Deciphering soybean molecular stress response via high-throughput approach

  • Agata Tyczewska Institute of Bioorganic Chemistry PAS Noskowskiego 12/14 61-704 Poznań
  • Joanna Gracz Institute of Bioorganic Chemistry PAS Noskowskiego 12/14 61-704 Poznań
  • Jakub Kuczyński Institute of Bioorganic Chemistry PAS Noskowskiego 12/14 61-704 Poznań
  • Tomasz Twardowski Institute of Bioorganic Chemistry PAS Noskowskiego 12/14 61-704 Poznań
Keywords: soybean, transcriptome, miRNA, proteome, stress conditions


As a result of thousands years of agriculture humans created many crop varieties, which became the basis of our daily diet, animal feed and also industrial application. Soybean is one of the most important crops worldwide and because of its high economic value, the demand for soybean products is constantly growing. On the European continent, due to unfavorable climate conditions, soybean cultivation is restricted and we are forced to rely on imported plant material. The development of agriculture requires continuous improvements in quality and yield of crop varieties to changing or adverse conditions, namely stresses. To achieve this goal we need to recognize and understand molecular dependencies underlying plant stress responses. With the advent of new technologies in studies of plant transcriptomes and proteomes, now we have tools to fast and more precisely elucidate of desirable crop traits. Here we present an overview of high-throughput techniques used to analyze soybean’s responses to different abiotic (drought, flooding, cold stress, salinity, phosphate deficiency) and biotic (infection of F. oxysporum, cyst nematode, SMV) stress conditions on the level of transcriptome (mRNAs and miRNAs) and proteome.


Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V et al. (2005) Computational prediction of miRNAs in Arabidopsis thaliana. 15:78-91. doi: 10.1101/gr.2908205

Agarwal P, Parida SK, Mahto A, Das S, Mathew IE et al. (1997) Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnol J. 9:1480-92. doi: 10.1002/biot.201400063

Arias MM, Leandro LF, Munkvold GP (2013) Aggressiveness of Fusarium species and impact of root infection on growth and yield of soybeans. Phytopathology. 103:822-32. doi: 10.1094/PHYTO-08-12-0207-R

Armstrong W (1979) Aeration in higher plants. Adv Bot Res. 7:225-232.

Augusto Guimaraes FV, de Lacerda CF, Marques EC, Alcantara de Miranda MR, Braga de A et al. (2011) Calcium can moderate changes on membrane structure and lipid composition in cowpea plants under salt stress. Plant Growth Regul. 65:55-63. doi: 10.1007/s10725-011-9574-1

Balestrasse KB, Tomaro ML, Batlle A, Noriega GO (2010) The role of 5-aminolevulinic acid in the response to cold stress in soybean plants. Phytochemistry. 71:2038-2045. doi: 10.1016/j.phytochem.2010.07.012

Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297. doi:10.1016/S0092-8674(04)00045-5

Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S et al.(2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37:766-770. doi:10.1038/ng1590

Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. Environ Mol Mutagen. 49:61-72.

Chaves MM, Flexas J, Pinheiro C (2009) Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot. 103:551-60. doi: 10.1093/aob/mcn125

Chen LM, Zhou XA, Li WB, Chang W, Zhou R et al. (2013) Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions. BMC Genomics. 6:687. doi: 10.1186/1471-2164-14-687

Chen Z, Cui Q, Liang C, Sun L, Tian J (2011) Identification of differentially expressed proteins in soybean nodules under phosphorus deficiency through proteomic analysis, Proteomics. 11:4648-4659. doi: 10.1002/pmic.201100231

Chinnusamy V, Zhu J, Zhu JK (2007) Cold stress regulation of gene expression in plants. Trends in Plant Science. 12:444-451.

Cozzone AJ (1988) Protein phosphorylation in prokaryotes. Annu. Rev. Microbiol. 42:97-125. doi:10.1146/annurev.mi.42.100188.000525

Cruz-Ramírez A, Oropeza-Aburto A, Razo-Hernández F, Ramírez-Chávez E, Herrera-Estrella L (2006) Phospholipase DZ2 plays an important role in extraplastidic galactolipid biosynthesis and phosphate recycling in Arabidopsis roots. Proc Natl Acad Sci U S A. 103:6765-70

Dong Z, Shi L, Wang Y, Chen L, Cai Z, Wang Y, Jin J, Li X (2013) Identification and dynamic regulation of microRNAs involved in salt stress responses in functional soybean nodules by high-throughput sequencing. Int. J. Mol. Sci., 14: 2717-2738. doi: 10.3390/ijms14022717

Fu H, Tie Y, Xu C, Zhang Z, Zhu J et al. (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett. 579:3849-3854. doi: 10.1016/j.febslet.2005.05.064

Garrett RD, Rueda X, Lambin EF (2014) Globalization’s unexpected impact on soybean production in South America: linkages between preferences for non-genetically modified crops, eco-certifications, and land use. Environ. Res. Lett. 8:1-11.

Gibbs J, Greenway H (2003) Mechanisms of anoxia tolerance in plants. I. Growth, survival and anaerobic catabolism. Funct Plant Biol. 30:353. doi:10.1071/PP98095.

Githiri SM, Watanabe S, Harada K, Takahashi R (2006) QTL analysis of flooding tolerance in soybean at an early vegetative growth stage. Plant Breed. 125:613-8. doi: 10.1111/j.1439-0523.2006.01291.x

Gracz J (2016) Alternative splicing in plant stress response. BioTechnologia. 97:9-17 doi: 10.5114/bta.2016.57719

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40:D1178-86. doi: 10.1093/nar/gkr944

Han X, Aslanian A, Yates JRIII (2008) Mass Spectrometry for Proteomics. Curr Opin Chem Biol. 12: 483–490. doi: 10.1016/j.cbpa.2008.07.024

Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Ann. Rev. of Plant Physiol. and Plant Mol. Biol. 51:463-499.

Hu Z, Jiang Q, Ni Z, Chen R, Xu S, Zhang H (2013) Analyses of a Glycine max degradome library identify microRNA targets and microRNAs that trigger secondary siRNA biogenesis. Journal of Integrative Plant Biology. 55:160-176. doi: 10.1111/jipb.12002

Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biol. 47: 377-403.

Jackson MB, Colmer TD (2005) Response and adaptation by plants to flooding stress. Ann Bot. 96:501-5

Kavar T, Maras M, Kidric M, Sustar-Vozlic J, Meglic V (2007) Identification of genes involved in the response of leaves of Phaseolus vulgaris to drought stress, Mol. Breed. 21:159-172. doi: 10.1007/s11032-007-9116-8

Khan MN, Sakata K, Komatsu S (2015) Proteomic analysis of soybean hypocotyl during recovery after flooding stress, J. Proteomics. 121:15-27. doi: 10.1016/j.jprot.2015.03.020

Komatsu S, Kobayashi Y, Nishizawa K, Nanjo Y, Furukawa K (2010) Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress, Amino Acids. 39:1435-1449. doi: 10.1007/s00726-010-0608-1

Komatsu S, Shirasaka N, Sakata KJ (2013) 'Omics' techniques for identifying flooding-response mechanisms in soybean. Proteomics. 93:169-178. doi: 10.1016/j.jprot.2012.12.016

Lanubile A, Muppirala UK, Severin AJ, Marocco A, Munkvold GP (2015)Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum. BMC Genomics. 16:1089. doi: 10.1186/s12864-015-2318-2

Le DT, Nishiyama R, Watanabe Y, Tanaka M, Seki M et al. (2012) Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis. PLoS One. 7:e49522. doi: 10.1371/journal.pone.0049522

Le Roux MR, Ward CL, Botha FC, Valentine AJ (2006) The route of pyruvate synthesis under Pi starvation in legume root systems. New Phytol. 169:399–408. doi/10.1111/j.1469-8137.2005.01594.x

Levitt J (1980) Responses of plants to environmental stresses. Vol 2. Water, radiation, salt and other stresses. Academic Press, New York, pp 93–128

Li H, Dong Y, Yin H, Wang N, Yang J et al. (2011) Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biology 11:170. doi: 10.1186/1471-2229-11-170

Li Q, Cao J, Yu L, Li M, Liao J et al. (2012) Effects on physiological characteristics of honeysuckle (Lonicera japonica Thunb) and the role of exogenous calcium under drought stress. Plant Omics. 2012: 5:1–5.

Li X, Wang X, Zhang S, Liu D, Duan Y et al. (2012) Identification of soybean microRNAs involved in soybean cyst nematode infection by deep sequencing. PLoS ONE 7: e39650. doi:10.1371

Li Y, Li W, Jin YX (2005) Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa. Acta Biochim. Biophys. Sin. 37:75-87. doi: 10.1093/abbs/37.2.75

Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev. 17:991-1008. doi: 10.1101/gad.1074403

Ma G, Chen P, Buss GR, Tolin SA (2004) Genetics of resistance to two strains of Soybean mosaic virus in differential soybean genotypes. Journal of Heredity 95:322-326. doi: 10.1093/jhered/esh059

Ma H, Song L, Shu Y, Wang S, Niu J et al. (2012) Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes, J. Proteomics. 75:1529-1546. doi: 10.1016/j.jprot.2011.11.026

Mańkowski D, Laudański Z, Flaszka M (2012) Propozycja metody oceny postępu biologicznego i technologicznego w uprawie roślin na przykładzie pszenicy ozimej. Biuletyn IHAR. 263:91-104.

Mazzucotelli E, Mastrangelo AM, Crosatti C, Guerra D, Stanca AM et al. (2008) Abiotic stress response in plants: When post-transcriptional and post-translational regulations control transcription. Plant Sci. 174:420-431. doi:10.1016/j.plantsci.2008.02.005

Mitulović G, Mechtler K (2006) HPLC techniques for proteomics analysis—a short overview of latest developments. Brief Funct Genomic Proteomic. 5:249-60.

Munns, R, Tester M (2008) Mechanisms of salinity tolerance. Annual Rev. of Plant Biol. 59:651-681. doi: 10.1146/annurev.arplant.59.032607.092911

Nanjo Y, Maruyama K, Yasue H, Yamaguchi-Shinozaki K, Shinozaki K (2011) Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings. Plant Mol Biol. 77:129-44. doi: 10.1007/s11103-011-9799-4

Nanjo Y, Skultety L, Ashraf Y, Komatsu S (2010) Comparative proteome analysis of early-stage sybean seedlings responses to flooding by using gel and gel-free techniques. J Proteome Res. 9:3989-4002. doi: 10.1021/pr100179f

Nanjo Y, Skultety L, Uváčková LU, Klubicová K, Hajduch M et al. (2011) Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. J Proteome Res. 11:372-85. doi: 10.1021/pr100179f

Olivera M, Tejera N, Iribarne C, Ocan´a A, Lluch C (2004) Growth, nitrogen fixation and ammonium assimilation in common bean (Phaseolus vulgaris): effect of phosphorus. Physiol. Plantarum. 121:498-505. doi: 10.1111/j.0031-9317.2004.00355.x

Oliveira BM, Coorssen JR, Martins-de-Souza D (2014) 2DE: the phoenix of proteomics. J Proteomics. 104:140-150. doi: 10.1016/j.jprot.2014.03.035

Price AH, Cairns JE, Horton P, Jones HG, Griffiths H (2002) Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses. J Exp Bot. 53:989-1004.

Qiu Y, Xi J, Du L, Suttle JC, Poovaiah BW (2012) Coupling calcium/calmodulin-mediated signaling and herbivore-induced plant response through calmodulin-binding transcription factor AtSR1/CAMTA3. Plant Mol Biol. 79:89-99. doi: 10.1007/s11103-012-9896-z

Ranjeva R, Boudet AM (1987) Phosphorylation of proteins in plants: regulatory effects and potential involvement in stimulus/response coupling. Annu Rev Plant Biol. 38:73-94. doi: 10.1146/annurev.pp.38.060187.000445.

Sa TM, Israel DW (1991) Energy status and functioning of phosphorus–deficient soybean nodules. Plant Physiol. 97:928-935.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature. 463:178-83. doi: 10.1038/nature08670

Shao HB, Chu LY, Jaleel CA, Zhao CX (2008) Water-deficit stress-induced anatomical changes in higher plants. C R Biol. 331:215-25. doi: 10.1016/j.crvi.2008.01.002

Shin JH, Vaughn JN, Abdel-Haleem H, Chavarro C, Abernathy B et al. (2015) Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance. BMC Plant Biol. 3:26. doi: 10.1186/s12870-015-0422-8

Sun Z, Wang Y, Mou F, Tian Y, Chen L et al. (2016) Genome-wide small RNA analysis of soybean reveals auxin-responsive microRNAs that are differentially expressed in response to salt stress in root. Apex. Front. Plant Sci. 6:1273. doi: 10.3389/fpls.2015.01273

Sunkar R (2010) MicroRNAs with macro-effects on plant stress responses. Seminars in Cell & Developmental Biology. 21:805-811. doi:10.1016/j.semcdb.2010.04.001

Sunkar R, Girke T, Zhu JK (2005) Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res. 33:4443-4454. doi: 10.1093/nar/gki758

Tang C, Hinsinger P, Drevon JJ, Jaillard B (2001) Phosphorus deficiency impairs early nodule functioning and enhances proton release in roots of Medicago truncatula. L. Ann. Bot. 88:131-138. doi: 10.1006/anbo.2001.1440

Tian X, Liu Y, Huang Z, Duan H, Tong J (2015) Comparative proteomic analysis of seedling leaves of cold-tolerant and -sensitive spring soybean cultivars. Mol Biol Rep. 42:581-601. doi: 10.1007/s11033-014-3803-4.

Timperio AM, Egidi MG, Zolla L (2008) Proteomics applied on plant abiotic stresses: Role of heat shock proteins (HSP). Journal of Proteomics. 71:391-411. doi:10.1016/j.jprot.2008.07.005

Thao NP, Tran LS (2011) Potentials toward genetic engineering of drought tolerant soybean. Crit Rev Biotechnol. 32:349-62 doi:10.3109/07388551.2011.643463

Trindade I, Santos D, Dalmay T, Fevereiro P (2011) Facing the environment: small RNAs and the regulation of gene expression under abiotic stress in plants. In Abiotic Stress Response in Plants - Physiological, Biochemical and Genetic Perspectives. Shanker A, Venkateswarlu B eds, pp 113-136. InTech. doi: 10.5772/22250

Tripathi P, Rabara RC, Reese RN, Miller MA, Rohila JS et al. (2016) A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes. BMC Genomics. 17:102. doi: 10.1186/s12864-016-2420-0

Turner NC, Wright GC, Siddique KHM (2001) Adaptation of grain legumes (pulses) to water-limited environments, Adv. Agron. 71:123-231. doi:10.1016/S0065-2113(01)71015-2

Tuteja N, Mahajan S (2007) Calcium signaling network in plants: an overview. Plant Signal Behav. 2:79-85.

Tyczewska A, Gracz J, Twardowski T, Malyska A (2014) Soja przyszłością polskiego rolnictwa? Nauka. 4/2014:121-138.

Vance CP, Uhde-stone C, Allan DL (2003) Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytol. 157:423-447. doi: 10.1046/j.1469-8137.2003.00695.x

Wang Q, Wang J, Yang Y, Du W, Zhang D et al. (2016) A genome-wide expression profile analysis reveals active genes and pathways coping with phosphate starvation in soybean. BMC Genomics. 17:192. doi: 10.1186/s12864-016-2558-9.

Wang WX, Vinocur B, Altman A. (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta. 218:1-14.

Wrather JA, Koenning SR (2009) Effects of diseases on soybean yields in the United States 1996 to 2007. Online. Plant Health Progress. doi:10.1094/PHP-2009-0401-01-RS.

Xu F, Liu Q, Chen L, Kuang J, Walk T, Wang J, Liao H (2013) Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation. BMC Genomics 14:66. doi: 10.1186/1471-2164-14-66

Yin X, Komatsu S (2015) Quantitative proteomics of nuclear phosphoproteins in the root tip of soybean during the initial stages of flooding stress, J. Proteomics. 119:183 – 195. doi: 10.1016/j.jprot.2015.02.004.

Yin X, Sakata K, Nanjo Y, Komatsu S (2014) Analysis of initial changes in the proteins of soybean root tip under flooding stress using gel-free and gel-based proteomic techniques. J. Proteomics. 106: 1-16. doi: 10.1016/j.jprot.2014.04.004

Yin X, Wang J, Cheng H, Wang X, Yu D (2013) Detection and evolutionary analysis of soybean miRNAs responsive to soybean mosaic virus. Planta 237:1213–1225. doi: 10.1007/s00425-012-1835-3

Yin Y, Yang R, Guo Q, Gu Z (2014) NaCl stress and supplemental CaCl2 regulating GABA metabolism pathways in germinating soybean. Eur Food Res Technol. 238:781–788. doi: 10.1007/s00217-014-2156-5

Yin Y, Yang R, Han Y, Gu Z (2015) Comparative proteomic and physiological analyses reveal the protective effect of exogenous calcium on the germinating soybean response to salt stress, J. Proteomics. 113:110-126. doi: 10.1016/j.jprot.2014.09.023

Yuan H, Liu D (2008) Signaling components involved in plant responses to phosphate starvation. J Integr Plant Biol 50:849−859. doi: 10.1111/j.1744-7909.2008.00709.x

Zeng H, Wang G, Zhang Y, Hu X, Pi E et al. (2015) Genome-wide identification of phosphate-deficiency-responsive genes in soybean roots by high-throughput sequencing. Plant and Soil. 398:207-227. doi:10.1007/s11104-015-2657-4

Zenga HQ, Zhub YY, Huanga SQ, Yanga ZM (2010) Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.). Journal of Plant Physiology 167:1289-1297. doi:10.1016/j.jplph.2010.04.017

Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA: A small regulatory molecule with big impact. Developmental Biology 289: 3 – 16. doi: 10.1016/j.ydbio.2005.10.036

Zhu JK (2007) Plant Salt Stress. eLS. doi: 10.1002/9780470015902.a0001300.pub2