Edited by: Nobuhiro Suzuki, Okayama University, Japan
Reviewed by: Richard S. Nelson, Samuel Roberts Noble Foundation, Inc., USA; Mikhail M. Pooggin, University of Basel, Switzerland; Monica Höfte, Ghent University, Belgium
*Correspondence: Shoshi Kikuchi, Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kan-nondai, Tsukuba, Ibaraki, 305-8602, Japan e-mail:
This article was submitted to Virology, a section of the journal Frontiers in Microbiology.
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Grassy stunt disease of rice caused by
Plant disease symptoms caused by virus infection are accompanied by changes in the expression of the genes involved in morphogenesis and development (Dardick,
In this study, we analyzed the gene expression profile in rice plants infected with RGSV to gain insight into RGSV-induced gene responses associated with the symptoms. The results suggested that symptoms such as stunting and leaf chlorosis caused by RGSV infection were associated with the suppression of genes related to cell wall, hormone synthesis and chlorophyll synthesis while excess tillering specific to RGSV infection is associated with the suppression of strigolactone signaling and GA metabolism.
RGSV was maintained in rice plants (
Total RNA was extracted from leaf samples pooled from five independent RGSV-infected or mock-inoculated plants by the RNeasy Maxi kit (Qiagen, UK). A microarray experiment involving complementary RNA synthesis, hybridization, array scanning, and image processing was performed as described previously (Satoh et al.,
Complementary DNA (cDNA) fragments for transcripts of selected rice genes were synthesized using 1.0 μg of total RNA with 50 ng/μL of random hexamer primers by SuperScript III reverse transcriptase (Invitrogen, USA). The resultant reaction mixtures containing cDNA were diluted four times. Four μL of diluted mixture was used for PCR. Primers for selected rice genes are shown in Supplementary Material
RGSV-infected and mock-inoculated rice plants were prepared as described previously and grown for 6 weeks. Then, the plants (
Rice plants infected with RGSV showed disease symptoms such as excessive tillering, stunting, and leaf yellowing. The symptoms became more severe after 28 DPI (Figure
Changes in gene expression caused by RGSV infection were examined by direct comparison between RGSV- and mock-inoculated rice plants at 28 DPI. The numbers of expressed genes and DEGs were 24,911 and 8203, respectively (Table
Component | GO:0016020 | Membrane | 3193 | 2.53E-05 | 671 | 517 | |
GO:0005618 | Cell wall | 1645 | 3.25E-10 | 377 | 311 | ||
GO:0005623 | Cell | 233 | 7.88E-03 | 54 | 46 | ||
GO:0005622 | Intracellular | 627 | 1.50E-04 | 103 | 49 | ||
GO:0005840 | Ribosome | 301 | 1.73E-08 | 18 | 25 | ||
GO:0005829 | Cytosol | 264 | 9.08E-04 | 33 | 23 | ||
Process | GO:0009719 | Response to endogenous stimulus | 2619 | 9.56E-13 | 615 | 457 | |
GO:0007582 | Physiological process | 2105 | 5.78E-08 | 499 | 337 | ||
GO:0007165 | Signal transduction | 2022 | 3.87E-06 | 485 | 300 | ||
GO:0006950 | Response to stress | 1804 | 4.11E-05 | 411 | 283 | ||
GO:0009628 | Response to abiotic stimulus | 1527 | 1.14E-14 | 404 | 272 | ||
GO:0008150 | Biological process | 1388 | 1.63E-09 | 357 | 229 | ||
GO:0009607 | Response to biotic stimulus | 1348 | 2.12E-11 | 321 | 264 | ||
GO:0009058 | Biosynthetic process | 1222 | 7.94E-06 | 214 | 278 | ||
GO:0006519 | Amino acid and derivative metabolic process | 803 | 4.23E-05 | 152 | 179 | ||
GO:0019748 | Secondary metabolic process | 659 | 1.14E-11 | 133 | 184 | ||
GO:0006629 | Lipid metabolic process | 655 | 1.26E-04 | 132 | 140 | ||
GO:0006118 | Electron transport | 481 | 4.12E-05 | 98 | 112 | ||
GO: 0005975 | Carbohydrate metabolic process | 473 | 1.82E-08 | 107 | 119 | ||
GO: 0007275 | Multicellular organismal development | 463 | 2.09E-05 | 128 | 77 | ||
GO:0030154 | Cell differentiation | 426 | 3.10E-04 | 120 | 63 | ||
GO:0009908 | Flower development | 342 | 1.29E-06 | 92 | 72 | ||
GO: 00096 53 | Anatomical structure morphogenesis | 204 | 6.87E-04 | 61 | 34 | ||
GO:0016043 | Cellular component organization and biogenesis | 784 | 1.09E-04 | 117 | 79 | ||
GO:0006412 | Translation | 516 | 2.60E-11 | 39 | 44 | ||
GO:0006139 | Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 453 | 9.20E-06 | 59 | 36 | ||
24911 | 8204 | 3896 | 4307 |
We classified the DEGs in RGSV-infected plants according to gene ontology. For many ontology categories, the ratio of the number of DEGs to the number of expressed genes was significantly higher (
The expression of genes related to cell wall components was affected by RGSV infection (Table
Cellulose synthase | LOC_Os0lg54620 | −0.70 | D |
LOC_Os05g08370 | −0.68 | D | |
LOC_Os07g2419 | −1.03 | D | |
LOC_Os10g32980 | −1.09 | D | |
LOC_Os12g29300 | −0.77 | D | |
Cellulose synthase-like family A | LOC_Os02g09930 | −2.20 | D |
LOC_Os02g51060 | −0.60 | D | |
LOC_Os06g12460 | −1.28 | D | |
LOC_Os08g33740 | −2.03 | D | |
Cellulose synthase-like family C | LOC_Os01g56130 | −0.68 | D |
LOC_Os03g56060 | 1.10 | U | |
LOC_Os08g15420 | −0.84 | D | |
Cellulose synthase-like family E | LOC_Os09g30120 | 1.13 | U |
LOC_Os09g30130 | −1.21 | D | |
Cellulose synthase-like family F | LOC_Os07g36610 | −0.89 | D |
LOC_Os07g36690 | −2.80 | D | |
LOC_Os07g36700 | −1.99 | D | |
LOC_Os07g36740 | −1.34 | D | |
LOC_Os08g06380 | −0.92 | D | |
Cellulose synthase-like family H | LOC_Os04g35030 | 1.35 | U |
Fasci din-like arabinogalactan protein | LOC_Os03g57460 | −1.07 | D |
LOC_Os07g06680 | −0.73 | D | |
LOC_Os08g38270 | −1.03 | D | |
LOC_Os05g07060 | −1.76 | D | |
LOC_Os05g48900 | −0.73 | D | |
LOC_Os08g39270 | 1.38 | U | |
LOC_Os05g38500 | −0.99 | D | |
LOC_Os03g03600 | −1.38 | D | |
LOC_Os08g23180 | −1.02 | D | |
LOC_Os09g07350 | −1.39 | D | |
LOC_Os09g30010 | 1.78 | U | |
α-Expansin | LOC_Os01g14660 | −2.34 | D |
LOC_Os02g51040 | −1.28 | D | |
LOC_Os03g60720 | 2.28 | U | |
LOC_Os04g15840 | −1.12 | D | |
LOC_Os05g39990 | −0.77 | D | |
LOC_Os06g41700 | 0.90 | U | |
LOC_Os10g30340 | −1.24 | D | |
β-Expansin | LOC_Os03g01270 | −2.06 | D |
LOC_Os 10g40710 | −2.26 | D | |
Expansin-like | LOC_Os03g04020 | −0.90 | D |
LOC_Os06g50960 | −0.66 | D | |
LOC_Os10g39640 | −1.36 | D | |
Extensin | LOC_Os01g67390 | −2.86 | D |
LOC_Os04g32850 | −1.66 | D | |
LOC_Os11g41120 | 1.73 | U | |
OsNACs/Ostiin | LOC_Os04g38720 | 0.58 | U |
RCN1 | LOC_Os03g17350 | 2. 47 | U |
SPL14 | LOC_Os03g39890 | −0.65 | D |
One of the major symptoms caused by RGSV infection is excessive tillering. The genes
Expression of many genes functioning in chloroplasts was affected by RGSV infection (Supplementary Material
We examined the expression patterns of genes involved in plant hormone biosynthesis and signaling processes. Rice genes for hormone biosynthesis and signaling and their orthologous genes in
GH3 converts IAA into an inactive form by conjugating IAA to amino acids (Domingo et al.,
Enzymes such as
SL was recently classified as a plant hormone. The expression of genes involved in SL biosynthesis such as those encoding Dwarf 17 (D17), D10, and D27 was not changed by RGSV infection (Figure
We previously reported gene responses of rice to RSV and
RGSV infection induces stunting of rice plants. Many cellulose synthase (-like) genes were suppressed in RGSV-infected plants (Table
The expression of the Rubisco genes was suppressed by RGSV infection (Figure
The difference in leaf chlorosis pattern may be related to chlorophyll degradation process (Figure
Cell elongation is controlled by plant hormones such as GA and IAA. The expression of genes for GA biosynthesis such as those for KS, KO, and GA20ox, and those involved in GA inactivation such as the genes for GA2ox increased in RGSV-infected plants (Figure
RGSV infection suppressed the genes for IAA biosynthesis, and induced the genes for IAA inactivation (Figure
Overexpression of a SAUR gene resulted in various morphological changes in rice plants (Kant et al.,
Excess tillering (shoot branching) is RGSV-specific symptoms. Shoot branching is controlled by plant hormones (Dill and Sun,
Rice genes
A reduction in active GA also promotes the formation of axillary buds (Curtis et al.,
Overall, excessive tillers induced specifically by RGSV infection might be a consequence from the additive actions of SL, GA, and the genes regulating shoot branching, such as
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
We thank Dr. Bill Hardy for editing this manuscript and Ms. Setsuko Kimura and Hiromi Satoh for their support in the microarray and semi-quantitative RT-PCR experiments. This work was supported by a grant from the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN).
The Supplementary Materials for this article can be found online at: