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The homologous identification of the stem rust resistance genes Rpg5, Adf3 and RGA1 in the relatives of barley

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Abstract

The barley genes Rpg5, RGA1 and Adf3, which provide a strong resistance to many pathotypes of stem rust, were cloned a few years ago, but it was still unclear whether their homologues were represented in wheat and in related species. The paper describes the results of a bioinformatic research to determine the homologues of Rpg5, RGA1 and Adf3 in the genomes of Triticum aestivum and several wild grasses, which breeders usually use as sources of stem rust resistance, and which are available in the genome databases. It was found that the Th. elongatum sequence Q9FEC6 and T. aestivum sequence Q43655 were the highly identical homologues of the Adf3 sequence. T. urartu M8A999 sequence and T. aestivum W5FCU1 sequence were found to be the closest homologues of Rpg5 complete protein sequence, but the identity of their kinase domains was not as clear as that of the other domains. The separate Rpg5 kinase part analysis did not provide the strong evidences that its orthologs were present in our corn species. T. urartu M7ZZX9 sequence and T. aestivum W5FFP0 and W5FI33 sequences were shown to be the homologues of RGA1. The analysis of the predicted active sites allowed finding out the difference between sequences of Rpg5, RGA1, Adf3 protein and their homologues.

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References

  1. Schumann, G.L. and Leonard, K.J., Stem rust of wheat (black rust), Plant Health Instr. DOI: 10.1094/PHI-I2000-0721-01, Updated 2011.

    Google Scholar 

  2. Arora, D., Gross, T., and Brueggeman, R., Allele characterization of genes required for rpg4-mediated wheat stem rust resistance identifies Rpg5 as the R gene, Phytopathology, 2013, vol. 103, no. 11, pp. 1153–1161.

    Article  CAS  PubMed  Google Scholar 

  3. Brueggeman, R., Druka, A., Nirmala, J., Cavileer, T., Drader, T., Rostoks, N., Mirlohi, A., Bennypaul, H., Gill, U., Kudrna, D., Whitelaw, C., Kilian, A., Han, F., Sun, Y., Gill, K., Steffenson, B., and Kleinhofs, A., The stem rust resistance gene rpg5 encodes a protein with nucleotide-binding-site, leucine-rich, and protein kinase domains, Proc. Natl. Acad. Sci. U.S.A., 2008, vol. 105, no. 39, pp. 14970–14975.

    Article  CAS  PubMed  Google Scholar 

  4. Rudrabhatla, P., Reddy, M., and Rajasekharan, R., Genome-wide analysis and experimentation of plant serine/threonine/tyrosine-specific protein kinases, Plant. Mol. Biol., 2006, vol. 60, no. 2, pp. 293–319.

    Article  CAS  PubMed  Google Scholar 

  5. van der Linden, C.G., Wouters, D.C., Mihalka, V., Kochieva, E.Z., Smulders, M.J., and Vosman, B., Efficient targeting of plant disease resistance loci using NBS profiling, Theor. Appl. Genet., 2004, vol. 109, no. 2, pp. 384–393.

    Article  CAS  PubMed  Google Scholar 

  6. McHale, L., Tan, X., Koehl, P., and Michelmore, R.W., Plant NBS-LRR proteins: adaptable guards, Genome Biol., 2006, vol. 7, no. 4, p. 212.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Lukasik, E. and Takken, F.L., Standing strong, resistance proteins instigators of plant defense, Curr. Opin. Plant Biol., 2009, vol. 12, no. 4, pp. 427–436.

    Article  CAS  Google Scholar 

  8. Kobe, B. and Kajava, A.V., The leucine-rich repeat as a protein recognition motif, Curr. Opin. Struct. Biol., 2001, vol. 11, no. 6, pp. 725–732.

    Article  CAS  PubMed  Google Scholar 

  9. Helft, L., Reddy, V., Chen, X., Koller, T., Federici, L., Fernandez-Recio, J., Gupta, R., and Bent, A., LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains, PLoS One, 2011, vol. 6, no. 7, p. e21614.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Wang, X., Richards, J., Gross, T., Druka, A., Kleinhofs, A., Steffenson, B., Acevedo, M., and Brueggeman, R., The rpg4-mediated resistance to wheat stem rust (Puccinia graminis) in barley (Hordeum vulgare) requires Rpg5, a second NBS-LRR gene, and an actin depolymerization factor, Mol. Plant Microbe Interact., 2013, vol. 26, no. 4, pp. 407–418.

    CAS  PubMed  Google Scholar 

  11. Porter, K. and Day, B., Actin branches out to link pathogen perception and host gene regulation, Plant Signal. Behav., 2013, vol. 8, no. 3, p. e23468.1.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Fu, Y., Duan, X., Tang, C., Li, X., Voegele, R.T., Wang, X., Wei, G., and Kang, Z., TaADF7, an actindepolymerizing factor, contributes to wheat resistance against Puccinia striiformis f. sp. tritici, Plant J., 2014, vol. 78, no. 1, pp. 16–30.

  13. The Universal Protein Resource (UniProt), The UniProt Consortium, Nucl. Acids Res., 2008, vol. 36, iss. suppl. 1, pp. D190–D195.

  14. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L., BLAST+: architecture and applications, BMC Bioinformatic, 2009, vol. 10, p. 421.

    Article  Google Scholar 

  15. Letunic, I., Doerks, T., and Bork, P., Smart 7: recent updates to the protein domain annotation resource, Nucleic Acids Res., 2012, vol. 40, no. D1, pp. D302–D305.

  16. Finn, R.D., Clements, J., and Eddy, S.R., HMMER web server: interactive sequence similarity searching, Nucleic Acids Res., 2011, vol. 139, suppl. 2, pp. W29–W37.

    Article  Google Scholar 

  17. Notredame, C., Higgins, D.G., and Heringa, J., TCoffee: a novel method for fast and accurate multiple sequence alignment, J. Mol. Biol., 2000, vol. 302, no. 1, pp. 205–217.

    Article  CAS  PubMed  Google Scholar 

  18. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., and Barton, G.J., Jalview Version 2—a multiple sequence alignment editor and analysis workbench, Bioinformatics, 2009, vol. 25, no. 9, pp. 1189–1191.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S., MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 2013, vol. 30, no. 12, pp. 2725–2729.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Felsenstein, J., Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 1985, vol. 39, no. 4, pp. 783–791.

    Article  Google Scholar 

  21. Jones, D.T., Taylor, W.R., and Thornton, J.M., The rapid generation of mutation data matrices from protein sequences, Comput. Appl. Biosci., 1992, vol. 8, no. 3, pp. 275–282.

    CAS  PubMed  Google Scholar 

  22. Saitou, N. and Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, vol. 4, no. 4, pp. 406–425.

    CAS  PubMed  Google Scholar 

  23. Kelley, L.A. and Stenberg, M.J., Protein structure prediction on the web: a case study using the Phyre server, Nat. Protoc., 2009, vol. 4, no. 3, pp. 363–371.

    Article  CAS  PubMed  Google Scholar 

  24. Brueggeman, R., Steffenson, B.J., and Kleinhofs, A., The rpg4/Rpg5 stem rust resistance locus in barley: resistance genes and cytoskeleton dynamics, Cell Cycle, 2009, vol. 8, no. 7, pp. 977–981.

    Article  CAS  PubMed  Google Scholar 

  25. Braun, P., Carvunis, A.R., Charloteau, B., Dreze, M., Ecker, J.R., Hill, D.E., et al., Evidence for network evolution in an Arabidopsis interactome map, Science, 2011, vol. 333, no. 6042, pp. 601–607.

    Article  CAS  Google Scholar 

  26. Ding, Y., Wang, J., Chun Lai, J.H., Ling Chan, V.H., Wang, X., Cai, Y., Tan, X., Bao, Y., Xia, J., Robinson, D.G., and Jiang, L., Exo70E2 is essential for exocyst subunit recruitment and expo formation in both plants and animals, Mol. Biol. Cell, 2014, vol. 25, no. 3, pp. 412–426.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Sumimoto, H., Kamakura, S., and Ito, T., Structure and function of the pb1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants, Sci. STKE, 2007, vol. 2007, no. 401, p. re6.

    Google Scholar 

  28. Ellis, J.G., Lagudah, E.S., Spielmeyer, W., and Dodds, P.N., The past, present and future of breeding rust resistant wheat, Front. Plant Sci., 2014, vol. 5, p. 641.

    PubMed  Google Scholar 

  29. Henty-Ridilla, J.L., Li, J., Day, B., and Staigera, C.J., Actin depolymerizing factor4 regulates actin dynamics during innate immune signaling in Arabidopsis, Plant Cell, 2014, vol. 26, no. 1, pp. 340–352.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Mago, R., Tabe, L., Vautrin, S., Simkova, H., Kubalakova, M., Upadhyaya, N., Berges, H., Kong, X., Breen, J., Dolezel, J., Appels, R., Ellis, J.G., and Spielmeyer, W., Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus, BMC Plant Biol., 2014, vol. 14, p. 379.

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Institute of Food Biotechnology and Genomics, NAS of Ukraine, Kyiv, Ukraine

    B. V. Ivaschuk, D. O. Samofalova, Ya. V. Pirko & Ya. B. Blume

  2. Eastern Cereal and Oilseed Research Centre, Agriculture and Agrifood Canada, Ottawa, Canada

    G. Fedak

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  1. B. V. Ivaschuk
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  2. D. O. Samofalova
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  3. Ya. V. Pirko
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  4. G. Fedak
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  5. Ya. B. Blume
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Correspondence to B. V. Ivaschuk.

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Ivaschuk, B.V., Samofalova, D.O., Pirko, Y.V. et al. The homologous identification of the stem rust resistance genes Rpg5, Adf3 and RGA1 in the relatives of barley. Cytol. Genet. 50, 96–105 (2016). https://doi.org/10.3103/S0095452716020055

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  • DOI: https://doi.org/10.3103/S0095452716020055

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