Zhang B, Wang Q, Pan X. MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol. 2007;210(2):279–89.
Article
CAS
PubMed
Google Scholar
Yates Luke A, Norbury Chris J, Gilbert Robert JC. The long and short of MicroRNA. Cell. 2013;153(3):516–9.
Article
CAS
PubMed
Google Scholar
Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. Control of leaf morphogenesis by microRNAs. Nature. 2003;425(6955):257–63.
Article
CAS
PubMed
Google Scholar
Sunkar R, Zhu J-K. Novel and stress-regulated MicroRNAs and other small RNAs from Arabidopsis. Plant Cell. 2004;16(8):2001–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brosnan CA, Voinnet O. The long and the short of noncoding RNAs. Curr Opin Cell Biol. 2009;21(3):416–25.
Article
CAS
PubMed
Google Scholar
Simon SA, Meyers BC. Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol. 2011;14(2):148–55.
Article
CAS
PubMed
Google Scholar
Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009;10(2):94–108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nobuta K, McCormick K, Nakano M, Meyers BC: Bioinformatics Analysis of Small RNAs in Plants Using Next Generation Sequencing Technologies. In: Plant MicroRNAs: Methods and Protocols. Edited by Meyers BC, Green PJ. Totowa, NJ: Humana Press; 2010: 89–106.
Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol. 2006;57(1):19–53.
Article
CAS
PubMed
Google Scholar
Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones JDG. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science. 2006;312(5772):436–9.
Article
CAS
PubMed
Google Scholar
Guo N, Ye W-W, Wu X-L, Shen D-Y, Wang Y-C, Xing H, Dou D-L. Microarray profiling reveals microRNAs involving soybean resistance to Phytophthora sojae. Genome. 2011;54(11):954–8.
Article
CAS
PubMed
Google Scholar
Li X, Wang X, Zhang S, Liu D, Duan Y, Dong W. Identification of soybean microRNAs involved in soybean cyst nematode infection by deep sequencing. PLoS One. 2012;7(6):e39650.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yan Z, Hossain MS, Valdes-Lopez O, Hoang NT, Zhai J, Wang J, Libault M, Brechenmacher L, Findley S, Joshi T, et al. Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Plant Biotechnol J. 2016;14:332–41. doi:10.1111/pbi.12387.
Mantri N, Basker N, Ford R, Pang E, Pardeshi V. The Role of Micro-Ribonucleic Acids in Legumes with a Focus on Abiotic Stress Response. The Plant Genome. 2013;6(3):1–14.
Navarro L, Jay F, Nomura K, He SY, Voinnet O. Suppression of the MicroRNA pathway by bacterial effector proteins. Science. 2008;321(5891):964–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qiao Y, Liu L, Xiong Q, Flores C, Wong J, Shi J, Wang X, Liu X, Xiang Q, Jiang S, et al. Oomycete pathogens encode RNA silencing suppressors. Nat Genet. 2013;45(3):330–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koenning SR, Wrather JA. Suppression of soybean yield potential in the continental United States from plant diseases estimated from 2006 to 2009. Plant Health Progress. 2010. doi:10.1094/PHP-2010-1122-01-RS.
Davis EL, Tylka GL. soybean cyst nematode disease: The Plant Health Instructor; 2000. doi:10.1094/PHI-I-2000-0725-01. (http://www.apsnet.org/edcenter/intropp/lessons/Nematodes/Pages/SoyCystNema.aspx).
Mitchum MG. Soybean resistance to the soybean cyst nematode Heterodera glycines: an update. Phytopathology. 2016;106(12):1444–50.
Article
PubMed
Google Scholar
Klink VP, Matthews BF. Emerging approaches to broaden resistance of soybean to soybean cyst nematode as supported by gene expression studies. Plant Physiol. 2009;151(3):1017–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong K, Barker KR, Opperman CH. Genetics of soybean-Heterodera glycines interactions. J Nematol. 1997;29(4):509–22.
CAS
PubMed
PubMed Central
Google Scholar
Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu J-K, Yu O. Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics. 2008;9(1):160.
Article
PubMed
PubMed Central
Google Scholar
Song Q-X, Liu Y-F, Hu X-Y, Zhang W-K, Ma B, Chen S-Y, Zhang J-S. Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol. 2011;11(1):5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Joshi T, Yan Z, Libault M, Jeong D-H, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, et al. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics. 2010;11(1):S14.
Article
PubMed
PubMed Central
Google Scholar
Goettel W, Liu Z, Xia J, Zhang W, Zhao PX, An Y-Q. Systems and evolutionary characterization of MicroRNAs and their underlying regulatory networks in soybean cotyledons. PLoS One. 2014;9(1):e86153.
Article
PubMed
PubMed Central
Google Scholar
Kulcheski FR, de Oliveira LF, Molina LG, Almerão MP, Rodrigues FA, Marcolino J, Barbosa JF, Stolf-Moreira R, Nepomuceno AL, Marcelino-Guimarães FC, et al. Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics. 2011;12(1):307.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu M, Li Y, Zhang Q, Xu T, Qiu L, Fan Y, Wang L. Novel MiRNA and PhasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4. PLoS One. 2014;9(10):e110051.
Article
PubMed
PubMed Central
Google Scholar
Xu S, Liu N, Mao W, Hu Q, Wang G, Gong Y. Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.). Sci Rep. 2016;6:26619.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Dong Y, Yin H, Wang N, Yang J, Liu X, Wang Y, Wu J, Li X. Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol. 2011;11(1):170.
Article
PubMed
PubMed Central
Google Scholar
Zeng HQ, Zhu YY, Huang SQ, Yang ZM. Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.). J Plant Physiol. 2010;167(15):1289–97.
Article
CAS
PubMed
Google Scholar
Li J, Todd TC, Oakley TR, Lee J, Trick HN. Host-derived suppression of nematode reproductive and fitness genes decreases fecundity of Heterodera glycines Ichinohe. Planta. 2010;232(3):775–85.
Article
CAS
PubMed
Google Scholar
Schapaugh B, Todd T: SDS and SCN Ratings of 2016 Entries. In: 2016 Soybean Performance Test.
https://webapp.agron.ksu.edu/agr_social/eu_article.throck?article_id=111; 2016. Accessed 5 June 2017.
Mazarei M, Liu W, Al-Ahmad H, Arelli PR, Pantalone VR, Stewart CN. Gene expression profiling of resistant and susceptible soybean lines infected with soybean cyst nematode. Theor Appl Genet. 2011;123(7):1193–206.
Article
CAS
PubMed
Google Scholar
Puthoff DP, Nettleton D, Rodermel SR, Baum TJ. Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. Plant J. 2003;33(5):911–21.
Article
CAS
PubMed
Google Scholar
Hosseini P, Matthews BF. Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. BMC Plant Biol. 2014;14(1):300.
Wang Y, Lan QK, Zhao X, Xu WT, Li FW, Wang QY, Chen R. Comparative Profiling of microRNA Expression in Soybean Seeds from Genetically Modified Plants and their Near-Isogenic Parental Lines. PLoS One. 2016;11(5):e0155896. https://doi.org/10.1371/journal.pone.0155896.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
Article
PubMed
PubMed Central
Google Scholar
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178–83.
Article
CAS
PubMed
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):D1178–86.
Article
CAS
PubMed
Google Scholar
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006;34(suppl_1):D140–4.
Article
CAS
PubMed
Google Scholar
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotech. 2008;26(4):407–15.
Article
Google Scholar
Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012;40(1):37–52.
Article
PubMed
Google Scholar
Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011;39(Web Server issue):W155–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010;38(Web Server issue):W64–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hewezi T, Howe P, Maier TR, Baum TJ. Arabidopsis small RNAs and their targets during cyst nematode parasitism. Mol Plant-Microbe Interact. 2008;21(12):1622–34.
Article
CAS
PubMed
Google Scholar
Zhao H, Sun R, Albrecht U, Padmanabhan C, Wang A, Coffey MD, Girke T, Wang Z, Close TJ, Roose M, et al. Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus Huanglongbing disease. Mol Plant. 2013;6(2):301–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang W, Gao S, Zhou X, Chellappan P, Chen Z, Zhou X, Zhang X, Fromuth N, Coutino G, Coffey M, et al. Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol. 2011;75(1):93–105.
Article
CAS
PubMed
Google Scholar
Feng H, Zhang Q, Wang Q, Wang X, Liu J, Li M, Huang L, Kang Z. Target of tae-miR408, a chemocyanin-like protein gene (TaCLP1), plays positive roles in wheat response to high-salinity, heavy cupric stress and stripe rust. Plant Mol Biol. 2013;83(4):433–43.
Article
CAS
PubMed
Google Scholar
Gupta OP, Permar V, Koundal V, Singh UD, Praveen S. MicroRNA regulated defense responses in Triticum Aestivum L. during Puccinia Graminis f.Sp. tritici infection. Mol Biol Rep. 2012;39(2):817–24.
Article
CAS
PubMed
Google Scholar
Li H, Deng Y, Wu T, Subramanian S, Yu O. Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol. 2010;153(4):1759–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grant D, Nelson RT, Cannon SB, Shoemaker RC. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010;38(suppl_1):D843–6.
Article
CAS
PubMed
Google Scholar
Scharte J, Schön H, Tjaden Z, Weis E, von Schaewen A. Isoenzyme replacement of glucose-6-phosphate dehydrogenase in the cytosol improves stress tolerance in plants. Proc Natl Acad Sci. 2009;106(19):8061–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Proels RK, Westermeier W, Hückelhoven R. Infection of barley with the parasitic fungus Blumeria graminis f.Sp. hordei results in the induction of HvADH1 and HvADH2. Plant Signal Behav. 2011;6(10):1584–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hren M, Nikolić P, Rotter A, Blejec A, Terrier N, Ravnikar M, Dermastia M, Gruden K: ‘Bois noir’ phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine. BMC Genomics 2009, 10:460–460.
Uehara T, Sugiyama S, Matsuura H, Arie T, Masuta C. Resistant and susceptible responses in tomato to cyst nematode are differentially regulated by salicylic acid. Plant Cell Physiol. 2010;51(9):1524–36.
Article
CAS
PubMed
Google Scholar
Kumar D, Rampuria S, Singh NK, Kirti PB. A novel zinc-binding alcohol dehydrogenase 2 from Arachis diogoi, expressed in resistance responses against late leaf spot pathogen, induces cell death when transexpressed in tobacco. FEBS Open Bio. 2016;6(3):200–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qiao Y, Shi J, Zhai Y, Hou Y, Ma W. Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection. Proc Natl Acad Sci. 2015;112(18):5850–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhai J, Jeong D-H, De Paoli E, Park S, Rosen BD, Li Y, González AJ, Yan Z, Kitto SL, Grusak MA, et al. MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev. 2011;25(23):2540–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA. MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum. PLoS Pathog. 2014;10(10):e1004464.
Article
PubMed
PubMed Central
Google Scholar
Sunkar R, Kapoor A, Zhu J-K. Posttranscriptional induction of two cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell. 2006;18(8):2051–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu C, Ding Y, Liu H. MiR398 and plant stress responses. Physiol Plant. 2011;143(1):1–9.
Article
CAS
PubMed
Google Scholar
Fridovich I. Superoxide radical and superoxide dismutases. Annu Rev Biochem. 1995;64:97–112.
Article
CAS
PubMed
Google Scholar
Thiebaut F, Rojas CA, Grativol C, Motta MR, Vieira T, Regulski M, Martienssen RA, Farinelli L, Hemerly AS, Ferreira PC. Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics. 2014;15:766.
Article
PubMed
PubMed Central
Google Scholar
Li Y, Zhang Q, Zhang J, Wu L, Qi Y, Zhou J-M. Identification of MicroRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol. 2010;152(4):2222–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Y, Lu Y-G, Shi Y, Wu L, Xu Y-J, Huang F, Guo X-Y, Zhang Y, Fan J, Zhao J-Q, et al. Multiple Rice MicroRNAs are involved in immunity against the blast fungus Magnaporthe oryzae. Plant Physiol. 2014;164(2):1077–92.
Article
CAS
PubMed
Google Scholar
Schurch NJ, Schofield P, Gierliński M, Cole C, Sherstnev A, Singh V, Wrobel N, Gharbi K, Simpson GG, Owen-Hughes T, et al. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA. 2016;22(6):839–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gierliński M, Cole C, Schofield P, Schurch NJ, Sherstnev A, Singh V, Wrobel N, Gharbi K, Simpson G, Owen-Hughes T, et al. Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. Bioinformatics. 2015;31(22):3625–30.
Article
PubMed
PubMed Central
Google Scholar
Tang G, Yan J, Gu Y, Qiao M, Fan R, Mao Y, Tang X. Construction of short tandem target mimic (STTM) to block the functions of plant and animal microRNAs. Methods. 2012;58(2):118–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yan J, Gu Y, Jia X, Kang W, Pan S, Tang X, Chen X, Tang G. Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. Plant Cell. 2012;24(2):415–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jia X, Ding N, Fan W, Yan J, Gu Y, Tang X, Li R, Tang G. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic. Plant Sci. 2015;233(0):11–21.
Article
CAS
PubMed
Google Scholar
Yan J, Zhao C, Zhou J, Yang Y, Wang P, Zhu X, Tang G, Bressan RA, Zhu J-K. The miR165/166 mediated regulatory module plays critical roles in ABA homeostasis and response in Arabidopsis thaliana. PLoS Genet. 2016;12(11):e1006416.
Article
PubMed
PubMed Central
Google Scholar
Jia X, Ding N, Fan W, Yan J, Gu Y, Tang X, Li R, Tang G. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic. Plant Sci. 2015;233:11–21.
Article
CAS
PubMed
Google Scholar
Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Chan V, Xiong Q, Yan J, et al. Roles of small RNAs in soybean defense against Phytophthora sojae infection. Plant J. 2014;79(6):928–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tian B, Li J, Oakley T, Todd T, Trick H. Host-derived artificial MicroRNA as an alternative method to improve soybean resistance to soybean cyst nematode. Genes. 2016;7(12):122.
Article
PubMed Central
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/; 2010. Accessed 29 July 2017.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJ. 2011;17(1):10.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
PubMed
Google Scholar
Liu WC, Deng Y, Zhou YG, Chen H, Dong YY, Wang N, Li XW, Jameel A, Yang H, Zhang M, et al. Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses. PLoS One. 2016;11(5):e0155606. https://doi.org/10.1371/journal.pone.0155606.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25(4):402–8.
Article
CAS
PubMed
Google Scholar