Abstract
Soil alkalinity is an important environmental problem limiting agricultural productivity. Wild soybean (Glycine soja) shows strong alkaline stress tolerance, so it is an ideal plant candidate for studying the molecular mechanisms of alkaline tolerance and identifying alkaline stress-responsive genes. However, limited information is available about G. soja responses to alkaline stress on a genomic scale. Therefore, in the present study, we used RNA sequencing to compare transcript profiles of G. soja root responses to sodium bicarbonate (NaHCO3) at six time points, and a total of 68,138,478 pairs of clean reads were obtained using the Illumina GAIIX. Expression patterns of 46,404 G. soja genes were profiled in all six samples based on RNA-seq data using Cufflinks software. Then, t12 transcription factors from MYB, WRKY, NAC, bZIP, C2H2, HB, and TIFY families and 12 oxidation reduction related genes were chosen and verified to be induced in response to alkaline stress by using quantitative real-time polymerase chain reaction (qRT-PCR). The GO functional annotation analysis showed that besides “transcriptional regulation” and “oxidation reduction,” these genes were involved in a variety of processes, such as “binding” and “response to stress.” This is the first comprehensive transcriptome profiling analysis of wild soybean root under alkaline stress by RNA sequencing. Our results highlight changes in the gene expression patterns and identify a set of genes induced by NaHCO3 stress. These findings provide a base for the global analyses of G. soja alkaline stress tolerance mechanisms.
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References
Agarwal PK, Jha B (2010) Transcription factors in plants and ABA dependent and independent abiotic stress signalling. Biol Plant 54:201–212
Ashraf M, Akram NA (2009) Improving salinity tolerance of plants through conventional breeding and genetic engineering: An analytical comparison. Biotechnol Adv 27:744–752. doi:10.1016/j.biotechadv.2009.05.026
Begara-Morales JC, Sanchez-Calvo B, Luque F, Leyva-Perez MO, Leterrier M, Corpas FJ, Barroso JB (2014) Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between arabidopsis roots and leaves. Plant Cell Physiol 55:1080–1095. doi:10.1093/pcp/pcu044
Chen L, Song Y, Li S, Zhang L, Zou C, Yu D (2012) The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta 1819:120–128. doi:10.1016/j.bbagrm.2011.09.002
Cordat E, Casey JR (2009) Bicarbonate transport in cell physiology and disease. Biochem J 417:423–439. doi:10.1042/BJ20081634
Dang ZH, Zheng LL, Wang J, Gao Z, Wu SB, Qi Z, Wang YC (2013) Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna. BMC Genomics 14:29. doi:10.1186/1471-2164-14-29
Day-Williams AG, Zeggini E (2011) The effect of next-generation sequencing technology on complex trait research. Eur J Clin Investig 41:561–567. doi:10.1111/j.1365-2362.2010.02437.x
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–W70. doi:10.1093/nar/gkq310
Fan XD, Wang JQ, Yang N, Dong YY, Liu L, Wang FW, Wang N, Chen H, Liu WC, Sun YP, Wu JY, Li HY (2013) Gene expression profiling of soybean leaves and roots under salt, saline-alkali and drought stress by high-throughput Illumina sequencing. Gene 512:392–402. doi:10.1016/j.gene.2012.09.100
Gao C, Wang Y, Liu G, Yang C, Jiang J, Li H (2008) Expression profiling of salinity-alkali stress responses by large-scale expressed sequence tag analysis in Tamarix hispid. Plant Mol Biol 66:245–258. doi:10.1007/s11103-007-9266-4
Ge Y, Li Y, Zhu YM, Bai X, Lv DK, Guo D, Ji W, Cai H (2010) Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC Plant Biol 10:153. doi:10.1186/1471-2229-10-153
Ge Y, Li Y, Lv DK, Bai X, Ji W, Cai H, Wang AX, Zhu YM (2011) Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. Funct Integr Genomics 11:369–379. doi:10.1007/s10142-010-0191-2
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186. doi:10.1093/nar/gkr944
Guide MUs (1998) The mathworks. Inc, Natick, MA 5:333
Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J (2008) PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res 36:D966–D969. doi:10.1093/nar/gkm841
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J Cell Mol Biol 61:1041–1052. doi:10.1111/j.1365-313X.2010.04124.x
Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J 9:922–931. doi:10.1111/j.1467-7652.2011.00625.x
Hiz MC, Canher B, Niron H, Turet M (2014) Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PLoS One 9, e92598. doi:10.1371/journal.pone.0092598
Howe EA, Sinha R, Schlauch D, Quackenbush J (2011) RNA-Seq analysis in MeV. Bioinformatics 27:3209–3210. doi:10.1093/bioinformatics/btr490
Jiang Y, Deyholos MK (2006) Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol 6:25. doi:10.1186/1471-2229-6-25
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J Cell Mol Biol 50:347–363. doi:10.1111/j.1365-313X.2007.03052.x
Koropatkin NM, Koppenaal DW, Pakrasi HB, Smith TJ (2007) The structure of a cyanobacterial bicarbonate transport protein, CmpA. J Biol Chem 282:2606–2614. doi:10.1074/jbc.M610222200
Kyndt T, Denil S, Haegeman A, Trooskens G, De Meyer T, Van Criekinge W, Gheysen G (2012) Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J Exp Bot 63:2141–2157. doi:10.1093/jxb/err435
Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059. doi:10.1038/ng.715
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:R25. doi:10.1186/gb-2009-10-3-r25
Li C, Ng CKY, Fan L-M (2014) MYB transcription factors, active players in abiotic stress signaling. Environ Exp Bot 114:80–91. doi:10.1016/j.envexpbot.2014.06.014
Liu ZQ, Yan L, Wu Z, Mei C, Lu K, Yu YT, Liang S, Zhang XF, Wang XF, Zhang DP (2012) Cooperation of three WRKY-domain transcription factors WRKY18, WRKY40, and WRKY60 in repressing two ABA-responsive genes ABI4 and ABI5 in Arabidopsis. J Exp Bot 63:6371–6392. doi:10.1093/jxb/ers293
Llorente F, Lopez-Cobollo RM, Catala R, Martinez-Zapater JM, Salinas J (2002) A novel cold-inducible gene from Arabidopsis, RCI3, encodes a peroxidase that constitutes a component for stress tolerance. Plant J Cell Mol Biol 32:13–24
Luo X, Bai X, Zhu D, Li Y, Ji W, Cai H, Wu J, Liu B, Zhu Y (2012) GsZFP1, a new Cys2/His2-type zinc-finger protein, is a positive regulator of plant tolerance to cold and drought stress. Planta 235:1141–1155. doi:10.1007/s00425-011-1563-0
Luo X, Bai X, Sun X, Zhu D, Liu B, Ji W, Cai H, Cao L, Wu J, Hu M, Liu X, Tang L, Zhu Y (2013) Expression of wild soybean WRKY20 in Arabidopsis enhances drought tolerance and regulates ABA signalling. J Exp Bot 64:2155–2169. doi:10.1093/jxb/ert073
Ma X, Sukiran NL, Ma H, Su Z (2014) Moderate drought causes dramatic floral transcriptomic reprogramming to ensure successful reproductive development in Arabidopsis. BMC Plant Biol 14:164. doi:10.1186/1471-2229-14-164
Miller G, Shulaev V, Mittler R (2008) Reactive oxygen signaling and abiotic stress. Physiol Plant 133:481–489. doi:10.1111/j.1399-3054.2008.01090.x
Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405–410
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. doi:10.1038/nmeth.1226
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349. doi:10.1126/science.1158441
Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) NAC transcription factors in plant abiotic stress responses. Biochim Biophys Acta 1819:97–103. doi:10.1016/j.bbagrm.2011.10.005
Paz RC, Rocco RA, Jimenez-Bremont JF, Rodriguez-Kessler M, Becerra-Flora A, Menendez AB, Ruiz OA (2014) Identification of differentially expressed genes potentially involved in the tolerance of Lotus tenuis to long-term alkaline stress. Plant Physiol Biochem PPB Soc Fr Physiol Veg 82:279–288. doi:10.1016/j.plaphy.2014.06.009
Postnikova OA, Shao J, Nemchinov LG (2013) Analysis of the alfalfa root transcriptome in response to salinity stress. Plant Cell Physiol 54:1041–1055. doi:10.1093/pcp/pct056
Qing DJ, Lu HF, Li N, Dong HT, Dong DF, Li YZ (2009) Comparative profiles of gene expression in leaves and roots of maize seedlings under conditions of salt stress and the removal of salt stress. Plant Cell Physiol 50:889–903. doi:10.1093/pcp/pcp038
Rushton PJ, Somssich IE, Ringler P, Shen QJ (2010) WRKY transcription factors. Trends Plant Sci 15:247–258. doi:10.1016/j.tplants.2010.02.006
Shan H, Chen S, Jiang J, Chen F, Chen Y, Gu C, Li P, Song A, Zhu X, Gao H, Zhou G, Li T, Yang X (2012) Heterologous expression of the chrysanthemum R2R3-MYB transcription factor CmMYB2 enhances drought and salinity tolerance, increases hypersensitivity to ABA and delays flowering in Arabidopsis thaliana. Mol Biotechnol 51:160–173. doi:10.1007/s12033-011-9451-1
Shi D, Sheng Y (2005) Effect of various salt–alkaline mixed stress conditions on sunflower seedlings and analysis of their stress factors. Environ Exp Bot 54:8–21
Shi SQ, Shi Z, Jiang ZP, Qi LW, Sun XM, Li CX, Liu JF, Xiao WF, Zhang SG (2010) Effects of exogenous GABA on gene expression of Caragana intermedia roots under NaCl stress: regulatory roles for H2O2 and ethylene production. Plant Cell Environ 33:149–162. doi:10.1111/j.1365-3040.2009.02065.x
Singh K, Foley RC, Onate-Sanchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436
Smil V (2000) Magic beans. Nature 407:567. doi:10.1038/35036653
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111. doi:10.1093/bioinformatics/btp120
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515. doi:10.1038/nbt.1621
Villarino GH, Bombarely A, Giovannoni JJ, Scanlon MJ, Mattson NS (2014) Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing. PloS one 9(5):e99146. doi:10.1371/journal.pone.0099146
Wang Y, Yang C, Liu G, Jiang J (2007) Development of a cDNA microarray to identify gene expression of Puccinellia tenuiflora under saline-alkali stress. Plant Physiol Biochem PPB Soc Fr Physiol Veg 45:567–576. doi:10.1016/j.plaphy.2007.05.006
Wang Y, Zhou B, Sun M, Li Y, Kawabata S (2012) UV-A light induces anthocyanin biosynthesis in a manner distinct from synergistic blue + UV-B light and UV-A/blue light responses in different parts of the hypocotyls in turnip seedlings. Plant Cell Physiol 53:1470–1480. doi:10.1093/pcp/pcs088
Wang Y, Tao X, Tang XM, Xiao L, Sun JL, Yan XF, Li D, Deng HY, Ma XR (2013) Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid. BMC Genomics 14:841. doi:10.1186/1471-2164-14-841
Wen Z, Ding Y, Zhao T, Gai J (2009) Genetic diversity and peculiarity of annual wild soybean (G. soja Sieb. et Zucc.) from various eco-regions in China. TAG Theor Appl Genet Theor Angew Genet 119:371–381. doi:10.1007/s00122-009-1045-y
Willems E, Leyns L, Vandesompele J (2008) Standardization of real-time PCR gene expression data from independent biological replicates. Anal Biochem 379:127–129. doi:10.1016/j.ab.2008.04.036
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297. doi:10.1093/nar/gkl031
Yong HY, Zou Z, Kok EP, Kwan BH, Chow K, Nasu S, Nanzyo M, Kitashiba H, Nishio T (2014) Comparative transcriptome analysis of leaves and roots in response to sudden increase in salinity in Brassica napus by RNA-seq. Biomed Res Int 2014:467395. doi:10.1155/2014/467395
Zahaf O, Blanchet S, de Zelicourt A, Alunni B, Plet J, Laffont C, de Lorenzo L, Imbeaud S, Ichante JL, Diet A, Badri M, Zabalza A, Gonzalez EM, Delacroix H, Gruber V, Frugier F, Crespi M (2012) Comparative transcriptomic analysis of salt adaptation in roots of contrasting Medicago truncatula genotypes. Mol Plant 5:1068–1081. doi:10.1093/mp/sss009
Zhai H, Bai X, Zhu Y, Li Y, Cai H, Ji W, Ji Z, Liu X, Liu X, Li J (2010) A single-repeat R3-MYB transcription factor MYBC1 negatively regulates freezing tolerance in Arabidopsis. Biochem Biophys Res Commun 394:1018–1023. doi:10.1016/j.bbrc.2010.03.114
Zhang L, Zhao G, Xia C, Jia J, Liu X, Kong X (2012) A wheat R2R3-MYB gene, TaMYB30-B, improves drought stress tolerance in transgenic Arabidopsis. J Exp Bot 63:5873–5885. doi:10.1093/jxb/ers237
Zhou QY, Tian AG, Zou HF, Xie ZM, Lei G, Huang J, Wang CM, Wang HW, Zhang JS, Chen SY (2008) Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnol J 6:486–503. doi:10.1111/j.1467-7652.2008.00336.x
Zhu D, Bai X, Chen C, Chen Q, Cai H, Li Y, Ji W, Zhai H, Lv D, Luo X, Zhu Y (2011) GsTIFY10, a novel positive regulator of plant tolerance to bicarbonate stress and a repressor of jasmonate signaling. Plant Mol Biol 77:285–297. doi:10.1007/s11103-011-9810-0
Zhu D, Cai H, Luo X, Bai X, Deyholos MK, Chen Q, Chen C, Ji W, Zhu Y (2012) Over-expression of a novel JAZ family gene from Glycine soja, increases salt and alkali stress tolerance. Biochem Biophys Res Commun 426:273–279. doi:10.1016/j.bbrc.2012.08.086
Zhu D, Bai X, Luo X, Chen Q, Cai H, Ji W, Zhu Y (2013) Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress. Plant Cell Rep 32:263–272. doi:10.1007/s00299-012-1360-7
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This work was supported by the National Natural Science Foundation of China (31171578), the Innovation Research Team in Higher School of Heilongjiang Province (2011TD005), and the Genome Alberta funded 1KP project.
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Huizi DuanMu, Yang Wang and Xi Bai contributed equally to this work.
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Gene Ontology (GO) functional categorizations of genes responding to alkaline stress at different time points. GO enrichment analysis was performed on genes whose expression changed at each time point using agriGO. The significance of the GO term was evaluated by P-values of the hypergeometric distribution algorithm. The heat map reflects the significance of GO terms enriched in these expression-changed genes at each time point. Rows indicate enriched GO terms, and columns indicate the time of stress; the color represents the –log10Pvalue: the deeper the color, the smaller the P-value (PNG 442 kb)
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DuanMu, H., Wang, Y., Bai, X. et al. Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress. Funct Integr Genomics 15, 651–660 (2015). https://doi.org/10.1007/s10142-015-0439-y
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DOI: https://doi.org/10.1007/s10142-015-0439-y