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Identification of Fusarium graminearum-responsive miRNAs and their targets in wheat by sRNA sequencing and degradome analysis

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Abstract

Fusarium head blight (FHB), a prevalent disease of bread wheat (Triticum aestivum L.) caused by Fusarium graminearum, leads to considerable losses of yield and quality in wheat production. MicroRNAs (miRNAs) are important regulators of plant defense responses. Here, to better understand the F. graminearum-responsive miRNAs, we constructed sRNA libraries for wheat cultivar Sumai 3 challenged with F. graminearum and sterile water, respectively. As a result, a total of 203 known miRNAs from 46 families and 68 novel miRNAs were identified. Among them, 18 known and six novel miRNAs were found to be differentially expressed between the F. graminearum-infected samples and the controls and thus were considered to be responsive to F. graminearum. The expression patterns of eight miRNAs were further validated by stem-loop qRT-PCR. Meanwhile, target genes were validated by degradome sequencing. Integrative analysis of the differentially expressed miRNAs and their targets revealed complex miRNA-mediated regulatory networks involved in the response of wheat to F. graminearum infection. Our findings are expected to facilitate a better understanding of the miRNA regulation in wheat-F. graminearum interaction.

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References

  1. Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25:130–131. https://doi.org/10.1093/bioinformatics/btn604

  2. Akpinar BA, Kantar M, Budak H (2015) Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct Integr Genomics 15:587–598. https://doi.org/10.1007/s10142-015-0453-0

  3. Alptekin B, Langridge P, Budak H (2017) Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 17:145–170. https://doi.org/10.1007/s10142-016-0525-9

  4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. https://doi.org/10.1038/75556

  5. Bai G, Shaner G (2004) Management and resistance in wheat and barley to Fusarium head blight. Annu Rev Phytopathol 42:135–161. https://doi.org/10.1146/annurev.phyto.42.040803.140340

  6. Bi C, Chen F, Jackson L, Gill BS, Li W (2011) Expression of lignin biosynthetic genes in wheat during development and upon infection by fungal pathogens. Plant Mol Biol Rep 29:149–161. https://doi.org/10.1007/s11105-010-0219-8

  7. Biselli C, Bagnaresi P, Faccioli P, Hu X, Balcerzak M, Mattera MG, Yan Z, Ouellet T, Cattivelli L, Vale G (2018) Comparative transcriptome profiles of near-isogenic hexaploid wheat lines differing for effective alleles at the 2DL FHB resistance QTL. Front Plant Sci 9:37. https://doi.org/10.3389/fpls.2018.00037

  8. Budak H, Akpinar BA (2015) Plant miRNAs: biogenesis, organization and origins. Funct Integr Genomics 15:523–531. https://doi.org/10.1007/s10142-015-0451-2

  9. Budak H, Zhang B (2017) MicroRNAs in model and complex organisms. Funct Intergr Genomics 17:121–124. https://doi.org/10.1007/s10142-017-0544-1

  10. Budak H, Kantar M, Bulut R, Akpinar BA (2015a) Stress responsive miRNAs and isomiRs in cereals. Plant Sci 235:1–13. https://doi.org/10.1016/j.plantsci.2015.02.008

  11. Budak H, Khan Z, Kantar M (2015b) History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress. Brief Funct Genomics 14:189–198. https://doi.org/10.1093/bfgp/elu021

  12. Buerstmayr H, Ban T, Anderson JA (2009) QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review. Plant Breed 128:1–26. https://doi.org/10.1111/j.1439-0523.2008.01550.x

  13. Buhrow LM, Cram D, Tulpan D, Foroud NA, Loewen MC (2016) Exogenous abscisic acid and gibberellic acid elicit opposing effects on Fusarum graminearum infection in what. Phytopathology 9:986–996. https://doi.org/10.1094/PHYTO-01-16-0033-R

  14. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179. https://doi.org/10.1093/nar/gni178

  15. Chen Y, Gao Q, Huang M, Liu Y, Liu Z, Liu X, Ma Z (2015) Characterization of RNA silencing components in the plant pathogenic fungus Fusarium graminearum. Sci Rep 5:12500. https://doi.org/10.1038/srep12500

  16. Chen W, Kastner C, Nowara D, Oliveira-Garcia E, Rutten T, Zhao Y, Deising HB, Kumlehn J, Schweizer P (2016) Host-induced silencing of Fusarium culmorum genes protects wheat from infection. J Exp Bot 67:4979–4991. https://doi.org/10.1093/jxb/erw263

  17. Cheng W, Song XS, Li HP, Cao LH, Sun K, Qiu XL, Xu YB, YangP HT, Zhang JB, Qu B, Liao YC (2015) Host-induced gene silencing of an essential chitin synthase gene confers durable resistance to Fusarium head blight and seedling blight in wheat. Plant Biotechnol J 13:1335–1345. https://doi.org/10.1111/pbi.12352

  18. Dhokane D, Karre S, Kushalappa AC, McCartney C (2016) Integrated metabolo-transcriptomics reveals Fusarium head blight candidate resistance genes in wheat QTL-Fhb2. PLoS One 11:e0155851. https://doi.org/10.1371/journal.pone.0155851

  19. Ding L, Xu H, Yi H, Yang L, Kong Z, Zhang L, Xue S, Jia H, Ma Z (2011) Resistance to hemi-biotrophic F. graminearum infection is associated with coordinated and ordered expression of diverse defense signaling pathways. PLoS One 6:e19008. https://doi.org/10.1371/journal.pone.0019008

  20. Feng H, Wang B, Zhang Q, Fu Y, Huang L, Wang X, Kang Z (2015) Exploration of microRNAs and their targets engaging in the resistance interaction between wheat and stripe rust. Front Plant Sci 6:469. https://doi.org/10.3389/fpls.2015.00469

  21. Fu ZQ, Dong X (2013) Systemic acquired resistance: turning local infection into global defense. Annu Rev Plant Biol 64:839–863. https://doi.org/10.1146/annurev-arplant-042811-105606

  22. Gao MJ, Li X, Huang J, Groop GM, Gjetvaj B, Lindsay DL, Wei S, Coutu C, Chen Z, Wan XC, Hannoufa A, Lydiate DJ, Gruber MY, Chen ZJ, Hegedus DD (2015) SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme. Nat Commun 6:7234. https://doi.org/10.1038/ncomms8243

  23. German MA, Luo S, Schroth G, Meyers BC, Green PJ (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 4:356–362. https://doi.org/10.1038/nprot.2009.8

  24. Golkari S, Gilbert J, Ban T, Procunier JD (2009) QTL-specific microarray gene expression analysis of wheat resistance to Fusarium head blight in Sumai-3 and two susceptible NILs. Genome 52:409–418. https://doi.org/10.1139/g09-018

  25. Goswami RS, Kistler HC (2004) Heading for disaster: Fusarium graminearum on cereal crops. Mol Plant Pathol 5:515–525. https://doi.org/10.1111/j.1364-3703.2004.00252.x

  26. Gottwald S, Samans B, Luck S, Friedt W (2012) Jasmonate and ethylene dependent defence gene expression and suppression of fungal virulence factors: two essential mechanisms of Fusarium head blight resistance in wheat? BMC Genomics 13:369. https://doi.org/10.1186/1471-2164-13-369

  27. Gunnaiah R, Kushalappa AC, Duggavathi R, Fox S, Somers DJ (2012) Integrated metabolo-proteomic approach to decipher the mechanisms by which wheat QTL (Fhb1) contributes to resistance against Fusarium graminearum. PLoS One 7:e40695. https://doi.org/10.1371/journal.pone.0040695

  28. Hofstad AN, Nussbaumer T, Akhunov E, Shin S, Kugler KG, Kistler HC, Mayer KF, Muehlbauer GJ (2016) Examining the transcriptional response in wheat Fhb1 near-isogenic lines to Fusarium graminearum infection and deoxynivalenol treatment. Plant Genome 9:1–15. https://doi.org/10.3835/plantgenome2015.05.0032

  29. Jagadeeswaran G, Saini A, Sunkar R (2009) Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis. Planta 229:1009–1014. https://doi.org/10.1007/s00425-009-0889-3

  30. Ji HM, Zhao M, Gao Y, Cao XX, Mao HY, Zhou Y, Fan WY, Borkovich KA, Quyang SQ, Liu P (2018) FRG3, a target of slmiR482e-3p, provides resistance against the fungal pathogen Fusarium oxysporum in tomato. Front Plant Sci 9:26. https://doi.org/10.3389/fpls.2018.00026

  31. Jia H, Cho S, Muehlbauer GJ (2009) Transcriptome analysis of a wheat near-isogenic line pair carrying Fusarium head blight-resistant and -susceptible alleles. Mol Plant-Microbe Interact 22:1366–1378. https://doi.org/10.1094/MPMI-22-11-1366

  32. Jia H, Zhou J, Xue S, Li G, Yan H, Ran C, Zhang Y, Shi J, Jia L, Wang X, Luo J, Ma Z (2018) A journey to understand wheat Fusarium head blight resistance in the Chinese wheat landrace Wangshuibai. Crop J 6:48–59. https://doi.org/10.1016/j.cj.2017.09.006

  33. Jiao J, Peng D (2018) Wheat microRNA1023 suppresses invasion of Fusarium graminearum via targeting and silencing FGSG_03101. J Plant Interact 13:514–521. https://doi.org/10.1080/17429145.2018.1528512

  34. Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329. https://doi.org/10.1038/nature05286

  35. Koch A, Kumar N, Weber L, Keller H, Imani J, Kogel KH (2013) Host-induced gene silencing of cytochrome P450 lanosterol C14α-demethylase–encoding genes confers strong resistance to Fusarium species. Proc Natl Acad Sci U S A 110:19324–19329. https://doi.org/10.1073/pnas.1306373110

  36. Koch A, Biedenkopf D, Furch A, Weber L, Rossbach O, Abdellatef E, Linicus L, Johannsmeier J, Jelonek L, Goesmann A, Cardoza V, McMillan J, Mentzel T, Kogel KH (2016) An RNAi-based control of Fusarium graminearum infections through spraying of long dsRNAs involves a plant passage and is controlled by the fungal silencing machinery. PLoS Pathog 12:e1005901. https://doi.org/10.1371/journal.ppat.1005901

  37. Kong L, Ohm HW, Anderson JM (2007) Expression analysis of defense-related genes in wheat in response to infection by Fusarium graminearum. Genome 50:1038–1048. https://doi.org/10.1139/g07-085

  38. Kugler KG, Siegwart G, Nussbaumer T, Ametz C, Spannagl M, Steiner B, Lemmens M, Mayer KF, Buerstmayr H, Schweiger W (2013) Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.). BMC Genomics 14:728. https://doi.org/10.1186/1471-2164-14-728

  39. Kumar D, Dutta S, Singh D, Prabhu KV, Kumar M, Mukhopadhyay K (2017) Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis. Planta 245:161–182. https://doi.org/10.1007/s00425-016-2600-9

  40. Lee HI, Leon J, Raskin I (1995) Biosynthesis and metabolism of salicylic acid. Proc Natl Acad Sci U S A 92:4076–4079

  41. Li G, Yen Y (2008) Jasmonate and ethylene signaling pathway may mediate Fusarium head blight resistance in wheat. Crop Sci 48:1888–1896. https://doi.org/10.2135/cropsci2008.02.0097

  42. Li C, Zhang B (2016) MicroRNAs in control of plant development. J Cell Physiol 231:303–313. https://doi.org/10.1002/jcp.25125

  43. Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B (2012) MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci U S A 109:1790–1795. https://doi.org/10.1073/pnas.1118282109

  44. Li D, Wang F, Wang C, Zou L, Wang Z, Chen Q, Niu C, Zhang R, Ling Y, Wang B (2016a) MicroRNA-mediated susceptible poplar gene expression regulation associated with the infection of virulent Melampsora larici-populina. BMC Genomics 17:59. https://doi.org/10.1186/s12864-015-2286-6

  45. Li X, Shahid MQ, Wu J, Wang L, Liu X, Lu Y (2016b) Comparative small RNA analysis of pollen development in autotetraploid and diploid rice. Int J Mol Sci 17:499. https://doi.org/10.3390/ijms17040499

  46. Liu J, Cheng X, Liu D, Xu W, Wise R, Shen QH (2014) The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling. PLoS Genet 10:e1004755. https://doi.org/10.1371/journal.pgen.1004755

  47. Liu H, Able AJ, Able JA (2016) SMARTER de-stressed cereal breeding. Trends Plant Sci 21:909–925. https://doi.org/10.1016/j.tplants.2016.07.006

  48. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262

  49. Long XY, Balcerzak M, Gulden S, Cao W, Fedak G, Wei YM, Zheng YL, Somers D, Ouellet T (2015) Expression profiling identifies differentially expressed genes associated with the Fusarium head blight resistance QTL 2DL from the wheat variety Wuhan-1. Physiol Mol Plant Pathol 90:1–11. https://doi.org/10.1016/j.pmpp.2015.02.002

  50. Machado AK, Brown NA, Urban M, Kanyuka K, Hammond-Kosack KE (2018) RNAi as an emerging approach to control Fusarium head blight disease and mycotoxin contamination in cereals. Pest Manag Sci 74:790–799. https://doi.org/10.1002/ps.4748

  51. Makandar R, Nalam VJ, Lee H, Trick HN, Dong Y, Shah J (2012) Salicylic acid regulates basal resistance to Fusarium head blight in wheat. Mol Plant-Microbe Interact 25:431–439. https://doi.org/10.1094/MPMI-09-11-0232

  52. Marin-Rodriguez MC, Orchard J, Seymour GB (2002) Pectate lyases, cell wall degradation and fruit softening. J Exp Bot 53:2115–2119. https://doi.org/10.1093/jxb/erf089

  53. Muhovski Y, Batoko H, Jacquemin JM (2012) Identification, characterization and mapping of differentially expressed genes in a winter wheat cultivar (Centenaire) resistant to Fusarium graminearum infection. Mol Biol Rep 39:9583–9600. https://doi.org/10.1007/s11033-012-1823-5

  54. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones JD (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312:436–439. https://doi.org/10.1126/science.1126088

  55. Nussbaumer T, Warth B, Sharma S, Ametz C, Bueschl C, Parich A, Pfeifer M, Siegwart G, Steiner B, Lemmens M, Schuhmacher R, Buerstmayr H, Mayer KF, Kugler KG, Schweiger W (2015) Joint transcriptomic and metabolomic analyses reveal changes in the primary metabolism and imbalances in the subgenome orchestration in the bread wheat molecular response to Fusarium graminearum. G3 5:2579–2592. https://doi.org/10.1534/g3.115.021550

  56. Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA (2014) MircoRNAs supress NB domain genes in tomato that confer resistance to Fusarium oxysporum. PLoS Pathog 10:e1004464. https://doi.org/10.1371/journal.ppat.1004464

  57. Palusa SG, Golovkin M, Shin SB, Richardson DN, Reddy AS (2007) Organ-specific, developmental, hormonal and stress regulation of expression of putative pectate lyase genes in Arabidopsis. New Phytol 174:537–550. https://doi.org/10.1111/j.1469-8137.2007.02033.x

  58. Pestka JJ (2010) Deoxynivalenol: mechanisms of action, human exposure, and toxicological relevance. Arch Toxicol 84:663–679. https://doi.org/10.1007/s00204-010-0579-8

  59. Pritsch C, Muehlbauer GJ, Bushnell WR, Somers DA, Vance CP (2000) Fungal development and induction of defense response genes during early infection of wheat spikes by Fusarium graminearum. Mol Plant-Microbe Interact 13:159–169. https://doi.org/10.1094/MPMI.2000.13.2.159

  60. Qi PF, Balcerzak M, Rocheleau H, Leung W, Wei YM, Zheng YL, Ouellet T (2016) Jasmonic acid and abscisic acid play important roles in host-pathogen interaction between Fusarium graminearum and wheat during the early stages of Fusarium head blight. Phsiol Mol Plant Pathol 93:39–48. https://doi.org/10.1016/j.pmpp.2015.12.004

  61. Ragupathy R, Ravichandran S, Mahdi MSR, Huang D, Reimer E, Domaratzki M, Cloutier S (2016) Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV. Sci Rep 6:39373. https://doi.org/10.1038/srep39373

  62. Rawat N, Pumphrey MO, Liu S, Zhang X, Tiwari VK, Ando K, Trick HN, Bockus WW, Akhunov E, Anderson JA, Gill BS (2016) Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight. Nat Genet 48:1576–1580. https://doi.org/10.1038/ng.3706

  63. Schweiger W, Steiner B, Ametz C, Siegwart G, Wiesenberger G, Berthiller F, Lemmens M, Jia H, Adam G, Muehlbauer GJ, Kreil DP, Buerstmayr H (2013) Transcriptomic characterization of two major Fusarium resistance quantitative trait loci (QTLs), Fhb1 and Qfhs.ifa-5A, identifies novel candidate genes. Mol Plant Pathol 14:772–785. https://doi.org/10.1111/mpp.12048

  64. Song G, Zhang R, Zhang S, Li Y, Gao J, Han X, Chen M, Wang J, Li W, Li G (2017) Response of microRNAs to cold treatment in the young spikes of common wheat. BMC Genomics 18:212. https://doi.org/10.1186/s12864-017-3556-2

  65. Stefanowicz K, Lannoo N, Van Damme EJM (2015) Plant F-box proteins – judges between life and death. Crit Rev Plant Sci 34:523–552. https://doi.org/10.1080/07352689.2015.1024566

  66. Sun XL, Jones WT, Rikkerink E (2012) GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signaling. Biochem J 442:1–12. https://doi.org/10.1042/bj20111766

  67. Vogel JP, Raab TK, Schiff C, Somerville SC (2002) PMR6, a pectate lyase-like gene required for powdery mildew susceptibility in Arabidopsis. Plant Cell 14:2095–2106. https://doi.org/10.1105/tpc.003509

  68. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687. https://doi.org/10.1016/j.cell.2009.01.046

  69. Wang H, Guo Y, Lv F, Zhu H, Wu S, Jiang Y, Li F, Zhou B, Guo W, Zhang T (2010) The essential role of GhPEL gene, encoding a pectate lyase, in cell wall loosening by depolymerization of the de-esterified pectin during fiber elongation in cotton. Plant Mol Biol 72:397–406. https://doi.org/10.1007/s11103-009-9578-7

  70. Wang L, Li Q, Liu Z, Surendra A, Pan Y, Li Y, Zaharia LI, Ouellet T, Fobert PR (2018) Intergrated transcriptome and hormone profiling highlight the role of multiple phytohormone pathways in wheat resistance against Fusarium head blight. PLoS One 13:e0207036. https://doi.org/10.1371/journal.pone.0207036

  71. Wu HB, Wang B, Chen Y, Liu YG, Chen L (2013) Characterization and fine mapping of the rice premature senescence mutant ospse1. Theor Appl Genet 126:1897–1907. https://doi.org/10.1007/s00122-013-2104-y

  72. Xiao J, Jin X, Jia X, Wang H, Cao A, Zhao W, Pei H, Xue Z, He L, Chen Q, Wang X (2013) Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai. BMC Genomics 14:197. https://doi.org/10.1186/1471-2164-14-197

  73. Xin M, Wang Y, Yao Y, Xie C, Peng H, Ni Z, Sun Q (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10:123. https://doi.org/10.1186/1471-2229-10-123

  74. Zhang B (2015) MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot 66:1749–1761. https://doi.org/10.1093/jxb/erv013

  75. Zhang X, Fu J, Hiromasa Y, Pan H, Bai G (2013) Differentially expressed proteins associated with Fusarium head blight resistance in wheat. PLoS One 8:e82079. https://doi.org/10.1371/journal.pone.0082079

  76. Zhu QH, Fan L, Liu Y, Xu H, Llewellyn D, Wilson I (2013) miR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. PLoS One 8:e84390. https://doi.org/10.1371/journal.pone.0084390

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Correspondence to Xiaojie Jin or Dongfa Sun.

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Jin, X., Jia, L., Wang, Y. et al. Identification of Fusarium graminearum-responsive miRNAs and their targets in wheat by sRNA sequencing and degradome analysis. Funct Integr Genomics 20, 51–61 (2020) doi:10.1007/s10142-019-00699-8

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Keywords

  • Wheat
  • Fusarium graminearum
  • MicroRNA
  • Wheat-F. graminearum interaction