Article Details: Received: 2020-03-26 | Accepted: 2020-05-19 | Available online: 2020-09-30 https://doi.org/10.15414/afz.2020.23.03.139-146

Plants are often exposed to adverse environmental conditions that can significantly interfere with their genomic response. Soil compaction induced by heavy field machinery represents a major problem for crop production mainly due to restricted root growth and penetration into soil and therefore reduced water and nutrient uptake by the plants. Tested hypotheses were to declare whether the plant‘s genome responds to soil compaction and whether the microRNA-based markers are suitable to determine this response. A long term field scale experiment was established in 2009 where different levels of soil compaction are researched from the soil and crop point of view. The analyzed barley (Hordeum vulgare L.) plants were collected during the growing season in 2019. The effect of soil compaction was analysed by four different DNA-based markers corresponding to miRNA sequences of dehydratation stress-responsive barley miRNAs (hvu-miR156, and hvu-miR408) and nutrition-sensitive markers (hvu-miR399 and hvu-miR827), within the leaf, stem and root tissues of barley plants. Our preliminary data support hypotheses that plant genome response was tissue-specific due to significant induction of the biomarkers to dehydratation and nutrition stress. The most affected part of the plant by dehydration, were roots and lack of nutrient supply was most pronounced on leaves.

Keywords: abiotic stress, crop yield, miRNAs, root growth

References

ANTILLE, D.L. et al. (2019). Review: Soil compaction and controlled traffic farming in arable and grass cropping systems. Agronomy Research, 17(3), 653–682. https://doi.org/10.15159/AR.19.133

ARVIDSSON J. (1999). Nutrient uptake and growth of barley as affected by soil compaction. Plant and Soil, 208, 9–19.

AXTELL, M.J. et al. (2011). Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biology, 12(4), pp. 221. https://doi.org/10.1186/gb-2011-12-4-221

BARTEL, B. and CITOVSKY, V. (2012). Focus on ubiquitin in plant biology. Plant Physiology, 160. https://doi.org/10.1104/pp.112.203208

BARTEL, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116 (2), 281–297. https://doi.org/10.1016/S0092-8674(04)00045-5

BARVKAR, V.T. et al. (2013). Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes. Planta, 237(4), 1149–1161. https://doi.org/10.1007/s00425-012-1833-5

BATEY, T. (2009). Soil compaction and soil management – a review. Soil Use and Management, 25,  335–345. https://doi.org/10.1111/j.1475-2743.2009.00236.x

BEJ, S. and BASAK, J. (2014). MicroRNAs: The potential biomarkers in plant stress response. American Journal of Plant Sciences, 5(5), 748–759. https://doi.org/10.4236/ajps.2014.55089

BENGOUGH, A.G. et al. (2011). Root elongation, water stress, and mechanical impedance: a review of limiting stresses and beneficial root tip traits. Journal of Experimental Botany, 62(1), 59–68. https://doi.org/10.1093/jxb/erq350

BERISSO, F.E. et al. (2012). Persistent effects of subsoil compaction on pore size distribution and gas transport in a loamy soil. Soil and Tillage Research,122, 42–51.

BIELEK P. (2003). Soils in Slovakia: Status quo, trends, and developments. Journal of Soils and Sediments, 3, 254–254.

BIELEK, P. et al. (2005). Soil survey and managing of soil data in Slovakia. In Jones, R.J. et al. (eds.) Soil Resources of Europe. (2. ed.). Ispra, Italy: European Soil Bureau (pp. 317–329).

CANARACHE, A. et al. (1974). Effect of induced compaction by wheel traffic on soil physical properties and yield of maize in Romania. Soil and Tillage Research, 4(2), 199–213. https://doi.org/10.1016/0167-1987(84)90048-5

CHAMEN, T. (2015). Controlled traffic farming: From worldwide research to adoption in Europe and its future prospects. Acta Technologica Agriculturae, 18(3), 64–73. https://doi.org/10.1515/ata-2015-0014

CHAMEN, W.C.T. and LONGSTAFF, D.J. (1995). Traffic and tillage effects on soil conditions and crop growth on a swelling clay soil. Soil Use and Management, 11(4), 168–176. https://doi.org/10.1111/j.1475-2743.1995.tb00951.x

CHANCELLOR, W. J. and SCHMIDT, R. H. (1962). Soil deformation beneath surface loads. Transactions of ASABE 5, 240–246.

COLOMBI, T. and KELLER, T. (2019). Developing strategies to recover crop productivity after soil compaction-A plant ecophysiological perspective. Soil and Tillage Research, 191, 156– 161. https://doi.org/10.1016/j.still.2019.04.008

CORREA, J. et al. (2019). Soil compaction and the architectural plasticity of root systems. Journal of Experimental Botany, 70(21), 6019–6034. https://doi.org/10.1093/jxb/erz383

COLOMBI, T. and WALTER, A. (2017). Genetic Diversity under Soil Compaction in Wheat: Root Numbers as a Promising Trait for Early Plant Vigor. Frontiers in Plant Science, 8(420). https://doi.org/10.3389/fpls.2017.00420

CUPERUS, J.T. et al. (2011). Evolution and functional diversification of MIRNA genes. Plant Cell, 23 (2), 431–442. https://doi.org/10.1105/tpc.110.082784

DING, Y. et al. (2013). Emerging roles of microRNAs in the mediation of drought stress response in plants. Journal of Experimental Botany, 64(11), 3077–3086. https://doi.org/10.1093/jxb/ert164

EC. (2006). Proposal for a Directive of the European Parliament and of the Council establishing a framework for the protection of soil and amending Directive 2004/35/EC. 232 Final. 2006. Brussels: European Commission.

ESDAC (2020). Soil Compaction. Retrieved December 14, 2019 form https://esdac.jrc.ec.europa.eu/themes/soil-compaction

FU, D. et al. (2013). MicroRNA-based molecular markers: a  novel PCR-based genotyping technique in Brassica species. Plant Breeding, 132 (4), 375–381. https://doi.org/10.1111/pbr.12069

FULAJTAR, E. (2000). Assessment and determination of the compacted soils in Slovakia. Advances of Geoecology, 32, 384–387

GALAMBOŠOVÁ, J. et al. (2017). Field evaluation of controlled traffic farming in Central Europe using commercially available machinery. Transaction of ASABE, 60 (3), 657–669. https://doi.org/10.13031/trans.11833

GANIE, S.A. and MONDAL, T.K. (2015). Genome-wide development of novel miRNA-based microsatellite markers of rice (Oryza sativa) for genotyping applications. Molecular Breeding, 35. https://doi.org/10.1007/s11032-015-0207-7

HAJYZADEH, M. et al. (2015). miR408 overexpression causes increased drought tolerance in chickpea. Gene, 555, 186–193. https://doi.org/10.1016/j.gene.2014.11.002

HLAVAČKOVÁ, L. and RAŽNÁ, K. (2015). Polymorphism of specific miRNAs in the context of flax (Linum usitatissimum L.) genome adaptability to abiotic stress. MendelNet 2015. Brno: Mendel University. 615 pp. I

HOUŠKOVÁ, B. (2002). Assessment of the state of soil compaction in Slovakia. Adv Geoecol, 35, 379–385.

HOUŠKOVÁ, B. and MONTANARELLA, L. (2008). The natural susceptibility of European soils to compaction. In Tóth, G. et al. (eds.) Threats to Soil Quality in Europe. Luxembourg: Office for Official Publications of the European Communities.

HSIEH, L.C. et al. (2009). Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiology, 151, 2120–2132. https://doi.org/10.1104/pp.109.147280

JONES-RHOADES, M.W. et al. (2006). MicroRNAs and their regulatory roles in plants. Annual Reviews in Plant Biology, 57, 19–53. https://doi.org/10.1146/annurev.arplant.57.032905.105218

KANT, S. et al. (2011). Genetic regulation by NLA and microRNA827 for maintaining nitrate-dependent phosphate homeostasis in Arabidopsis. PLoS Genetics, 7, e1002021. https://doi.org/10.1371/journal.pgen.1002021

KANTAR, M. et al. (2010). Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Functional & Integrative Genomics, 493–507. https://doi.org/10.1007/s10142-010-0181-4

KEHR, L. (2013). Systemic regulation of mineral homeostasis by micro RNA. Frontiers in Plant Sciences, 4. https://doi.org/10.3389/fpls.2013.00145

KELLER, T. et al. (2019). Historical increase in agricultural machinery weights enhanced soil stress levels and adversely affected soil functioning. Soil and Tillage Research, 194. https://doi.org/10.1016/j.still.2019.104293

KHANUJA, S.P.S. et al. (1999). Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Molecular Biology Reporter, 17, 74–84.

KOBZA, J. (2018). Actual status of agricultural soils in Slovakia as the basic atribute of their fertility. In Slovak.

KROULÍK, M. et al. (2011). Procedures of soil farming allowing reduction of compaction. Precision Agriculture, 12, 317–333. https://doi.org/10.1007/s11119-010-9206-1

KRUSZKA, K. et al. (2014). Transcriptionally and posttranscriptionally regulated microRNAs in heat stress response in barley. Journal of Experimental Botany, 65(20), 6123–6135. https://doi.org/10.1093/jxb/eru353

KRUSZKA, K. et al. (2012). Role of microRNAs and other sRNAs of plants in their changing environments. Journal of Plant Physiology, 169, 1664–1672. https://doi.org/10.1016/j.jplph.2012.03.009

LHOTSKÝ, J. et al. (1991). Degradation of soil by increasing compression. Soil and Tillage Research, 19(2-3), 287–295. https://doi.org/10.1016/0167-1987(91)90096-G

LIANG, G. et al. (2015). Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis. Scientific Reports, 5. https://doi.org/10.1038/srep11813

LIN, S.I. et al. (2008). Regulatory Network of MicroRNA399 and PHO2 by Systemic Signaling. Plant Physiology, 147, 732–746. https://doi.org/10.1104/pp.108.116269

LIPIEC, J. and HATANO, R. (2003). Quantification of compaction effects on soil physical properties and crop growth. Geoderma, 116(1-2), 107–136. https://doi.org/10.1016/S0016-7061(03)00097-1

LIU, H.H. et al. (2008). Microarray-based analysis of stressregulated microRNAs in Arabidopsis thaliana. RNA, 14(5), 836–843. https://doi.org/10.1261/rna.895308

MA, Ch. et al. (2015). miR408 is involved in abiotic stress responses in Arabidopsis. Plant Journal, 84(1), 169–187. https:// doi.org/10.1111/tpj.12999

MACÁK, M. et al. (2018). Comparison of two sowing systems for CTF using commercially available machinery. Agronomy Research, 16(2), 523–533. https://doi.org/10.15159/AR.18.060

MELNIKOVA, N.V. et al. (2016). Identification, expression analysis, and target prediction of flax genotroph microRNAs under normal and nutrient stress conditions. Frontiers in Plant Sciences, 7(399). https://doi.org/10.3389/fpls.2016.00399

MELNIKOVA, N.V. et al. (2015). Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L. Biochemie, 109, 36– 41. https://doi.org/10.1016/j.biochi.2014.11.017

MONDAL, T.K. and GANIE, S.A. (2014). Identification and characterization of salt responsive miRNA-SSR. Gene, 535(2), 204–209. https.//doi.org/10.1016/j.gene.2013.11.033

PANT, B.D. et al. (2008). MicroRNA 399 is a  longdistance Signal for the Regulation of plant phosphate homeostasis. Plant Journal, 53(5), 731–738, https://doi.org/10.1111/j.1365-313X.2007.03363.x

RADFORD, B.J. et al. (2007). Changes in the properties of a Vertisol and responses of wheat after compaction with harvester traffic. Soil and Tillage Research, 54(3-4), 155–170. https://doi.org/10.1016/S0167-1987(00)00091-X

RADFORD, B.J. et al. (2001). Crop responses to applied soil compaction and to compaction repair treatments. Soil and Tillage Research, 61(3-4), 157–166. https://doi.org/10.1016/S0167-1987(01)00194-5

RAJWANSHI, R. et al. (2014). Orthologous plant microRNAs: microregulators with great potential for improving stress tolerance in plants. Theoretical and Applied Genetics, 127(12), 2525–2543. https://doi.org/10.1007/s00122-014-2391-y

RAŽNÁ, K. and HLAVAČKOVÁ, L. (2017). The applicability of genetic markers based on molecules microRNA in agriculturel research. Open Access Journal of Agricultural Research, 2, 000125. https://doi.org/10.23880/OAJAR-16000125

REIS, R.S. et al. (2015). Missing Pieces in the Puzzle of Plant MicroRNAs. Trends in Plant Science, 20(11), 721–728. https://doi.org/10.1016/j.tplants.2015.08.003

RIVERA, M. et al. (2019). Soil compaction induced changes in morpho-physiological characteristics of common bean. Journal of Soil Science and Plant Nutrition, 19, 217–227. https://doi.org/10.1007/s42729-019-0007-y

SCHÄFER-LANDEFELD, L. et al. (2004). Effects of agricultural machinery with high axle load on soil properties of normally managed fields. Soil and Tillage Research, 75(1), 75–86. https://doi.org/10.1016/S0167-1987(03)00154-5

SCHREIBER, A.W. et al. (2011). Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics, 12, 129. http://www.biomedcentral.com/1471-2164/12/129

SINGH, N. et al. (2020). Stress physiology and metabolism in hybrid rice. III. Puddling and soil compaction regulate water status and internal metabolism during drought. Journal Of Crop Improvement. https://doi.org/10.1080/15427528.2020.1723766

SOUMITRA, P. et al. (2015). miRNA regulation of nutrient homeostasis in plants. Frontiers in Plant Science, 6, 232. https://doi.org/10.3389/fpls.2015.00232

SUN, X. et al. (2019). Regulation mechanism of microRNA in plant response to abiotic stress and breeding. Molecular Biology Reports, 46, 1447–1457. https://doi.org/10.1007/s11033-018-4511-2

TRINDADE, I. et al. (2010). miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula Planta, 231, 705–716. https://doi.org/10.1007/s00425-009-1078-0

UNGER, P. W. and KASPAR, T. C. (1994). Soil compaction and root growth: A review. Agronomy Journal, 86, 759–766. https://doi.org/10.2134/agronj1994.00021962008600050004x

VAN den AKKER, J.J.H. and CANARACHE, A. (2001). Two European concerted actions on subsoil compaction. Landnutzung und Landentwicklung, 42(1), 15–22.

VERO, S.E. et al. (2014). Field evaluation of soil moisture deficit thresholds for limits to trafficability with slurry spreading equipment on grassland. Soil Use and Management, 30(1), 69– 77. https://doi.org/10.1111/sum.12093

WU, X. et al. (2014). In silico identification and characterization of conserved plant microRNAs in barley. Central European Journal of Biology, 9, 841–852. https://doi.org/10.2478/s11535-014-0308-z

YADAV, C.B.Y. et al. (2014). Development of novel microRNAbased genetic markers in foxtail millet for genotyping applications in related grass species. Molecular Breeding, 34, 2219–2224. https://doi.org/10.1007/s11032-014-0137-9

ZHANG, B. (2015). MicroRNA: a new target for improving plant tolerance to abiotic stress. Journal of Experimental Botany, 66, 1749–1761. https://doi.org/10.1093/jxb/erv013

ZHOU, L. et al. (2010). Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. Journal of Experimental Botany, 61, 4157–4168. https://doi.org/10.1093/jxb/erq237