang et al., 2012). For quantitative real-time PCR, we carried out 561

the reaction in a total volume of 10 μl containing 5 μl FastStart Universal SYBR 562

Green Master (Rox) (Roche), 1 μl cDNA sample, 3 μM each primer on ABI ViiA™7 563

system. The primers for PCR and RT-qPCR are listed in Supplemental Table S4. The 564

gene profilin (Os06g05880) was used as the internal control in RT-qPCR (Yang et al., 565

2012). 566

Histological staining 567

The fresh florets were fixed with FAA solution (50% ethanol, 5% acetic acid, 3.7% 568

formaldehyde) at 4°C overnight, dehydrated with ethanol in a series of concentrations 569

(50%, 70%, 85%, 95%, 100%), infiltrated with xylene and finally embedded in 570

paraffin. The materials were cut into 10 μm-thick sections and then washed in a 571

xylene/ethanol series (0–50% ethanol). For callose staining, the rehydrated sections 572

were stained with 0.1% aniline blue solution for 60 min. For cellulose staining, the 573

rehydrated sections were stained with 0.01% Pontamine Fast Scarlet 4B solution for 574

20 min or 0.1% calcofluor white (Sigma) for 5 min. The stained sections were 575

scanned under fluorescence microscopy. The florets for observation of ovule 576

development process were stained with ehrlich haematoxylin. After fixation, the 577



28

materials were rehydrated, infiltrated with ehrlich haematoxylin for four days, then 578

dehydrated with ethanol, infiltrated with xylene and embedded in paraffin. The 10 579

μm-thick sections were dewaxed with xylene and sealed with Canada balsam (Sigma). 580

The slides were scanned under light microscopy. 581

Cellulose content determination 582

The cellulose content was determined as described previously (Guo et al., 2014). 583

In brief, the materials were suspended with potassium phosphate buffer (pH 7.0), 584

chloroform-methanol (1:1, v/v), dimethylsulphoxide (DMSO)-water (9:1, v/v), 0.5% 585

(w/v) ammonium oxalate, 4 M KOH containing 1.0 mg/mL sodium borohydride in 586

turn. The remaining pellet was collected and extracted further with H2SO4 (67%, v/v) 587

and the supernatants were collected for the determination of cellulose. 588

589

SUPPLEMENTAL DATA 590

Supplemental Figure S1. The fertility of BL, BL5+, and BL3+5+. 591

Supplemental Figure S2. RNA in situ hybridization of ORF3+ and ORF4+. 592

Supplemental Figure S3. DEGs in “Biotic stress” in BL5+ compared with BL at 593

MMC (A) and MEI (B). 594

Supplemental Figure S4. qPCR verification for expression of the cellulose 595

biosynthetic genes in pistils of BL, BL5+, and BL3+5+ at MMC, MEI, and AME, 596

respectively. 597

Supplemental Figure S5. Expression change of genes involved in callose 598

metabolism. 599

Supplemental Figure S6. The number of DEGs involved in RNA transcription, 600

protein synthesis and processing. 601

Supplemental Table S1. The number of expressed genes in BL, BL5+, and BL3+5+ 602

at different stages. 603

Supplemental Table S2. The number of differentially expressed genes identified in 604

different comparisons. 605

Supplemental Table S3. Full list of significantly enriched GO terms (FDR < 0.005) 606

for DEGs in BL5+ vs. BL. 607



29

Supplemental Table S4. Full list of significantly enriched GO terms (FDR < 0.005) 608

for DEGs in BL3+5+ vs. BL. 609

Supplemental Table S5. The list of cell wall modifying or degrading genes and their 610

expression changes based on log2 fold. 611

Supplemental Table S6. The primers used in this study. 612

Supplemental Dataset 1. The differentially expressed genes in BL5+ compared with 613

BL. 614

Supplemental Dataset 2. The differentially expressed genes in BL3+5+ compared 615

with BL. 616

617

ACKNOWLEDGMENTS 618

We thank Yihua Zhou from Institute of Genetics and Developmental Biology for 619

kindly providing the Pontamine Fast Scarlet 4B solution. 620

621



30

622

FIGURE LEGENDS 623

Figure 1. The ovule development process of BL, BL5+, and BL3+5+. 624

(A-E) Ovule development of BL (gametes fertile). (F-J) Ovule development of BL5+ 625

(gametes sterile). (K-O) Ovule development of BL3+5+ (gametes fertile). (A, F, K) 626

The megaspore mother cell stage. (B, G, L) The dyad stage. (C, H, M) The tetrad 627

stage. (D, I, N) The functional megaspore stage. (E, J, O) The mature embryo sac. 628

MMC, megaspore mother cell; Dy, dyad; Te, tetrad; FM, functional megaspore; DM, 629

degenerated megaspore; AFM, aborted functional megaspore; ANC, abnormal 630

nucellus cells; ES, embryo sac; AES, aborted embryo sac. Bars = 30 μm. The grey 631

bars at the top indicate the corresponding stage in transcriptome data. MMC indicated 632

the megaspore mother cell stage. MEI indicates the meiosis stage. AME indicates the 633

stage after meiosis. 634

635

Figure 2. Analysis of genes differentially expressed in BL5+ compared to BL. 636

(A) Numbers of the up- and down-regulated DEGs at MMC and MEI. (B) Numbers of 637

DEGs in different MapMan functional categories at MMC, MEI and AME, 638

respectively. (C) The heat map of “Metabolism overview” and “Cellular response” in 639

BL5+ at MMC based on the MapMan results. Each small square represents a gene 640

differentially expressed in BL5+ vs. BL. The color of the square represents the level 641

of up-regulation (red) or down-regulation (green) based on the log2 fold change of the 642

DEGs. 643

644

Figure 3. Partial significantly (FDR < 0.005) enriched GO terms for up-regulated 645

genes in BL5+ compared to BL. 646

The color in each cell represents the significance of enrichment based on the FDR 647

value. The cells without color indicate not significantly enriched. The full list of GO 648

terms is given in Supplemental Table S3. 649

650

Figure 4. Differential regulation of cell wall genes in BL5+ and BL3+5+ compared 651



31

with BL. 652

(A) The number of differentially expressed genes involved in cell wall modification 653

and degradation in BL5+ and BL3+5+. The X-axis indicates the gene numbers. The 654

Y-axis indicates the gene families at different stages. (B) Heat map of expression 655

change of genes involved in cell wall modification and degradation. The color in each 656

cell represents the level of expression change based on the log2 fold. The cell without 657

color indicates the gene was not differentially expressed. Full list of genes and their 658

expressions is given in Supplemental Table S5. (C) Expression change of cellulose 659

biosynthetic genes. 660

661

Figure 5. Cellulose deposition in the mature ovules of BL, BL5+, and BL3+5+. 662

(A-F) Cellulose deposition in BL (A, D), BL5+ (B, E) and BL3+5+ (C, F). (A-C) 663

S4B staining. (D-F) Calcofluor white staining. The strong red or blue fluorescence 664

indicates where the cellulose accumulated. Bars = 50 μm. (G) Cellulose content in the 665

panicles of BL and BL5+. The data are means ± SEM (n = 3). *** significant 666

difference at P < 0.001. 667

668

Figure 6. Callose deposition (green fluorescence) in the developing ovule of BL, 669

BL5+, and BL3+5+ by aniline blue staining. 670

(A-F) The dyad stage. The red arrowheads indicate the callose bands around the dyad. 671

(G-L) The tetrad stage. The red arrowheads indicate the callose bands around the 672

tetrad. (M-R) The functional megaspore stage. The red arrowheads indicate the 673

degenerated megaspores. (S-X) The mature embryo-sac. (I, O, U) The grey 674

arrowheads indicate abnormally deposited callose. Bars = 25 μm. 675

676

Figure 7. Differential regulation of ER stress and PCD genes. 677

(A) Log2 fold change of the expression level of ER stress and PCD genes in BL5+ 678

against BL. The color in each cell represents the levels of expression change based on 679

the log2 fold. The cell without color indicates the gene was not differentially 680

expressed. (B) Splicing of OsbZIP50 mRNA in BL, BL5+ and BL3+5+ at each stage. 681



32

(C) qPCR verification for expression of tapetal PCD-related genes in BL and BL5+. 682

The X-axis represents different stages. The Y-axis represents the expression level 683

relative to profilin (Os06g05880). The data are means ± SEM (n = 3). 684

685

Figure 8. Analysis of genes differentially expressed in BL3+5+ compared to BL. 686

(A) Number of DEGs detected in the BL3+5+/BL and BL5+/BL comparisons at 687

different stages. The overlapping areas indicate the genes differentially expressed in 688

both BL3+5+ and BL5+. (B) The number of DEGs in different functional categories 689

of “Metabolism Overview” and “Cellular response” by MapMan at MMC, MEI and 690

AME, respectively. (C) Partial significantly (FDR < 0.005) enriched GO terms for 691

up-regulated genes in BL3+5+ compared with BL. The color in each cell represents 692

the significance of enrichment based on the FDR value. The cells without color 693

indicate not significantly enriched. The full list of GO terms is given in Supplemental 694

Table S4. 695

696

Fig. 9. A model for S5 locus-mediated ovule abortion. 697

698



33

699

700



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

http://scholar.google.com/scholar?as_q=Real-time imaging of cellulose reorientation during cell wall expansion in Arabidopsis roots&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=Real-time imaging of cellulose reorientation during cell wall expansion in Arabidopsis roots&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Anderson&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bellincampi D%2C Cervone F%2C Lionetti V %282014%29 Plant cell wall dynamics and wall%2Drelated susceptibility in plant%2Dpathogen interactions%2E Front Plant Sci 5%3A 228&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bellincampi D, Cervone F, Lionetti V (2014) Plant cell wall dynamics and wall-related susceptibility in plant-pathogen interactions. Front Plant Sci 5: 228

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http://scholar.google.com/scholar?as_q=Plant cell wall dynamics and wall-related susceptibility in plant-pathogen interactions.&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=Plant cell wall dynamics and wall-related susceptibility in plant-pathogen interactions.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bellincampi&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bosch M%2C Ycheung A%2C Khepler P %282005%29 Pectin methylesterase%2C a regulator of pollen tube growth%2E Plant Physiol 138%3A 1334%2D1346&dopt=abstract

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Hayashi S, Takahashi H, Wakasa Y, Kawakatsu T, Takaiwa F (2013) Identification of a cis-element that mediates multiple pathwaysof the endoplasmic reticulum stress response in rice. Plant J 74: 248-257


Hayashi S, Wakasa Y, Takahashi H, Kawakatsu T, Takaiwa F (2012) Signal transduction by IRE1-mediated splicing of bZIP50 andother stress sensors in the endoplasmic reticulum stress response of rice. Plant J 69: 946-956


Hepler PK, Rounds CM, Winship LJ (2013) Control of cell wall extensibility during pollen tube growth. Mol Plant 6: 998-1017Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Howell SH (2013) Endoplasmic reticulum stress responses in plants. Annu Rev Plant Biol 64: 477-499Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H, Xie W, Liu H, Cui Y, Cao Y, Sun X, Xiao J, Li X, Zhang Q, Wang S (2017) Improvement ofmultiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nat Plants 3: 17009


Ikehashi H, Araki H (1986) Genetics of F1 sterility in remote crosses of rice. In: IRRI (eds) Rice genetics. IRRI, Manila, pp 119-130Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, ChildsKL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013)Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6: 4


Kourmpetli S, Lee K, Hemsley R, Rossignol P, Papageorgiou T, Drea S (2013) Bidirectional promoters in seed development andrelated hormone/stress responses. BMC Plant Biol 13: 1-16


Krysan DJ (2009) The cell wall and endoplasmic reticulum stress responses are coordinately regulated in Saccharomycescerevisiae. Commun Integr Biol 2: 233-235


Krysan DJ, Ting EL, Abeijon C, Kroos L, Fuller RS (2005) Yapsins are a family of aspartyl proteases required for cell wall integrity inSaccharomyces cerevisiae. Eukaryot Cell 4: 1364-1374


Kubo T, Takashi T, Ashikari M, Yoshimura A, Kurata N (2016) Two tightly linked genes at the hsa1 locus cause both F1 and F2hybrid sterility in rice. Mol Plant 9: 221-232


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http://search.crossref.org/?page=1&rows=2&q=Hara Y, Yokoyama R, Osakabe K, Toki S, Nishitani K (2014) Function of xyloglucan endotransglucosylase/hydrolases in rice. Ann Bot 114: 1309-1318

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http://search.crossref.org/?page=1&rows=2&q=Hayashi S, Takahashi H, Wakasa Y, Kawakatsu T, Takaiwa F (2013) Identification of a cis-element that mediates multiple pathways of the endoplasmic reticulum stress response in rice. Plant J 74: 248-257

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http://www.ncbi.nlm.nih.gov/pubmed?term=Hayashi S%2C Wakasa Y%2C Takahashi H%2C Kawakatsu T%2C Takaiwa F %282012%29 Signal transduction by IRE1%2Dmediated splicing of bZIP50 and other stress sensors in the endoplasmic reticulum stress response of rice%2E Plant J 69%3A 946%2D956&dopt=abstract

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

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http://www.ncbi.nlm.nih.gov/pubmed?term=Hepler PK%2C Rounds CM%2C Winship LJ %282013%29 Control of cell wall extensibility during pollen tube growth%2E Mol Plant 6%3A 998%2D1017&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hepler PK, Rounds CM, Winship LJ (2013) Control of cell wall extensibility during pollen tube growth. Mol Plant 6: 998-1017

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

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http://www.ncbi.nlm.nih.gov/pubmed?term=Howell SH %282013%29 Endoplasmic reticulum stress responses in plants%2E Annu Rev Plant Biol 64%3A 477%2D499&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Howell SH (2013) Endoplasmic reticulum stress responses in plants. Annu Rev Plant Biol 64: 477-499

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http://www.ncbi.nlm.nih.gov/pubmed?term=Kawahara Y%2C de la Bastide M%2C Hamilton JP%2C Kanamori H%2C McCombie WR%2C Ouyang S%2C Schwartz DC%2C Tanaka T%2C Wu J%2C Zhou S%2C Childs KL%2C Davidson RM%2C Lin H%2C Quesada%2DOcampo L%2C Vaillancourt B%2C Sakai H%2C Lee SS%2C Kim J%2C Numa H%2C Itoh T%2C Buell CR%2C Matsumoto T %282013%29 Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data%2E Rice 6%3A 4&dopt=abstract

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http://search.crossref.org/?page=1&rows=2&q=Krysan DJ (2009) The cell wall and endoplasmic reticulum stress responses are coordinately regulated in Saccharomyces cerevisiae. Commun Integr Biol 2: 233-235

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Ma N, Wang Y, Qiu S, Kang Z, Che S, Wang G, Huang J (2013) Overexpression of OsEXPA8, a root-specific gene, improves ricegrowth and root system architecture by facilitating cell extension. PLoS ONE 8: e75997


Maris A, Suslov D, Fry SC, Verbelen JP, Vissenberg K (2009) Enzymic characterization of two recombinant xyloglucanendotransglucosylase/hydrolase (XTH) proteins of Arabidopsis and their effect on root growth and cell wall extension. J Exp Bot60: 3959-3972


Miedes E, Suslov D, Vandenbussche F, Kenobi K, Ivakov A, Van Der Straeten D, Lorences EP, Mellerowicz EJ, Verbelen JP,Vissenberg K (2013) Xyloglucan endotransglucosylase/hydrolase (XTH) overexpression affects growth and cell wall mechanics inetiolated Arabidopsis hypocotyls. J Exp Bot 64: 2481-2497


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Niu N, Liang W, Yang X, Jin W, Wilson Z, Hu J, Zhang D (2013) EAT1 promotes tapetal cell death by regulating aspartic proteasesduring male reproductive development in rice. Nat Commun 4: 1445


Ouyang Y, Chen J, Ding J, Zhang Q (2009) Advances in the understanding of inter-subspecific hybrid sterility and wide-compatibility in rice. Chin Sci Bull 54: 2332-2341


Ouyang Y, Li G, Mi J, Xu C, Du H, Zhang C, Xie W, Li X, Xiao J, Song H, Zhang Q (2016) Origination and establishment of a trigenicreproductive isolation system in rice. Mol Plant 9: 1542-1545


Ouyang Y, Zhang Q (2013) Understanding reproductive isolation based on the rice model. Annu Rev Plant Biol 64: 111-135Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Paparella S, Tava A, Avato P, Biazzi E, Macovei A, Biggiogera M, Carbonera D, Balestrazzi A (2015) Cell wall integrity, genotoxicinjury and PCD dynamics in alfalfa saponin-treated white poplar cells highlight a complex link between molecule structure andactivity. Phytochemistry 111: 114-123


Pirselova B, Matusikova I (2012) Callose: the plant cell wall polysaccharide with multiple biological functions. Acta Physiol Plant 35:635-644


Pogorelko G, Lionetti V, Bellincampi D, Zabotina O (2013) Cell wall integrity: targeted post-synthetic modifications to reveal its rolein plant growth and defense against pathogens. Plant Signal Behav 8: e25435


Qiu SQ, Liu K, Jiang JX, Song X, Xu CG, Li XH, Zhang Q (2005) Delimitation of the rice wide compatibility gene S5n to a 40-kb DNAfragment. Theor Appl Genet 111: 1080-1086

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http://www.ncbi.nlm.nih.gov/pubmed?term=Ma N%2C Wang Y%2C Qiu S%2C Kang Z%2C Che S%2C Wang G%2C Huang J %282013%29 Overexpression of OsEXPA8%2C a root%2Dspecific gene%2C improves rice growth and root system architecture by facilitating cell extension%2E PLoS ONE 8%3A e75997&dopt=abstract

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http://scholar.google.com/scholar?as_q=Enzymic characterization of two recombinant xyloglucan endotransglucosylase/hydrolase (XTH) proteins of Arabidopsis and their effect on root growth and cell wall extension&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=Enzymic characterization of two recombinant xyloglucan endotransglucosylase/hydrolase (XTH) proteins of Arabidopsis and their effect on root growth and cell wall extension&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Maris&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Miedes E%2C Suslov D%2C Vandenbussche F%2C Kenobi K%2C Ivakov A%2C Van Der Straeten D%2C Lorences EP%2C Mellerowicz EJ%2C Verbelen JP%2C Vissenberg K %282013%29 Xyloglucan endotransglucosylase%2Fhydrolase %28XTH%29 overexpression affects growth and cell wall mechanics in etiolated Arabidopsis hypocotyls%2E J Exp Bot 64%3A 2481%2D2497&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=Mizuta Y%2C Harushima Y%2C Kurata N %282010%29 Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes%2E Proc Natl Acad Sci U S A 107%3A 20417%2D20422&dopt=abstract

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Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF (2005) Roles of the CBF2 and ZAT12 transcription factors inconfiguring the low temperature transcriptome of Arabidopsis. Plant J 41: 195-211

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Yu Z, Kang B, He X, Lv S, Bai Y, Ding W, Chen M, Cho H-T, Wu P (2011) Root hair-specific expansins modulate root hair elongationin rice. Plant J 66: 725-734


Zhang GY, Feng J, Wu J, Wang XW (2010) BoPMEI1, a pollen-specific pectin methylesterase inhibitor, has an essential role inpollen tube growth. Planta 231: 1323-1334


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Zhong R, Lee C, McCarthy RL, Reeves CK, Jones EG, Ye ZH (2011) Transcriptional activation of secondary wall biosynthesis byrice and maize NAC and MYB transcription factors. Plant Cell Physiol 52: 1856-1871


Zhou H, He S, Cao Y, Chen T, Du B, Chu C, Zhang J, Chen S (2006) OsGLU1, a putative membrane-bound endo-1,4-beta-D-glucanase from rice, affects plant internode elongation. Plant Mol Biol 60: 137-151



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http://www.ncbi.nlm.nih.gov/pubmed?term=Zhang J%2C Xu L%2C Wu Y%2C Chen X%2C Liu Y%2C Zhu S%2C Ding W%2C Wu P%2C Yi K %282012%29 OsGLU3%2C a putative membrane%2Dbound endo%2D1%2C4%2Dbeta%2Dglucanase%2C is required for root cell elongation and division in rice %28Oryza sativa L%2E%29%2E Mol Plant 5%3A 176%2D186&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=Zhong R%2C Lee C%2C McCarthy RL%2C Reeves CK%2C Jones EG%2C Ye ZH %282011%29 Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors%2E Plant Cell Physiol 52%3A 1856%2D1871&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhong R, Lee C, McCarthy RL, Reeves CK, Jones EG, Ye ZH (2011) Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors. Plant Cell Physiol 52: 1856-1871

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

http://scholar.google.com/scholar?as_q=Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors&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=Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhong&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhou H%2C He S%2C Cao Y%2C Chen T%2C Du B%2C Chu C%2C Zhang J%2C Chen S %282006%29 OsGLU1%2C a putative membrane%2Dbound endo%2D1%2C4%2Dbeta%2DD%2Dglucanase from rice%2C affects plant internode elongation%2E Plant Mol Biol 60%3A 137%2D151&dopt=abstract

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http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhou&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1


Documents

1 Running Head - Plant Physiology3 44 ABSTRACT 45 46 In rice (Oryza sativa L.), hybrids between indica and japonica subspecies are usually 47 highly sterile, which provides a model