Abstract

Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security1. Genetic resistance can reduce crop losses in the field and can be selected through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst)2. This highlights the need to (1) identify genes that, alone or in combination, provide broad-spectrum resistance, and (2) increase our understanding of the underlying molecular modes of action. Here we report the isolation and characterization of three major yellow rust resistance genes (Yr7, Yr5 and YrSP) from hexaploid wheat (Triticum aestivum), each having a distinct recognition specificity. We show that Yr5, which remains effective to a broad range of Pst isolates worldwide, is closely related yet distinct from Yr7, whereas YrSP is a truncated version of Yr5 with 99.8% sequence identity. All three Yr genes belong to a complex resistance gene cluster on chromosome 2B encoding nucleotide-binding and leucine-rich repeat proteins (NLRs) with a non-canonical N-terminal zinc-finger BED domain3 that is distinct from those found in non-NLR wheat proteins. We developed diagnostic markers to accelerate haplotype analysis and for marker-assisted selection to expedite the stacking of the non-allelic Yr genes. Our results provide evidence that the BED-NLR gene architecture can provide effective field-based resistance to important fungal diseases such as wheat yellow rust.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

References

  1. 1.

    Oerke, E. C. Crop losses to pests. J. Agric. Sci. 144, 31–43 (2006).

  2. 2.

    Hubbard, A. et al. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biol. 16, 23 (2015).

  3. 3.

    Aravind, L. The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases. Trends Biochem. Sci. 25, 421–423 (2000).

  4. 4.

    Jones, J. D. G. & Dangl, J. L. The plant immune system. Nature 444, 323–329 (2006).

  5. 5.

    Kourelis, J. & van der Hoorn, R. A. L. Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell. https://doi.org/10.1105/tpc.17.00579 (2018).

  6. 6.

    Sarris, P. F., Cevik, V., Dagdas, G., Jones, J. D. G. & Krasileva, K. V. Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens. BMC Biol. 14, 8 (2016).

  7. 7.

    Kroj, T., Chanclud, E., Michel-Romiti, C., Grand, X. & Morel, J.-B. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. New Phytol. 210, 618–626 (2016).

  8. 8.

    Bailey, P. C. et al. Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions. Genome Biol. 19, 23 (2018).

  9. 9.

    Bundock, P. & Hooykaas, P. An Arabidopsis hAT-like transposase is essential for plant development. Nature 436, 282–284 (2005).

  10. 10.

    Yoshimura, S. et al. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc. Natl Acad. Sci. USA. 95, 1663–1668 (1998).

  11. 11.

    Das, B., Sengupta, S., Prasad, M. & Ghose, T. Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces. BMC Genet. 15, 82 (2014).

  12. 12.

    Law, C. N. Genetic control of yellow rust resistance in T. spelta Album. Plant Breed. Institute, Cambridge, Annu. Rep. 1975, 108–109 (1976).

  13. 13.

    Johnson, R. & Dyck, P. L. Resistance to yellow rust in Triticum spelta var. Album and bread wheat cultivars Thatcher and Lee. Colloq. l’INRA (1984).

  14. 14.

    Zhang, P., McIntosh, R. A., Hoxha, S. & Dong, C. M. Wheat stripe rust resistance genes Yr5 and Yr7 are allelic. Theor. Appl. Genet. 120, 25–29 (2009).

  15. 15.

    Feng, J. Y. et al. Molecular mapping of YrSP and its relationship with other genes for stripe rust resistance in wheat chromosome 2BL. Phytopathology 105, 1206–1213 (2015).

  16. 16.

    Wellings, C. R. & McIntosh, R. A. Puccinia striiformis f. sp. tritici in Australasia: pathogenic changes during the first 10 years. Plant Pathol. 39, 316–325 (1990).

  17. 17.

    Zhan, G. et al. Virulence and molecular diversity of the Puccinia striiformis f. sp. tritici population in Xinjiang in relation to other regions of western China. Plant Dis. 100, 99–107 (2016).

  18. 18.

    Steuernagel, B. et al. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat. Biotechnol. 34, 652–655 (2016).

  19. 19.

    Sun, Q., Wei, Y., Ni, Z., Xie, C. & Yang, T. Microsatellite marker for yellow rust resistance gene Yr5 in wheat introgressed from spelt wheat. Plant Breed. 121, 539–541 (2002).

  20. 20.

    Yao, Z. J. et al. The molecular tagging of the yellow rust resistance gene Yr7 in wheat transferred from differential host Lee using microsatellite markers. Sci. Agric. Sin. 39, 1146–1152 (2006).

  21. 21.

    Brunner, S. et al. Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles. Plant J. 64, 433–445 (2010).

  22. 22.

    Ellis, J. G., Lawrence, G. J., Luck, J. E. & Dodds, P. N. Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell 11, 495–506 (1999).

  23. 23.

    Bai, S. et al. Structure-function analysis of barley NLR immune receptor MLA10 reveals its cell compartment specific activity in cell death and disease resistance. PLoS Pathog. 8, e1002752 (2012).

  24. 24.

    Periyannan, S. et al. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 341, 786–788 (2013).

  25. 25.

    Srichumpa, P., Brunner, S., Keller, B. & Yahiaoui, N. Allelic series of four powdery mildew resistance genes at the Pm3 locus in hexaploid bread wheat. Plant Physiol. 139, 885–895 (2005).

  26. 26.

    Sarris, P. F. et al. A plant immune receptor detects pathogen effectors that target WRKY transcription factors. Cell 161, 1089–1100 (2015).

  27. 27.

    Wingen, L. U. et al. Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat. Theor. Appl. Genet. 127, 1831–1842 (2014).

  28. 28.

    Reeves, J. C. et al. Changes over time in the genetic diversity of four major European crops - a report from the Gediflux Framework 5 project. In Proc. 17th EUCARPIA Gen. Congr. (Eds Grausgruber, J. V. H. & Ruckenbauer, P.) 3–7 (BOKU, 2004).

  29. 29.

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

  30. 30.

    Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254–267 (2006).

  31. 31.

    Ellis, J. G. Integrated decoys and effector traps: how to catch a plant pathogen. BMC Biol. 14, 13 (2016).

  32. 32.

    Dobon, A., Bunting, D. C. E., Cabrera-Quio, L. E., Uauy, C. & Saunders, D. G. O. The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression. BMC Genomics 17, 380 (2016).

  33. 33.

    Seeholzer, S. et al. Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection. Mol. Plant-Microbe Interact. 23, 497–509 (2010).

  34. 34.

    Krasileva, K. V. et al. Uncovering hidden variation in polyploid wheat. Proc. Natl Acad. Sci. USA. 6, E913–E921 (2017).

  35. 35.

    Hubbard, A. J., Fanstone, V. & Bayles, R. A. UKCPVS 2009 Annual report (NIAB, 2009).

  36. 36.

    Gassner, G. & Straib, W. Die Bestimmung der biologischen Rassen des Weizengelbrostes (Pucciniaglumarum f.sp. tritici Schmidt Erikss. u. Henn). Arb. Biol. Reichsanst. Land: Forstwirtsch. 20, 141–163 (1932).

  37. 37.

    McGrann, G. R. D. et al. Genomic and genetic analysis of the wheat race-specific yellow rust resistance gene Yr5. J. Plant Sci. Mol. Breed. 3, (2014).

  38. 38.

    Lagudah, E. S., Appels, R., Brown, A. H. D. & McNeil, D. The molecular–genetic analysis of Triticum tauschii, the D-genome donor to hexaploid wheat. Genome 34, 375–386 (1991).

  39. 39.

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

  40. 40.

    Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).

  41. 41.

    Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).

  42. 42.

    Lupas, A., Van Dyke, M. & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162–1164 (1991).

  43. 43.

    Warren, R. F., Henk, A., Mowery, P., Holub, E. & Innes, R. W. A mutation within the leucine-rich repeat domain of the arabidopsis disease resistance gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes. Plant Cell 10, 1439–1452 (1998).

  44. 44.

    Altschul, S. F. et al. Protein database searches using compositionally adjusted substitution matrices. FEBS J. 272, 5101–5109 (2005).

  45. 45.

    Pallotta, M. A. et al. Marker assisted wheat breeding in the southern region of Australia. in Proc. 10th Int. Wheat Genet. Symp. Instituto Sperimentale Cerealcoltura (Eds Pogna, N. & McIntosh, R.A.) 789–791 (Istituto Sperimentale per la Cerealicoltura, 2003).

  46. 46.

    Ramirez-Gonzalez, R. H. et al. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol. J. 13, 613–624 (2015).

  47. 47.

    Broman, K. W., Wu, H., Sen, S. & Churchill, G. A. R/qtl: QTL mapping in experimental crosses. Bioinformatics 19, 889–890 (2003).

  48. 48.

    Avni, R. et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 93–97 (2017).

  49. 49.

    Luo, M.-C. et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551, 498–502 (2017).

  50. 50.

    Jupe, F. et al. Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13, 75 (2012).

Download references

Acknowledgements

This work was supported by the UK Biotechnology and Biological Sciences Research Council Designing Future Wheat programme BB/P016855/1 and the Grains Research and Development Corporation, Australia. C.M. was funded by a PhD studentship from Group Limagrain and J.Z. is funded by PhD scholarships from the National Science Foundation (NSF) and the Monsanto Beachell-Borlaug International Scholars Programs (MBBISP). We thank the International Wheat Genome Sequencing Consortium for allowing pre-publication access to the RefSeq v1.0 assembly and gene annotation. We thank J. Dubcovsky and X. Zhang (University of California, Davis) for providing Yr5 cultivars. We thank the John Innes Centre Horticultural Services and Limagrain Rothwell staff for management of the wheat populations. We also thank S. Specel (Limagrain; Clermont-Ferrand) and R. Goram (JIC) for their help in designing and running KASP assays, and S. Hoxha (The University of Sydney) for technical assistance. This research was supported by the NBI Computing Infrastructure for Science (CiS) group in Norwich, UK.

Author information

Author notes

  1. These authors contributed equally: C. Marchal and J. Zhang.

Affiliations

  1. John Innes Centre, Norwich Research Park, Norwich, UK

    • Clemence Marchal
    • , Burkhard Steuernagel
    • , Nikolai M. Adamski
    • , Brande B. H. Wulff
    •  & Cristobal Uauy
  2. University of Sydney, Plant Breeding Institute, Cobbitty, New South Wales, Australia

    • Jianping Zhang
    • , Peng Zhang
    •  & Robert McIntosh
  3. Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture & Food, Canberra, Australian Capital Territory, Australia

    • Jianping Zhang
    •  & Evans Lagudah
  4. Henan Tianmin Seed Company Limited, Lankao County, Henan Province, China

    • Jianping Zhang
  5. Limagrain UK Ltd, Rothwell, Market Rasen, Lincolnshire, UK

    • Paul Fenwick
    •  & Simon Berry
  6. National Institute of Agricultural Botany (NIAB), Cambridge, UK

    • Lesley Boyd

Authors

  1. Search for Clemence Marchal in:

  2. Search for Jianping Zhang in:

  3. Search for Peng Zhang in:

  4. Search for Paul Fenwick in:

  5. Search for Burkhard Steuernagel in:

  6. Search for Nikolai M. Adamski in:

  7. Search for Lesley Boyd in:

  8. Search for Robert McIntosh in:

  9. Search for Brande B. H. Wulff in:

  10. Search for Simon Berry in:

  11. Search for Evans Lagudah in:

  12. Search for Cristobal Uauy in:

Contributions

C.M. performed the experiments to clone Yr7 and Yr5 and the subsequent analyses of their loci and BED domains, designed the gene-specific markers, analysed the genotype data in the studied panels, and designed and made the figures. J.Z. performed the experiments to clone YrSP, confirm the Yr7 and Yr5 genes in AvocetS-Yr7 and AvocetS-Yr5 mutants, and identified the full length of Yr5 and YrSP with their respective regulatory elements. C.M. and J.Z. developed the gene-specific markers. P.Z. and R.M. performed the EMS treatment, isolation, and confirmation of Yr7, Yr5 and YrSP mutants in AvocetS NILs. P.F. performed the pathology work on the Cadenza Yr7 mutants and the mapping populations. B.S. helped with the NLR -Annotator analysis and provided the bait library for target enrichment and sequencing of NLRs. N.M.A. provided DNA samples for allelic variation studies. L.B. provided Lemhi-Yr5 mutants. R.M., E.L., P.Z., B.W., S.B. and C.U. conceived, designed and supervised the research. C.M. and C.U. wrote the manuscript. J.Z., P.Z., R.M., B.W., N.M.A., L.B. and E.L. provided edits.

Competing interests

A patent application based on this work has been filed (United Kingdom Patent Application No. 1805865.1).

Data availability

The data that support the findings of this study are presented in the supplementary information. All sequencing data have been deposited in the NCBI Short Reads Archive under accession numbers listed in Supplementary Table 14 (SRP139043). Cadenza (Yr7) and Lemhi (Yr5) mutants are available through the JIC Germplasm Resource Unit (www.seedstor.ac.uk).

Corresponding author

Correspondence to Cristobal Uauy.

Supplementary information

  1. Supplementary Information

    Supplementary Notes and Supplementary Figures 1–10.

  2. Reporting Summary

  3. Supplementary Tables

    Supplementary Tables 1–13.

  4. Supplementary File 1

    Annotation of the Yr7 locus in Cadenza with exon/intron structure, positions of mutations and the position of primers for long-range PCR and nested PCRs that were carried out prior to Sanger sequencing.

  5. Supplementary File 2

    Annotation of the Yr5/YrSP locus in Lemhi-Yr5 and AvocetS-YrSP, respectively, with exon/intron structure, the position of mutations and the position of primers for long-range PCR and nested PCRs that were carried out prior to Sanger sequencing.

  6. Supplementary File 3

    Curation of the Yr7 locus in the Cadenza genome assembly based on Sanger sequencing results.

  7. Supplementary File 4

    Syntenic region across different grasses (Supplementary Table 6) and the NLR loci identified with NLR-Annotator.

  8. Supplementary File 5

    Curated sequences of BED-NLRs from chromosome 2B and Ta_2D7.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/s41477-018-0236-4