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Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair

Abstract

Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases3. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class4, which recognize pathogen effector proteins known as avirulence (Avr) proteins5. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. 6,7), and none in other cereal rusts8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye10. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat–rye hybrid and is a host for Pgt11,12. Sr27 is effective against Ug99 (ref. 13) and other recent Pgt strains14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.

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Fig. 1: Pgt mutants with virulence to Sr27.
Fig. 2: The AvrSr27 locus encodes two related secreted proteins.
Fig. 3: Differential expression of AvrSr27 alleles.
Fig. 4: Identification of the Sr27 resistance gene.

Data availability

All sequence data from this study are available in NCBI under BioProject PRJNA695305 (Sr27 MutRenSeq data) and PRJNA698655 (Pgt21-0 mutants). This includes raw data for Fig. 2b and Supplementary Figs. 2 and 8. Figure 3 is derived from raw sequence data available in NCBI BioProject PRJNA253722 and PRJNA415866. All other relevant data are available on request from the corresponding author.

Code availability

Scripts and files for MutRenSeq analysis are available at https://github.com/TC-Hewitt/MuTrigo.

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Acknowledgements

Work described here was supported by funding from the 2Blades foundation to P.N.D. J.C. was supported by a Chinese Scholarship Council postgraduate fellowship. J.S. was supported by an Australian Research Council Discovery Early Career Researcher Award (no. DE190100066). K.K. and V.P. acknowledge financial support by the Institute Strategic Program Grant ‘Designing Future Wheat’ (grant no. BB/P016855/1) from the Biotechnology and Biological Sciences Research Council of the UK. H.N.-P. was supported by USDA-NIFA grant no. 2018-67013-27819.

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P.N.D. conceptualized the project, acquired funding and supervised the work. N.M.U., R.M., V.P., M.L., A.W., D.O., J.C., J.Z., D.B., M.A. and L.H. acquired experimental data. N.M.U., R.M., J.S., H.N.-P., T.H., M.F., K.K., J.G.E. and P.N.D conducted data analysis. P.N.D. drafted the manuscript and all authors contributed to review and editing.

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Correspondence to Peter N. Dodds.

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Peer review information Nature Plants thanks Beat Keller, Simon Krattinger and Brande Wulff for their contribution to the peer review of this work.

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Supplementary Information

Supplementary Figs. 1–11, Tables 1 and 2 and source data as uncropped gel/blot images for Supplementary Figs. 3, 5a, 6 and 11.

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Upadhyaya, N.M., Mago, R., Panwar, V. et al. Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair. Nat. Plants 7, 1220–1228 (2021). https://doi.org/10.1038/s41477-021-00971-5

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