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Identification of genes associated with drought tolerance in barley

  • Original Papers
  • Published:
Biologia Plantarum

Abstract

Mapping of quantitative trait genes (QTGs) associated with drought related traits is essential for improving drought tolerance in crop species. In silico identification of candidate genes relies on annotation of critical QTGs to a variety of web resource-based datasets. The barley reference sequence was employed to map QTGs significantly associated with the proline accumulation and osmotic potential. Annotation of the critical QTGs contigs to the NCBI protein database identified 72 gene orthologs located on chromosomes 1H, 2H, and 7H, from which seven genes were identified as candidates. Expression analysis of all seven candidate genes revealed differential expression pattern between plants grown under well-watered conditions and drought-stress. The results represent a successful and highly powerful implementation of genome-wide scanning approach based on in silico mapping of QTGs to identify gene clusters having a common transcript pattern with similar function.

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Abbreviations

DArT:

diversity arrays technology

IBSC:

International Barley Sequencing Consortium

LD:

linkage disequilibrium

NCBI:

National Center for Biotechnology Information

OP:

osmotic potential

PA:

proline accumulation

QTGs:

quantitative trait genes

QTL:

quantitative trait loci

RT-PCR:

reverse transcription polymerase chain reaction.

References

  • Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., Yoshida, K., Mitsuoka, C., Tamiru, M., Innan, H., Cano, L., Kamoun, S., Terauchi, R.: Genome sequencing reveals agronomically important loci in rice using MutMap. - Natur. Biotechnol. 30: 174–178, 2012.

    Article  CAS  Google Scholar 

  • Abou-Elwafa, S.F.: Association mapping for drought tolerance in barley. - Gene Technol. 5: 1–2, 2016a.

    Article  Google Scholar 

  • Abou-Elwafa, S.F.: Association mapping for drought tolerance in barley at the reproductive stage. - Compt. rend. Biol. 339: 51–59, 2016b.

    Article  Google Scholar 

  • Abou-Elwafa, S.F.: Association mapping for yield and yieldcontributing traits in barley under drought conditions with genome-based SSR markers. - Compt. rend. Biol. 339: 153–162, 2016c.

    Article  Google Scholar 

  • Afzal, A.J., Wood, A.J., Lightfoot, D.A.: Plant receptor-like serine threonine kinases: roles in signaling and plant defense. - Mol. Plant Microbe Interact. 21: 507–517, 2008.

    Article  PubMed  CAS  Google Scholar 

  • Alcazar, R., Marco, F., Cuevas, J.C., Patron, M., Ferrando, A., Carrasco, P., Tiburcio, A.F., Altabella, T.: Involvement of polyamines in plant response to abiotic stress. - Biotechnol. Lett. 28: 1867–1876, 2006.

    Article  PubMed  CAS  Google Scholar 

  • Alcazar, R., Planas, J., Saxena, T., Zarza, X., Bortolotti, C., Cuevas, J., Bitrian, M., Tiburcio, A.F., Altabella, T.: Putrescine accumulation confers drought tolerance in transgenic Arabidopsis plants over-expressing the homologous arginine decarboxylase 2 gene. - Plant Physiol. Biochem. 48: 547–552, 2010.

    Article  PubMed  CAS  Google Scholar 

  • Alves, A.A.G., Setter, T.L.: Abscisic acid accumulation and osmotic adjustment in cassava under water deficit. - Environ. exp. Bot. 51: 259–279, 2004.

    Article  CAS  Google Scholar 

  • Ariyadasa, R., Mascher, M., Nussbaumer, T., Schulte, D., Frenkel, Z., Poursarebani, N., Zhou, R., Steuernagel, B., Gundlach, H., Taudien, S., Felder, M., Platzer, M., Himmelbach, A., Schmutzer, T., Hedley, P.E., Muehlbauer, G.J., Scholz, U., Korol, A., Mayer, K.F., Waugh, R., Langridge, P., Graner, A., Stein, N.: A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. - Plant Physiol. 164: 412–423, 2014.

    Article  PubMed  CAS  Google Scholar 

  • Boyes, D.C., Nam, J., Dangl, J.L.: The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. - PNAS 95: 15849–15854, 1998.

    Article  PubMed  CAS  Google Scholar 

  • Deepak, S., Shailasree, S., Kini, R.K., Hause, B., Shetty, S.H., Mithöfer, A.: Role of hydroxyproline-rich glycoproteins in resistance of pearl millet against downy mildew pathogen Sclerospora graminicola. - Planta 226: 323–333, 2007.

    Article  PubMed  CAS  Google Scholar 

  • Deepak, S., Shailasree, S., Kini, R.K., Muck, A., Mithöfer, A., Shetty S.H.: Hydroxyproline-rich glycoproteins and plant defence. - Phytopathology 158: 585–593, 2010.

    CAS  Google Scholar 

  • Ekblom, R., Galindo, J.: Applications of next generation sequencing in molecular ecology of non-model organisms. - Heredity 107: 1–15, 2011.

    Article  PubMed  CAS  Google Scholar 

  • Ersoz, E.S., Yu, J., Buckler, E.S.: Applications of linkage disequilibrium and association mapping in crop plants. - In: Varshney, R.K., Tuberosa, R. (ed.): Genomics Assisted Crop improvement, Genomics Approaches and Platforms. Vol. 1. Pp. 97–119. Springer, Dordrecht 2007.

    Chapter  Google Scholar 

  • Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J., Nekrutenko, A.: Galaxy, a platform for interactive large-scale genome analysis. - Genome Res. 15: 1451–1455, 2005.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Harhay, G.P., Keele, J.W.: Positional candidate gene selection from livestock EST databases using gene ontology. Bioinformatics 19: 249–255, 2003.

    Article  PubMed  CAS  Google Scholar 

  • Hayat, S., Hayat, Q., Alyemeni, M.N., Wani, A.S., Pichtel, J., Ahmad, A.: Role of proline under changing environments: a review. - Plant Signal. Behav. 7: 1456–1466, 2012.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hristovski, D., Peterlin, B., Mitchell, J.A., Humphrey, S.M.: Using literature based discovery to identify disease candidate genes. - Int. J. med. Inform. 74: 289–298, 2005.

    Article  PubMed  Google Scholar 

  • James, G.V., Patel, V., Nordström, K.J., Klasen, J.R., Salomé, P.A., Weigel, D., Schneeberger, K.: User guide for mapping-by-sequencing in Arabidopsis. - Genome Biol. 14: R61, 2013.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kumar, S., Stecher, G., Tamura, K.: MEGA7, molecular evolutionary genetics analysis version 7.0 for bigger datasets. - Mol. Biol. Evol. 33: 1870–1874, 2016a.

    Article  PubMed  CAS  Google Scholar 

  • Kumar, R., Vashisth, D., Misra, A., Akhtar, M.Q., Jalil, S.U., Shanker, K., Gupta, M.M., Rout, P.K., Gupta, A.K., Shasany, A.K.: RNAi down-regulation of cinnamate-4- hydroxylase increases artemisinin biosynthesis in Artemisia annua. - Natur. Rev. Sci. Rep. 25: 26458, 2016b.

    Article  CAS  Google Scholar 

  • Le Gall, H., Philippe, F., Domon, J.M., Gillet, F., Pelloux, J., Rayon, C.: Cell wall metabolism in response to abiotic stress. - Plants 4: 112–166, 2015.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Logemann, J., Schell, J., Willmitzer, L.: Improved method for the isolation of RNA from plant tissues. - Anal. Biochem. 163: 16–20, 1987.

    Article  PubMed  CAS  Google Scholar 

  • Man, D., Bao, Y.X., Han, L.B., Zhang, X.: Drought tolerance associated with proline and hormone metabolism in two tall fescue cultivars. - HortScience 46: 1027–1032, 2011.

    Google Scholar 

  • Milla, M.A., Townsend, J., Chang, I.F., Cushman, J.C.: The Arabidopsis AtDi19 gene family encodes a novel type of Cys2/His2 Zinc-finger protein implicated in ABA independent dehydration, high-salinity stress and light signaling pathways. - Plant mol. Biol. 61: 13–30, 2006.

    Article  PubMed  CAS  Google Scholar 

  • Nei, M.: Genome evolution: let’s stick together. - Heredity 90: 411–412, 2003.

    Article  PubMed  CAS  Google Scholar 

  • Nguyen, K.H., Hab, C.V., Nishiyamaa, R., Watanabea, Y., Leyva-Gonzálezc, M.A., Fujitad, Y., Trana, U.T., Lia, W., Tanakae, M., Sekie, M., Schallerg, G.E., HerreraEstrellah, L., Trana, L.S.P.: Arabidopsis type B cytokinin response regulators ARR1, ARR10, and ARR12 negatively regulate plant responses to drought. - PNAS 13: 3090–3095, 2016.

    Article  CAS  Google Scholar 

  • Peremarti, A., Bassie, L., Zhu, C.F., Christou, P., Capell, T.: Molecular characterization of the arginine decarboxylase gene family in rice. - Transgenic Res. 19: 785–797, 2010.

    Article  PubMed  CAS  Google Scholar 

  • Purugganan, D., Fuller, D.Q.: The nature of selection during plant domestication. - Nature 457: 843–848, 2009.

    Article  PubMed  CAS  Google Scholar 

  • Rossi, S., Masotti, D., Nardini, C., Bonora, E., Romeo, G., Macii, E., Benini, L., Volinia, S.: TOM: a web-based integrated approach for identification of candidate disease genes. - Nucl. Acids Res. 34: W285–W292, 2006.

    Article  PubMed  CAS  Google Scholar 

  • Seki, M., Umezawa, T., Urano, K., Shinozaki, K.: Regulatory metabolic networks in drought stress responses. - Curr. Opin. Plant Biol. 10: 296–302, 2007.

    Article  PubMed  CAS  Google Scholar 

  • Sujeeth, N., Deepak, S., Shailasree, S., Kini, R.K., Shetty, S.H., Hille, J.: Hydroxyproline-rich glycoproteins accumulate in pearl millet after seed treatment with elicitors of defense responses against Sclerospora graminicola. - Physiol. mol. Plant Pathol. 74: 230–237, 2010.

    Article  CAS  Google Scholar 

  • Takagi, H., Abe, A., Yoshida, K., Kosugi, S., Natsume, S., Mitsuoka, C., Uemura, A., Utsushi, H., Tamiru, M., Takuno, S., Innan, H., Cano, L.M., Kamoun, S., Terauchi, R.: QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. - Plant J. cell. mol. Biol. 74: 174–183, 2013.

    Article  CAS  Google Scholar 

  • Teer, J.K., Mullikin, J.C.: Exome sequencing: the sweet spot before whole genomes. - Human mol. Genet. 19: R145–R151, 2010.

    Article  CAS  Google Scholar 

  • Teichmann, S.A., Veitia, R.A.: Genes encoding subunits of stable complexes are clustered on the yeast chromosomes: an interpretation from a dosage balance perspective. - Genetics 167: 2121–2125, 2004.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yi, G., Sze, S.H., Thon, M.R.: Identifying clusters of functionally related genes in genomes. - Bioinformatics 23: 1053–1060, 2007.

    Article  PubMed  CAS  Google Scholar 

  • Yu, A.M., Li, P., Tang, T., Wang, J.C., Chen, Y., Liu, L.: Roles of Hsp70s in stress responses of microorganisms, plants, and animals. - Biomed. Res. Int. 2015: 1–8, 2015.

    Google Scholar 

  • Zhang, X., Ervin, E.H., Evanylo, G.K., Haering, K.C.: Impact of biosolids on hormone metabolism in drought-stressed tall fescue. - Crop Sci. 49: 1893–1901, 2009.

    Article  CAS  Google Scholar 

  • Zhou, Z., Ma, H., Lin, K., Zhao, Y., Chen, Y., Xiong, Z., Wang, L., Tian, B.: RNA-seq reveals complicated transcriptomic responses to drought stress in a nonmodel tropic plant, Bombax ceiba L. - Evol. Bioinformatics 11: 27–37, 2015.

    CAS  Google Scholar 

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Authors and Affiliations

  1. Agronomy department, College of Agriculture, Assiut University, 71526, Assiut, Egypt

    S. F. Abou-Elwafa

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  1. S. F. Abou-Elwafa
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Correspondence to S. F. Abou-Elwafa.

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Acknowledgements: The author gratefully acknowledge the City of Scientific Research & Technology Applications (SRTA-City), Egypt, for the excellent help in conducting expression analysis.

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Abou-Elwafa, S.F. Identification of genes associated with drought tolerance in barley. Biol Plant 62, 299–306 (2018). https://doi.org/10.1007/s10535-017-0765-0

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  • DOI: https://doi.org/10.1007/s10535-017-0765-0

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