Transcriptome Analysis Reveals Common and Distinct Mechanisms for Sheepgrass (Leymus chinensis) Responses to Defoliation Compared to Mechanical Wounding
Background Herbivore grazing is a multiple-component process that includes wounding, defoliation, and saliva deposition. Despite the extensive published research on mechanical wounding and defoliation, no analysis to identify the genes that specify defoliation and mechanical wounding has been performed. Moreover, the influence of the expression of these genes on plant regrowth after defoliation remains poorly understood. Results Seven cDNA libraries for RNA samples collected from stubble tissues that had been mechanically wounded or defoliated at 2, 6 and 24 h along with the control were sequenced using the Illumina/Solexa platform. A comparative transcriptomic analysis of the sequencing data was conducted. In total, 1,836 and 3,238 genes were detected with significant differential expression levels after wounding and defoliation, respectively, during one day. GO, KOG and pathway-based enrichment analyses were performed to determine and further understand the biological functions of those differentially expressed genes (DEGs). The results demonstrated that both wounding and defoliation activated the systemic synthesis of jasmonate (JA). However, defoliation specifically reduced the expression levels of ribosomal protein genes, cell division or cell expansion-related genes, and lignin biosynthesis genes and may have negatively affected plant growth. Further analysis revealed that the regrowth of elongating leaves was significantly retarded after defoliation at 6 h through the following 7 days of measurement, suggesting that the gene expression pattern and phenotype are consistent. Fifteen genes were selected, and their expression levels were confirmed by quantitative RT-PCR (qRT-PCR). Thirteen of them exhibited expression patterns consistent with the digital gene expression (DGE) data. Conclusions These sequencing datasets allowed us to elucidate the common and distinct mechanisms of plant responses to defoliation and wounding. Additionally, the distinct DEGs represent a valuable resource for novel gene discovery that may improve plant resistance to defoliation from various processes.
References
[1]
O'Mara FP (2012) The role of grasslands in food security and climate change. Ann Bot 110(6): 1263–1270.
[2]
Roche LM, Latimer AM, Eastburn DJ, Tate KW (2012) Cattle grazing and conservation of a meadow-dependent amphibian species in the Sierra Nevada. PLoS One 7(4): e35734. doi: 10.1371/journal.pone.0035734
[3]
de Villalobos AE, Zalba SM, Peláez DV (2011) Pinus halepensis invasion in mountain pampean grassland: effects of feral horses grazing on seedling establishment. Environ Res 111(7): 953–959. doi: 10.1016/j.envres.2011.03.011
[4]
Scohier A, Dumont B (2012) How do sheep affect plant communities and arthropod populations in temperate grasslands? Animal 6(7): 1129–1138. doi: 10.1017/s1751731111002618
[5]
Lapointe L, Bussières J, Crête M, Ouellet JP (2010) Impact of growth form and carbohydrate reserves on tolerance to simulated deer herbivory and subsequent recovery in Liliaceae. Am J Bot 97(6): 913–924. doi: 10.3732/ajb.0900200
[6]
Rueda M, Rebollo S, García-Salgado G (2013) Contrasting impacts of different-sized herbivores on species richness of Mediterranean annual pastures differing in primary productivity. Oecologia 172(2): 449–459. doi: 10.1007/s00442-012-2501-y
[7]
Meers T, Adams R (2003) The impact of grazing by Eastern Grey Kangaroos (Macropus giganteus) on vegetation recovery after fire at Reef Hills Regional Park, Victoria. Ecol Manage Rest 4: 126–132. doi: 10.1046/j.1442-8903.2003.00147.x
[8]
Chen S, Li XQ, Zhao A, Wang L, Li X, et al. (2009) Genes and pathways induced in early response to defoliation in rice seedlings. Curr Issues Mol Biol 11(2): 81–100.
[9]
Koo AJ, Howe GA (2009) The wound hormone jasmonate. Phytochemistry 70(13–14): 1571–1580. doi: 10.1016/j.phytochem.2009.07.018
[10]
Chung HS, Koo AJK, Gao X, Jayanty S, Thines B, et al. (2008) Regulation and function of Arabidopsis JASMONATE ZIM-domain genes in response to wounding and herbivory. Plant Physiol 146: 952–964. doi: 10.1104/pp.107.115691
[11]
Glauser G, Grata E, Dubugnon L, Rudaz S, Farmer EE, et al. (2008) Spatial and temporal dynamics of jasmonate synthesis and accumulation in Arabidopsis in response to wounding. J Biol Chem 283: 16400–16407. doi: 10.1074/jbc.m801760200
[12]
Strassner J, Schaller F, Frick U, Howe GA, Weiler EW, et al. (2002) Characterization and cDNA microarray expression analysis of 12-oxophytodienoate reductases reveals differential roles for octadecanoid biosynthesis in local versus systemic wound responses. Plant J 32: 585–601. doi: 10.1046/j.1365-313x.2002.01449.x
[13]
Lee JM, Sathish P, Donaghy DJ, Roche JR (2011) Impact of defoliation severity on photosynthesis, carbon metabolism and transport gene expression in perennial ryegrass. Funct Plant Biol 38: 808–817. doi: 10.1071/fp11048
[14]
Tamura KI, Sanada Y, Tase K, Komatsu T, Yoshida M (2011) Pp6-FEH1 encodes an enzyme for degradation of highly polymerized levan and is transcriptionally induced by defoliation in timothy (Phleum pratense L.). J Exp Bot 62(10): 3421–3431. doi: 10.1093/jxb/err018
[15]
Berthier A, Desclos M, Amiard V, Morvan-Bertrand A, Demmig-Adams B, et al. (2009) Activation of sucrose transport in defoliated Lolium perenne L.: an example of apoplastic phloem loading plasticity. Plant Cell Physiol 50(7): 1329–1344. doi: 10.1093/pcp/pcp081
[16]
Furet PM, Berthier A, Decau ML, Morvan-Bertrand A, Prud'homme MP, et al. (2012) Differential regulation of two sucrose transporters by defoliation and light conditions in perennial ryegrass. Plant Physiol Biochem 61: 88–96. doi: 10.1016/j.plaphy.2012.09.011
[17]
Castrillón-Arbeláez PA, Martínez-Gallardo N, Arnaut HA, Tiessen A, Délano-Frier JP (2012) Metabolic and enzymatic changes associated with carbon mobilization, utilization and replenishment triggered in grain amaranth (Amaranthus cruentus) in response to partial defoliation by mechanical injury or insect herbivory. BMC Plant Biol 12: 163. doi: 10.1186/1471-2229-12-163
Chen S, Huang X, Yan X, Liang Y, Wang Y, et al. (2013) Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe. PLoS One 8(7): e67974. doi: 10.1371/journal.pone.0067974
[20]
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3): R25. doi: 10.1186/gb-2009-10-3-r25
[21]
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7): 621–628. doi: 10.1038/nmeth.1226
[22]
Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26(1): 136–138. doi: 10.1093/bioinformatics/btp612
[23]
Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165–1188. doi: 10.1214/aos/1013699998
[24]
Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64–70. doi: 10.1093/nar/gkq310
[25]
Xie C, Mao X, Huang J, Ding Y, Wu J, et al. (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39: W316–322. doi: 10.1093/nar/gkr483
[26]
Lyons R, Manners JM, Kazan K (2013) Jasmonate biosynthesis and signaling in monocots: a comparative overview. Plant Cell Rep 32(6): 815–827. doi: 10.1007/s00299-013-1400-y
[27]
Wasternack C, Hause B (2013) Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Ann Bot 111(6): 1021–1058.
[28]
Zhang Y, Turner JG (2008) Wound-induced endogenous jasmonates stunt plant growth by inhibiting mitosis. PLoS One 3(11): e3699. doi: 10.1371/journal.pone.0003699
[29]
Koo AJ, Gao X, Jones AD, Howe GA (2009) A rapid wound signal activates the systemic synthesis of bioactive jasmonates in Arabidopsis. Plant J 59(6): 974–986. doi: 10.1111/j.1365-313x.2009.03924.x
[30]
Horiguchi G, Van Lijsebettens M, Candela H, Micol JL, Tsukaya H (2012) Ribosomes and translation in plant developmental control. Plant Sci 191–192: 24–34. doi: 10.1016/j.plantsci.2012.04.008
[31]
Byrne ME (2009) A role for the ribosome in development. Trends Plant Sci 14(9): 512–529. doi: 10.1016/j.tplants.2009.06.009
[32]
Schippers JHM, Mueller-Roeber B (2010) Ribosomal composition and control of leaf development. Plant Sci 179: 307–315. doi: 10.1016/j.plantsci.2010.06.012
[33]
Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, DiLoreto DS, et al. (2009) The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression. BMC Plant Biol 9: 26. doi: 10.1186/1471-2229-9-26
[34]
Guo D, Chen F, Inoue K, Blount JW, Dixon RA (2001) Downregulation of caffeic acid 3-O-methyltransferase and caffeoyl CoA 3-O-methyltransferase in transgenic alfalfa. impacts on lignin structure and implications for the biosynthesis of G and S lignin. Plant Cell 13(1): 73–88. doi: 10.2307/3871154
[35]
Day A, Neutelings G, Nolin F, Grec S, Habrant A, et al. (2009) Caffeoyl coenzyme A O-methyltransferase down-regulation is associated with modifications in lignin and cell-wall architecture in flax secondary xylem. Plant Physiol Biochem 47(1): 9–19. doi: 10.1016/j.plaphy.2008.09.011
[36]
Gallego-Giraldo L, Jikumaru Y, Kamiya Y, Tang Y, Dixon RA (2011) Selective lignin downregulation leads to constitutive defense response expression in alfalfa (Medicago sativa L.). New Phytol 190(3): 627–639. doi: 10.1111/j.1469-8137.2010.03621.x
[37]
Vargas-Ortiz E, Espitia-Rangel E, Tiessen A, Délano-Frier JP (2013) Grain amaranths are defoliation tolerant crop species capable of utilizing stem and root carbohydrate reserves to sustain vegetative and reproductive growth after leaf loss. PLoS One 8(7): e67879. doi: 10.1371/journal.pone.0067879
[38]
Ida TY, Harder LD, Kudo G (2012) Effects of defoliation and shading on the physiological cost of reproduction in silky locoweed Oxytropis sericea. Ann Bot 109(1): 237–246.
[39]
Akiyama R, ？gren J (2012) Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae). PLoS One 7(1): e30015. doi: 10.1371/journal.pone.0030015
