An RNA-Seq Analysis of Grape Plantlets Grown in vitro Reveals Different Responses to Blue, Green, Red LED Light, and White Fluorescent Light

Using an RNA sequencing (RNA-seq) approach, we analyzed the differentially expressed genes (DEGs) and physiological behaviors of “Manicure Finger” grape plantlets grown in vitro under white, blue, green, and red light. A total of 670, 1601, and 746 DEGs were identified in plants exposed to blue, green, and red light, respectively, compared to the control (white light). By comparing the gene expression patterns with the growth and physiological responses of the grape plantlets, we were able to link the responses of the plants to light of different spectral wavelengths and the expression of particular sets of genes. Exposure to red and green light primarily triggered responses associated with the shade-avoidance syndrome (SAS), such as enhanced elongation of stems, reduced investment in leaf growth, and decreased chlorophyll levels accompanied by the expression of genes encoding histone H3, auxin repressed protein, xyloglucan endotransglycosylase/hydrolase, the ELIP protein, and microtubule proteins. Furthermore, specific light treatments were associated with the expression of a large number of genes, including those involved in the glucan metabolic pathway and the starch and sucrose metabolic pathways; these genes were up/down-regulated in ways that may explain the increase in the starch, sucrose, and total sugar contents in the plants. Moreover, the enhanced root growth and up-regulation of the expression of defense genes accompanied with SAS after exposure to red and green light may be related to the addition of 30 g/L sucrose to the culture medium of plantlets grown in vitro. In contrast, blue light induced the up-regulation of genes related to microtubules, serine carboxypeptidase, chlorophyll synthesis, and sugar degradation and the down-regulation of auxin-repressed protein as well as a large number of resistance-related genes that may promote leaf growth, improve chlorophyll synthesis and chloroplast development, increase the ratio of chlorophyll a (chla)/chlorophyll b (chlb), and decrease the ratio of carbohydrates to proteins in plants. Although exposure to red and green light seems to impose “shade stress” on the plantlets, growth under blue light is comparable to growth observed under white or broad-spectrum light.

[1]  T. Nakayama,et al.  A wheat histone H3 promoter confers cell division-dependent and -independent expression of the gus A gene in transgenic rice plants. , 1993, The Plant journal : for cell and molecular biology.

[2]  D. Cosgrove.  Growth of the plant cell wall , 2005, Nature Reviews Molecular Cell Biology.

[3]  F. Baluška,et al.  Actin cytoskeleton in plants: From transport networks to signaling networks , 1999, Microscopy research and technique.

[4]  S. Dutta Gupta,et al.  Fundamentals and applications of light-emitting diodes (LEDs) in in vitro plant growth and morphogenesis , 2013, Plant Biotechnology Reports.

[5]  de Wit,et al.  Shade avoidance : phytochrome signalling and other aboveground neighbour detection cues , 2014 .

[6]  Takahisa Hayashi,et al.  Xyloglucans in the Primary Cell Wall , 1989 .

[7]  D. Nadeau,et al.  A micromethod for the quantitation of cellular proteins in Percoll with the Coomassie brilliant blue dye-binding assay. , 1983, Analytical biochemistry.

[8]  Jihong Liu Clarke,et al.  Artificial light from light emitting diodes (LEDs) with a high portion of blue light results in shorter poinsettias compared to high pressure sodium (HPS) lamps , 2012 .

[9]  M. Solursh,et al.  Induction of chondrogenesis in limb mesenchymal cultures by disruption of the actin cytoskeleton , 1984, The Journal of cell biology.

[10]  F. Skoog,et al.  A revised medium for rapid growth and bio assays with tobacco tissue cultures , 1962 .

[11]  A. Sæbø,et al.  Light quality affects photosynthesis and leaf anatomy of birch plantlets in vitro , 1995, Plant Cell, Tissue and Organ Culture.

[12]  Role of green light in physiological activity of plants , 2015, Russian Journal of Plant Physiology.

[13]  A. Bittner,et al.  Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells , 2014, PloS one.

[14]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[15]  S. Turner,et al.  Control of Cellulose Synthase Complex Localization in Developing Xylem Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012815. , 2003, The Plant Cell Online.

[16]  Y. Desjardins,et al.  Effects of sucrose on photosynthesis and phosphoenolpyruvate carboxylase activity of in vitro cultured strawberry plantlets , 2004, Plant Cell, Tissue and Organ Culture.

[17]  Andrea Furtado Macedo,et al.  The effect of light quality on leaf production and development of in vitro-cultured plants of Alternanthera brasiliana Kuntze , 2011 .

[18]  X. Zhigang,et al.  Effects of different spectral lights on Oncidium PLBs induction, proliferation, and plant regeneration , 2011, Plant Cell, Tissue and Organ Culture (PCTOC).

[19]  R. Chée.  In vitro culture of Vitis: the effects of light spectrum, manganese sulfate and potassium iodide on morphogenesis , 2004, Plant Cell, Tissue and Organ Culture.

[20]  K. Chapman,et al.  Commentary: why don't plant leaves get fat? , 2013, Plant science : an international journal of experimental plant biology.

[21]  J. Olsen,et al.  Antagonistic action of blue and red light on shoot elongation in petunia depends on gibberellin, but the effects on flowering are not generally linked to gibberellin , 2016 .

[22]  S. Turner,et al.  The roles of the cytoskeleton during cellulose deposition at the secondary cell wall. , 2008, The Plant journal : for cell and molecular biology.

[23]  A. Jerzmanowski,et al.  Histone H1 overexpressed to high level in tobacco affects certain developmental programs but has limited effect on basal cellular functions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Lin Fang,et al.  WEGO: a web tool for plotting GO annotations , 2006, Nucleic Acids Res..

[25]  W. Kim,et al.  Constitutive expression of CaXTH3, a hot pepper xyloglucan endotransglucosylase/hydrolase, enhanced tolerance to salt and drought stresses without phenotypic defects in tomato plants (Solanum lycopersicum cv. Dotaerang) , 2011, Plant Cell Reports.

[26]  F. K. Gyoeva.  Interaction of Molecular Motors , 2005, Molecular Biology.

[27]  Daniel J. Cosgrove,et al.  Loosening of plant cell walls by expansins , 2000, Nature.

[28]  I. Adamska.  Regulation of Early Light-Inducible Protein Gene Expression by Blue and Red Light in Etiolated Seedlings Involves Nuclear and Plastid Factors , 1995, Plant physiology.

[29]  P. Echlin,et al.  Scanning Electron Microscopy , 2014 .

[30]  R. Jennings,et al.  Suppression of Both ELIP1 and ELIP2 in Arabidopsis Does Not Affect Tolerance to Photoinhibition and Photooxidative Stress1 , 2006, Plant Physiology.

[31]  J. Kossmann,et al.  Downregulation of a chloroplast-targeted beta-amylase leads to a starch-excess phenotype in leaves. , 2002, The Plant journal : for cell and molecular biology.

[32]  Kazuhiro Shoji,et al.  Effect of green light wavelength and intensity on photomorphogenesis and photosynthesis in Lactuca sativa , 2012 .

[33]  I. Ohad,et al.  Synthesis of the early light-inducible protein is controlled by blue light and related to light stress. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Maureen C. McCann,et al.  Direct visualization of cross-links in the primary plant cell wall , 1990 .

[35]  R. Nagai,et al.  The plant cytoskeleton. , 1994, Current opinion in cell biology.

[36]  Anil Grover,et al.  Salt stress response in rice: genetics, molecular biology, and comparative genomics , 2006, Functional & Integrative Genomics.

[37]  C. Navarre,et al.  NtSCP1 from Tobacco Is an Extracellular Serine Carboxypeptidase III That Has an Impact on Cell Elongation1[C][W][OA] , 2012, Plant Physiology.

[38]  A. Aharoni,et al.  Novel Insight into Vascular, Stress, and Auxin-Dependent and -Independent Gene Expression Programs in Strawberry, a Non-Climacteric Fruit , 2002, Plant Physiology.

[39]  J. Pickett-Heaps.  The effects of colchicine on the ultrastructure of dividing plant cells, xylem wall differentiation and distribution of cytoplasmic microtubules , 1967 .

[40]  K. Dietz,et al.  AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling , 2010, Protoplasma.

[41]  Srinidhi V. Holalu,et al.  Abscisic Acid Regulates Axillary Bud Outgrowth Responses to the Ratio of Red to Far-Red Light1[C][W][OPEN] , 2013, Plant Physiology.

[42]  W. Schmidt,et al.  The conundrum of discordant protein and mRNA expression. Are plants special? , 2014, Front. Plant Sci..

[43]  R. Pierik,et al.  Shade avoidance: phytochrome signalling and other aboveground neighbour detection cues. , 2014, Journal of experimental botany.

[44]  A. Altman,et al.  Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. , 2004, Trends in plant science.

[45]  T. Sharkey,et al.  Maltose is the major form of carbon exported from the chloroplast at night , 2004, Planta.

[46]  Sunchung Park,et al.  An auxin-repressed gene (RpARP) from black locust (Robinia pseudoacacia) is posttranscriptionally regulated and negatively associated with shoot elongation. , 2003, Tree physiology.

[47]  Thomas Unger,et al.  Quantitative real-time RT-PCR data analysis: current concepts and the novel “gene expression’s CT difference” formula , 2006, Journal of Molecular Medicine.

[48]  Yi Wei,et al.  Abiotic Stress Resistance, a Novel Moonlighting Function of Ribosomal Protein RPL44 in the Halophilic Fungus Aspergillus glaucus , 2014, Applied and Environmental Microbiology.

[49]  Wenbin Li,et al.  A RAV-like transcription factor controls photosynthesis and senescence in soybean , 2008, Planta.

[50]  P. Mazzafera,et al.  Abiotic and biotic stresses and changes in the lignin content and composition in plants. , 2010, Journal of integrative plant biology.

[51]  G. Calder,et al.  The Microtubule-Associated Protein AtMAP70-5 Regulates Secondary Wall Patterning in Arabidopsis Wood Cells , 2010, Current Biology.

[52]  J. Palatnik,et al.  Morphogenesis of simple leaves: regulation of leaf size and shape , 2014, Wiley interdisciplinary reviews. Developmental biology.

[53]  B. Gunning,et al.  Cytoskeleton and integration of cellular function in cells of higher plants , 1984, Journal of Cell Biology.

[54]  J. Derksen,et al.  The plant cytoskeleton its significance in plant development , 1990 .

[55]  K. Baumann,et al.  Shaping in plant cells. , 2001, Current opinion in plant biology.

[56]  D. Kopsell,et al.  Increases in Shoot Tissue Pigments, Glucosinolates, and Mineral Elements in Sprouting Broccoli after Exposure to Short-duration Blue Light from Light Emitting Diodes , 2013 .

[57]  D. Inzé,et al.  Meristem, cell division and S phase-dependent activity of wheat histone H4 promoter in transgenic maize plants , 1999 .

[58]  D. Fairbairn.  The metabolism of Heterakis gallinae. II. Carbon dioxide fixation. , 1954, Experimental parasitology.

[59]  S. Blackmore,et al.  Scanning electron microscopy of chloroplast ultrastructure , 1984 .

[60]  L. Hadwiger,et al.  The non-host disease resistance response in peas; alterations in phosphorylation and ubiquitination of HMG A and histones H2A/H2B , 2009 .

[61]  Robert Ascenzi,et al.  A drought-stress-inducible histone gene in Arabidopsis thaliana is a member of a distinct class of plant linker histone variants , 1997, Plant Molecular Biology.

[62]  Jorge J Casal,et al.  Shade Avoidance , 2012, The arabidopsis book.

[63]  Junhui Wang,et al.  Transcriptome Analysis Reveals that Red and Blue Light Regulate Growth and Phytohormone Metabolism in Norway Spruce [Picea abies (L.) Karst.] , 2015, PloS one.

[64]  S. Klosterman,et al.  Analysis of pea HMG-I/Y expression suggests a role in defence gene regulation. , 2003, Molecular plant pathology.

[65]  Hong Wang,et al.  Effects of light quality on CO2 assimilation, chlorophyll-fluorescence quenching, expression of Calvin cycle genes and carbohydrate accumulation in Cucumis sativus. , 2009, Journal of photochemistry and photobiology. B, Biology.

[66]  C Lehfeldt,et al.  Cloning of the SNG1 Gene of Arabidopsis Reveals a Role for a Serine Carboxypeptidase-like Protein as an Acyltransferase in Secondary Metabolism , 2000, Plant Cell.

[67]  Shi-rong Guo,et al.  Evaluation of leaf morphology, structure and biochemical substance of balloon flower (Platycodon grandiflorum (Jacq.) A. DC.) plantlets in vitro under different light spectra , 2014 .

[68]  Eiji Goto,et al.  EFFECTS OF BLUE AND RED LIGHT ON STEM ELONGATION AND FLOWERING OF TOMATO SEEDLINGS , 2012 .

[69]  K. Folta,et al.  Green Light Adjusts the Plastid Transcriptome during Early Photomorphogenic Development1[W] , 2006, Plant Physiology.

[70]  Kee Yoeup Paek,et al.  Light quality affectsin Vitro growth of grape ‘Teleki 5BB’ , 2006, Journal of Plant Biology.

[71]  H. R. Gislerød,et al.  A high proportion of blue light increases the photosynthesis capacity and leaf formation rate of Rosa × hybrida but does not affect time to flower opening. , 2013, Physiologia plantarum.

[72]  J. Tibbits,et al.  beta-tubulin affects cellulose microfibril orientation in plant secondary fibre cell walls. , 2007, The Plant journal : for cell and molecular biology.

[73]  N. P. Voskresenskaya.  Blue Light and Carbon Metabolism , 1972 .

[74]  J. Kossmann,et al.  Leaf starch degradation comes out of the shadows. , 2005, Trends in plant science.

[75]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[76]  A. Conesa,et al.  Differential expression in RNA-seq: a matter of depth. , 2011, Genome research.

[77]  I. Kataoka,et al.  Effect of red- and blue-light-emitting diodes on growth and morphogenesis of grapes , 2008, Plant Cell, Tissue and Organ Culture.