Abstract
Wheat blast, caused by Magnaporthe oryzae pathotype Triticum (MoT), threatens global wheat production, yet durable resistance mechanisms remain elusive. Current strategies relying on race-specific resistance genes or fungicides are vulnerable to pathogen evolution and inefficacy. Here, we investigated field-derived transcriptomes from the 2016 Bangladesh wheat blast epidemic, a catastrophic event devastating all local varieties to identify host susceptibility (S) genes co-opted by MoT. By analyzing RNA-seq data from infected and healthy plants across geographically distinct regions, we pinpointed 273 consistently upregulated wheat genes, enriched in defense-related pathways. Ortholog analysis with rice, a model for blast resistance, identified three conserved susceptibility (S)-gene candidates: TaSULTR3-3B (an ortholog of a rice bacterial blight susceptibility gene), TaSTP3-4D (associated with stripe rust), and TaMLO1-5A (a wheat powdery mildew susceptibility gene). While all three candidates exhibited significant expression correlation with M. oryzae Triticum (MoT) effectors in field-derived samples, in planta spike assays revealed distinct expression dynamics. Only TaMLO1-5A was significantly upregulated in the susceptible cultivar BARI Gom 26 following MoT inoculation, with no induction observed in the resistant cultivar S-615 (carrying Rmg8). Conversely, TaSULTR3-3B and TaSTP3-4D did not show significant induction under the specific conditions and time points of the in planta spike assays. This discrepancy potentially arises from tissue-specific regulation (spike vs. leaf), environmental variations, or differences in sampling time points between the field and greenhouse experiments. Disruption of such S genes, validated in other cereals for durable resistance, offers a transformative strategy to engineer non-race-specific wheat blast resilience. Our findings shift the paradigm from transient resistance genes to foundational susceptibility networks, proposing CRISPR-based editing of the candidate gene as an actionable target. This approach, resilient to pathogen evolution, could preempt epidemics in climate-vulnerable regions, safeguarding global wheat security. By bridging field pathogenomics and evolutionary genomics, we provide a roadmap for sustainable disease management in an era of expanding fungal threats.
Data availability
The transcriptomics data for both wheat and blast can be freely accessed on Open Wheat Blast (http://openwheatblast.net/raw-data/). Data that support the findings of this study are available within the paper and its supplementary materials.
References
Latorre, S. M. et al. Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus. PLoS Biol. 21, e3002052. https://doi.org/10.1371/journal.pbio.3002052 (2023).
Islam, M. T. et al. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biol. 14, 84. https://doi.org/10.1186/s12915-016-0309-7 (2016).
Tembo, B. et al. Detection and characterization of Magnaporthe oryzae pathotype Triticum causing wheat blast disease on rain-fed wheat in Zambia. PLoS One. 15, e0238724. https://doi.org/10.1371/journal.pone.0238724 (2020).
Farman, M. et al. The Lolium pathotype of Magnaporthe oryzae recovered from a single blasted wheat plant in the united States. Plant Dis. 101, 684–692. https://doi.org/10.1094/PDIS-05-16-0700-RE (2017).
Barragan, A. C. et al. Wild grass isolates of Magnaporthe (Syn. Pyricularia) spp. From Germany can cause blast disease on cereal crops. BioRxiv 505667. https://doi.org/10.1101/2022.08.29.505667 (2022).
Islam, M. T. et al. Wheat blast: a new threat to food security. Phytopathol. Res. 2, 1–13 (2020).
Jones, J. D. & Dangl, J. L. The plant immune system. Nature 444, 323–329. https://doi.org/10.1038/nature05286 (2006).
Cruz, C. D. & Valent, B. Wheat blast disease: danger on the move. Trop. Plant. Pathol. 42, 210–222. https://doi.org/10.1007/s40858-017-0159-z (2017).
Nizolli, V. O. et al. Wheat blast: the last enemy of hunger fighters. Genet. Mol. Biol. 46, e20220002. https://doi.org/10.1590/1678-4685-GMB-2022-0002 (2023).
Ge, X. et al. Tempered Mlo broad-spectrum resistance to barley powdery mildew in an Ethiopian landrace. Sci. Rep. 6, 29558 (2016).
Kusch, S. & Panstruga, R. mlo-based resistance: an apparently universal weapon to defeat powdery mildew disease. Mol. Plant Microbe Interact. 30, 179–189. https://doi.org/10.1094/mpmi-12-16-0255-cr (2017).
Li, S. et al. Genome-edited powdery mildew resistance in wheat without growth penalties. Nature 602, 455–460. https://doi.org/10.1038/s41586-022-04395-9 (2022).
Islam, T., Ansary, M. W. R. & Rahman, M. M. Magnaporthe oryzae and its pathotypes: a potential plant pandemic threat to global food security. In Plant Relationships: Fungal-Plant Interactions, 425–462. https://doi.org/10.1007/978-3-031-16503-0_18 (Springer, 2022).
Nicolas, L. B. et al. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527. https://doi.org/10.1038/nbt.3519 (2016).
Chowdhury, R. H. et al. Drought-responsive genes in tomato: meta-analysis of gene expression using machine learning. Sci. Rep. 13, 19374 (2023).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140. https://doi.org/10.1093/bioinformatics/btp616 (2010).
Gupta, D. R. et al. Suitable methods for isolation, culture, storage and identification of wheat blast fungus Magnaporthe oryzae triticum pathotype. Phytopathol. Res. 2, 30. https://doi.org/10.1186/s42483-020-00070-x (2020).
Zhang, B., Han, X., Yuan, W. & Zhang, H. TALEs as double-edged swords in plant-pathogen interactions: progress, challenges and perspectives. Plant. Commun. 3, 100318. https://doi.org/10.1016/j.xplc.2022.100318 (2022).
Huai, B. et al. TaSTP13 contributes to wheat susceptibility to Stripe rust possibly by increasing cytoplasmic hexose concentration. BMC Plant Biol. 20, 49. https://doi.org/10.1186/s12870-020-2248-2 (2020).
Römer, P. et al. Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae. New Phytol. 187, 1048–1057. https://doi.org/10.1111/j.1469-8137.2010.03217.x (2010).
Yuan, T., Li, X., Xiao, J. & Wang, S. Characterization of Xanthomonas oryzae-responsive cis-acting element in the promoter of rice race-specific susceptibility gene Xa13. Mol. Plant. 4, 300–309. https://doi.org/10.1093/mp/ssq076 (2011).
Chen, Y. et al. The role of sugar transporters in the battle for carbon between plants and pathogens. Plant Biotechnol. J. 22, 2844–2858 (2024).
Ricardo et al. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat. Biotechnol. 37, 1344–1350 (2019).
Garcia-Ruiz, H., Szurek, B. & Van den Ackerveken, G. Stop helping pathogens: engineering plant susceptibility genes for durable resistance. Curr. Opin. Biotechnol. 70, 187–195. https://doi.org/10.1016/j.copbio.2021.05.005 (2021).
Schmitt-Keichinger, C. Manipulating cellular factors to combat viruses: a case study from plant eukaryotic translation initiation factors eIF4. Front. Microbiol. 10, 17. https://doi.org/10.3389/fmicb.2019.00017 (2019).
Cernadas, R. A. et al. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. PLoS Pathog. 10, e1003972 (2014).
Asuke, S. et al. Evolution of wheat blast resistance gene Rmg8 accompanied by differentiation of variants recognizing the powdery mildew fungus. Nat. Plants. 10, 971–983. https://doi.org/10.1038/s41477-024-01711-1 (2024).
O’Hara, T. et al. The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast. Nat. Plants. 10, 984–993. https://doi.org/10.1038/s41477-024-01718-8 (2024).
Islam, T. & Azad, R. B. Rmg8 gene against wheat blast. Nat. Plants. 10, 836–837. https://doi.org/10.1038/s41477-024-01690-3 (2024).
Kourelis, J. et al. NLR immune receptor–nanobody fusions confer plant disease resistance. Science 379, 934–939. https://doi.org/10.1126/science.abn4116 (2023).
Inoue, Y. et al. Suppression of wheat blast resistance by an effector of Pyricularia oryzae is counteracted by a host specificity resistance gene in wheat. New Phytol. 229, 488–500. https://doi.org/10.1111/nph.16894 (2021).
Horo, J. T. et al. Effectiveness of the wheat blast resistance gene Rmg8 in Bangladesh suggested by distribution of an AVR-Rmg8 allele in the Pyricularia oryzae population. Phytopathology 110, 1802–1807. https://doi.org/10.1094/PHYTO-03-20-0073-R (2020).
Anh, V. L. et al. Rmg8 and Rmg7, wheat genes for resistance to the wheat blast fungus, recognize the same avirulence gene AVR-Rmg8. Mol. Plant Pathol. 19, 1252–1256. https://doi.org/10.1111/mpp.12609 (2018).
Chen, L. Q. et al. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science 335, 207–211. https://doi.org/10.1126/science.1213351 (2012).
van Schie, C. C. & Takken, F. L. Susceptibility genes 101: how to be a good host. Annu. Rev. Phytopathol. 52, 551–581. https://doi.org/10.1146/annurev-phyto-102313-045854 (2024).
Saintenac, C. et al. Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to Zymoseptoria tritici. Nat. Genet. 50, 368–374. https://doi.org/10.1038/s41588-018-0051-x (2018).
Babaeizad, V. et al. Over-expression of the cell death regulator BAX inhibitor-1 in barley confers reduced or enhanced susceptibility to distinct fungal pathogens. Theor. Appl. Genet. 118, 455–463. https://doi.org/10.1007/s00122-008-0912-2 (2009).
Navia-Urrutia, M. et al. Effector genes in Magnaporthe oryzae triticum as potential targets for incorporating blast resistance in wheat. Plant Dis. 106, 1700–1712. https://doi.org/10.1094/PDIS-10-21-2209-RE (2022).
Castroagudín, V. L. et al. Resistance to QoI fungicides is widespread in Brazilian populations of the wheat blast pathogen Magnaporthe oryzae. Phytopathology. 105, 284–294 (2015).
Pequeno, D. N. et al. Production vulnerability to wheat blast disease under climate change. Nat. Clim. Change. 14, 1–6 (2024).
Pallab, B. et al. Management of wheat blast disease in Bangladesh caused by Magnaporthe oryzae pathotype Triticum. Plant. Health Cases. phcs20250025. https://doi.org/10.1079/planthealthcases.2025.0025 (2025).
Hasnat, S. et al. Structural insights into AVR-Rmg8 recognition mechanisms by the wheat blast resistance gene. Rmg8 Sci. Rep. 15, 45777. https://doi.org/10.1038/s41598-025-28559-5 (2025).
Sung, Y. C. et al. Wheat tandem kinase RWT4 directly binds a fungal effector to activate defense. Nat. Genet. 57, 1238–1249. https://doi.org/10.1038/s41588-025-02162-w (2025).
Acknowledgements
The authors would like to thank Sophien Kamoun, Thorsten Langner and Joe Win for helpful comments on the manuscript. We are thankful to Professor Yukio Tosa of Kobe University, Japan for generously providing wheat genotype, S-615, carrying Rmg8 blast resistance gene. We are sincerely thankful to the Open Wheat Blast (http://openwheatblast.net/), a unique platform which openly shares the RNA-seq data of both wheat and blast pathogen MoT of Bangladesh epidemic outbreak in 2016.
Funding
This study was funded by the Krishi Gobeshona Foundation, Bangladesh under the OFANS project (Project Code No: FT-92-FNS/21), and a grant from the National Natural Science Foundation of China (32261143468). The authors are also thankful to the Bill and Melinda Gates Foundation and the Foreign, Commonwealth & Development Office (FCDO), UK for partial funding to the DEWAS: Wheat Blast Diagnostics project (Grant Code: V0156.01).
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A.K. and T.I. conceived and designed the study. A.K. and T.I.S. collected and curated data sets and performed exploratory analyses. A.K. wrote the code, F.S.E. and T.I.S. performed final analyses. F.S.E., T.I.S. and D.R.G. made figures. H.K. and T.I. designed the in planta transcriptomics experiments. P.Y., R.B.A., and J.A. carried out the in planta experiment. A.K., T.I., S.A., Q.P, M.A.M., H.K., D.R.G., and T.I.S. wrote and edited the manuscript. All authors reviewed the manuscript.
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Khayer, A., Ye, P., Eti, F.S. et al. Field pathogenomics and evolutionary conservation unveil CRISPR-targetable susceptibility genes for wheat blast resistance. Sci Rep (2026). https://doi.org/10.1038/s41598-026-36547-6
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DOI: https://doi.org/10.1038/s41598-026-36547-6
