Discovery of functional NLRs using expression level, high-throughput transformation and large-scale phenotyping
Status Publisher Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic
Typ dokumentu časopisecké články
Grantová podpora
BBS/E/J/000PR9795
RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
CRIS #5062-21220-025-000D
United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)
ARS 0500-00093-001-00-D
United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)
PubMed
40987916
DOI
10.1038/s41477-025-02110-w
PII: 10.1038/s41477-025-02110-w
Knihovny.cz E-zdroje
- Publikační typ
- časopisecké články MeSH
Protecting crops from diseases is vital for the sustainable agricultural systems that are needed for food security. Introducing functional resistance genes to enhance the plant immune system is highly effective for disease resistance, but identifying new immune receptors is resource intensive. We observed that functional immune receptors of the nucleotide-binding domain leucine-rich repeat (NLR) class show a signature of high expression in uninfected plants across both monocot and dicot species. Here, by exploiting this signature combined with high-throughput transformation, we generated a wheat transgenic array of 995 NLRs from diverse grass species to identify new resistance genes for wheat. Confirming this proof of concept, we identified new resistance genes against the stem rust pathogen Puccinia graminis f. sp. tritici and the leaf rust pathogen Puccinia triticina, both major threats to wheat production. This pipeline facilitates the rapid identification of candidate NLRs and provides in planta gene validation of resistance. The accelerated discovery of new NLRs from a large gene pool of diverse and non-domesticated plant species will enhance the development of disease-resistant crops.
Agri Bio Research Center Kaneka Corporation Iwata Shizuoka Japan
Department of Integrated Plant Protection Kroměříž Czech Republic
Department of Plant Pathology University of Minnesota St Paul MN USA
Gatsby Charitable Foundation London UK
Plant Innovation Center Japan Tobacco Inc Iwata Japan
The Sainsbury Laboratory University of East Anglia Norwich UK
USDA ARS Cereal Disease Laboratory University of Minnesota St Paul MN USA
Zobrazit více v PubMed
Savary, S. et al. The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 3, 430–439 (2019). PubMed DOI
Ristaino, J. B. et al. The persistent threat of emerging plant disease pandemics to global food security. Proc. Natl Acad. Sci. USA 118, e2022239118 (2021). PubMed DOI PMC
Bebber, D. P. Range-expanding pests and pathogens in a warming world. Annu. Rev. Phytopathol. 53, 335–356 (2015). PubMed DOI
Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). PubMed DOI
Shaw, M. W. & Osborne, T. M. Geographic distribution of plant pathogens in response to climate change. Plant Pathol. 60, 31–43 (2011). DOI
Kettles, G. J. & Luna, E. Food security in 2044: how do we control the fungal threat? Fungal Biol. 123, 558–564 (2019). PubMed DOI
Hovmøller, M. S., Thach, T. & Justesen, A. F. Global dispersal and diversity of rust fungi in the context of plant health. Curr. Opin. Microbiol. 71, 102243 (2022). PubMed DOI
Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant–pathogen interactions. Nat. Rev. Genet. 11, 539–548 (2010). PubMed DOI
Luo, M. et al. A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat. Nat. Biotechnol. 39, 561–566 (2021). PubMed DOI
van Esse, H. P., Reuber, T. L. & van der Does, D. Genetic modification to improve disease resistance in crops. N. Phytol. 225, 70–86 (2020). DOI
Hafeez, A. N. et al. Creation and judicious application of a wheat resistance gene atlas. Mol. Plant 14, 1053–1070 (2021). PubMed DOI
Wulff, B. B. & Krattinger, S. G. The long road to engineering durable disease resistance in wheat. Curr. Opin. Biotechnol. 73, 270–275 (2022). PubMed DOI
Schulze-Lefert, P. & Panstruga, R. A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation. Trends Plant Sci. 16, 117–125 (2011). PubMed DOI
Panstruga, R. & Moscou, M. J. What is the molecular basis of nonhost resistance? Mol. Plant Microbe Interact. 33, 1253–1264 (2020). PubMed DOI
Bevan, M. W. et al. Genomic innovation for crop improvement. Nature 543, 346–354 (2017). PubMed DOI
Mascher, M. et al. Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding. Nat. Genet. 51, 1076–1081 (2019). PubMed DOI
Van Der Biezen, E. A. & Jones, J. D. Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem. Sci. 23, 454–456 (1998). PubMed DOI
Cesari, S., Bernoux, M., Moncuquet, P., Kroj, T. & Dodds, P. N. A novel conserved mechanism for plant NLR protein pairs: the ‘integrated decoy’ hypothesis. Front. Plant Sci. 5, 606 (2014). PubMed DOI PMC
Saur, I. M., Panstruga, R. & Schulze-Lefert, P. NOD-like receptor-mediated plant immunity: from structure to cell death. Nat. Rev. Immunol. 21, 305–318 (2021). PubMed DOI
Tian, D., Traw, M. B., Chen, J. Q., Kreitman, M. & Bergelson, J. Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature 423, 74–77 (2003). PubMed DOI
Xiao, S., Brown, S., Patrick, E., Brearley, C. & Turner, J. G. Enhanced transcription of the Arabidopsis disease resistance genes RPW8.1 and RPW8.2 via a salicylic acid–dependent amplification circuit is required for hypersensitive cell death. Plant Cell 15, 33–45 (2003). PubMed DOI PMC
Palma, K. et al. Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog. 6, e1001137 (2010). PubMed DOI PMC
Deng, Y. et al. Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science 355, 962–965 (2017). PubMed DOI
Lai, Y. & Eulgem, T. Transcript-level expression control of plant NLR genes. Mol. Plant Pathol. 19, 1267–1281 (2018). PubMed DOI
Brown, J. K. M. Yield penalties of disease resistance in crops. Curr. Opin. Plant Biol. 5, 339–344 (2002). PubMed DOI
Brown, J. K. M. & Rant, J. C. Fitness costs and trade-offs of disease resistance and their consequences for breeding arable crops. Plant Pathol. 62, 83–95 (2013). DOI
Richard, M. M. S., Gratias, A., Meyers, B. C. & Geffroy, V. Molecular mechanisms that limit the costs of NLR-mediated resistance in plants. Mol. Plant Pathol. 19, 2516–2523 (2018). PubMed DOI PMC
Bergelson, J. & Purrington, C. B. Surveying patterns in the cost of resistance in plants. Am. Nat. 148, 536–558 (1996). DOI
Tan, X. et al. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biol. 7, 56 (2007). PubMed DOI PMC
Balint‐Kurti, P. The plant hypersensitive response: concepts, control and consequences. Mol. Plant Pathol. 20, 1163–1178 (2019). PubMed DOI PMC
Karasov, T. L., Chae, E., Herman, J. J. & Bergelson, J. Mechanisms to mitigate the trade-off between growth and defense. Plant Cell 29, 666–680 (2017). PubMed DOI PMC
Stokes, T. L., Kunkel, B. N. & Richards, E. J. Epigenetic variation in Arabidopsis disease resistance. Genes Dev. 16, 171–182 (2002). PubMed DOI PMC
Howles, P. et al. Autoactive alleles of the flax L6 rust resistance gene induce non-race-specific rust resistance associated with the hypersensitive response. Mol. Plant Microbe Interact. 18, 570–582 (2005). PubMed DOI
Hatta, M. A. M. et al. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. Plant Biotechnol. J. 19, 273–284 (2021). PubMed DOI
Brabham, H. J. et al. Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae. Plant Cell 36, 447–470 (2024). PubMed DOI
Arora, S. et al. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat. Biotechnol. 37, 139–143 (2019). PubMed DOI
Chen, S., Zhang, W., Bolus, S., Rouse, M. N. & Dubcovsky, J. Identification and characterization of wheat stem rust resistance gene Sr21 effective against the Ug99 race group at high temperature. PLoS Genet. 14, e1007287 (2018). PubMed DOI PMC
Mago, R. et al. The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus. Nat. Plants 1, 15186 (2015). PubMed DOI
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). PubMed DOI
Saintenac, C. et al. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science 341, 783–786 (2013). PubMed DOI PMC
Zhang, J. et al. A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes. Nat. Commun. 12, 3378 (2021). PubMed DOI PMC
Zhang, W. et al. Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group. Proc. Natl Acad. Sci. USA 114, E9483–E9492 (2017). PubMed DOI PMC
Steuernagel, B. et al. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat. Biotechnol. 34, 652–655 (2016). PubMed DOI
Luo, J. et al. Identification and characterization of Sr22b, a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group. Plant Biotechnol. J. 20, 554–563 (2022). PubMed DOI
Zhang, J. et al. Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9. Nat. Commun. 14, 7354 (2023). PubMed DOI PMC
Upadhyaya, N. M. et al. Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair. Nat. Plants 7, 1220–1228 (2021). PubMed DOI
Cloutier, S. et al. Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family. Plant Mol. Biol. 65, 93–106 (2007). PubMed DOI
Feuillet, C. et al. Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc. Natl Acad. Sci. USA 100, 15253–15258 (2003). PubMed DOI PMC
Hewitt, T. et al. Wheat leaf rust resistance gene Lr13 is a specific Ne2 allele for hybrid necrosis. Mol. Plant 14, 1025–1028 (2021). PubMed DOI
Lin, G. et al. Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii. Nat. Commun. 13, 3044 (2022). PubMed DOI PMC
Mapuranga, J. et al. Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. Front. Plant Sci. https://doi.org/10.3389/fpls.2022.951095 (2022).
Sharma, D. et al. A single NLR gene confers resistance to leaf and stripe rust in wheat. Nat. Commun. 15, 9925 (2024). PubMed DOI PMC
Thind, A. K. et al. Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat. Biotechnol. 35, 793–796 (2017). PubMed DOI
Yan, X. et al. High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis. Mol. Plant 14, 1029–1032 (2021). PubMed DOI
Huang, L. et al. Evolution of new disease specificity at a simple resistance locus in a crop–weed complex: reconstitution of the Lr21 gene in wheat. Genetics 182, 595–602 (2009). PubMed DOI PMC
Ishida, Y., Tsunashima, M., Hiei, Y. & Komari, T. Wheat (Triticum aestivum L.) transformation using immature embryos. Methods Mol. Biol. 1223, 189–198 (2015). PubMed DOI
Bettgenhaeuser, J. et al. The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics. Nat. Commun. 12, 6915 (2021). PubMed DOI PMC
Kawashima, C. G. et al. A pigeonpea gene confers resistance to Asian soybean rust in soybean. Nat. Biotechnol. 34, 661–665 (2016). PubMed DOI
Witek, K. et al. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. Nat. Plants 7, 198–208 (2021). PubMed DOI PMC
Wu, C. H. et al. NLR network mediates immunity to diverse plant pathogens. Proc. Natl Acad. Sci. USA 114, 8113–8118 (2017). PubMed DOI PMC
Adachi, H. & Kamoun, S. NLR receptor networks in plants. Essays Biochem. 66, 541–549 (2022). PubMed DOI
Zhang, X.-C. & Gassmann, W. RPS4-mediated disease resistance requires the combined presence of RPS4 transcripts with full-length and truncated open reading frames. Plant Cell 15, 2333–2342 (2003). PubMed DOI PMC
Dinesh-Kumar, S. P. & Baker, B. J. Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance. Proc. Natl Acad. Sci. USA 97, 1908–1913 (2000). PubMed DOI PMC
Tang, F., Yang, S., Gao, M. & Zhu, H. Alternative splicing is required for RCT1-mediated disease resistance in Medicago truncatula. Plant Mol. Biol. 82, 367–374 (2013). PubMed DOI
Cesari, S. et al. The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding. Plant Cell 25, 1463–1481 (2013). PubMed DOI PMC
Periyannan, S. et al. Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat. Theor. Appl. Genet. 127, 947–955 (2014). PubMed DOI
Bailey, P. C. et al. Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions. Genome Biol. 19, 23 (2018). PubMed DOI PMC
Cesari, S. et al. The NB-LRR proteins RGA4 and RGA5 interact functionally and physically to confer disease resistance. EMBO J. 33, 1941–1959 (2014). PubMed DOI PMC
Wang, X. et al. 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. 26, 407–418 (2013). PubMed DOI
Rouse, M. N., Olson, E. L., Gill, B. S., Pumphrey, M. O. & Jin, Y. Stem rust resistance in Aegilops tauschii germplasm. Crop Sci. 51, 2074–2078 (2011). DOI
Maekawa, T. et al. Subfamily-specific specialization of RGH1/MLA immune receptors in wild barley. Mol. Plant Microbe Interact. 32, 107–119 (2018). PubMed DOI
Förderer, A. et al. A wheat resistosome defines common principles of immune receptor channels. Nature 610, 532–539 (2022). PubMed DOI PMC
Saur, I. M. et al. Multiple pairs of allelic MLA immune receptor–powdery mildew AVRA effectors argue for a direct recognition mechanism. eLife https://doi.org/10.7554/eLife.44471 (2019).
Contreras, M. P. et al. Resurrection of plant disease resistance proteins via helper NLR bioengineering. Sci Adv. 9, eadg3861 (2023). PubMed DOI PMC
Li, X., Clarke, J. D., Zhang, Y. & Dong, X. Activation of an EDS1-mediated R-gene pathway in the snc1 mutant leads to constitutive, NPR1-independent pathogen resistance. Mol. Plant Microbe Interact. 14, 1131–1139 (2001). PubMed DOI
Oldroyd, G. E. D. & Staskawicz, B. J. Genetically engineered broad-spectrum disease resistance in tomato. Proc. Natl Acad. Sci. USA 95, 10300–10305 (1998). PubMed DOI PMC
Yang, S. et al. Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease. Proc. Natl Acad. Sci. USA 110, 18572–18577 (2013). PubMed DOI PMC
Yi, H. & Richards, E. J. A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing. Plant Cell 19, 2929–2939 (2007). PubMed DOI PMC
Yi, H. & Richards, E. J. Phenotypic instability of Arabidopsis alleles affecting a disease resistance gene cluster. BMC Plant Biol. 8, 36 (2008). PubMed DOI PMC
Halterman, D. A., Wei, F. & Wise, R. P. Powdery mildew-induced Mla mRNAs are alternatively spliced and contain multiple upstream open reading frames. Plant Physiol. 131, 558–567 (2003). PubMed DOI PMC
Guo, H., Wang, S. & Jones, J. D. Autoactive Arabidopsis RPS4 alleles require partner protein RRS1-R. Plant Physiol. 185, 761–764 (2021). PubMed DOI
Shirano, Y., Kachroo, P., Shah, J. & Klessig, D. F. A gain-of-function mutation in an Arabidopsis Toll Interleukin1 Receptor–Nucleotide Binding Site–Leucine-Rich Repeat type R gene triggers defense responses and results in enhanced disease resistance. Plant Cell 14, 3149–3162 (2002). PubMed DOI PMC
Yang, X.-M. et al. Broad-spectrum resistance gene RPW8.1 balances immunity and growth via feedback regulation of WRKYs. Plant Biotechnol. J. 22, 116–130 (2024). PubMed DOI
Borrill, P. et al. An autoactive NB-LRR gene causes Rht13 dwarfism in wheat. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.2209875119 (2022).
Tong, M. et al. E3 ligase SAUL1 serves as a positive regulator of PAMP-triggered immunity and its homeostasis is monitored by immune receptor SOC3. N. Phytol. 215, 1516–1532 (2017). DOI
Lorang, J. et al. Tricking the guard: exploiting plant defense for disease susceptibility. Science 338, 659–662 (2012). PubMed DOI PMC
Innan, H. & Kondrashov, F. The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet. 11, 97–108 (2010). PubMed DOI
Ma, S. et al. Oligomerization-mediated autoinhibition and cofactor binding of a plant NLR. Nature 632, 869–876 (2024). PubMed DOI PMC
Wang, J. et al. Reconstitution and structure of a plant NLR resistosome conferring immunity. Science 364, eaav5870 (2019). PubMed DOI
Komori, T. et al. High-throughput phenotypic screening of random genomic fragments in transgenic rice identified novel drought tolerance genes. Theor. Appl. Genet. 133, 1291–1301 (2020). PubMed DOI
Moseman, J. G. Isogenic barley lines for reaction to Erysiphe graminis f. sp. hordei. Crop Sci. 12, 681–682 (1972). DOI
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics https://doi.org/10.1093/bioinformatics/btu170 (2014).
Mapleson, D. et al. KAT: a K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. Bioinformatics https://doi.org/10.1093/bioinformatics/btw663 (2016).
R Core Team R: A Language and Environment for Statistical Computing (R Core Team, 2025).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Halterman, D., Zhou, F., Wei, F., Wise, R. P. & Schulze-Lefert, P. The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria graminis f. sp. hordei in barley and wheat. Plant J. 25, 335–348 (2001). PubMed DOI
Gibson, D. G. Programming biological operating systems: genome design, assembly and activation. Nat. Methods 11, 521–526 (2014). PubMed DOI
Hensel, G., Kastner, C., Oleszczuk, S., Riechen, J. & Kumlehn, J. Agrobacterium-mediated gene transfer to cereal crop plants: current protocols for barley, wheat, triticale, and maize. Int. J. Plant Genom. https://doi.org/10.1155/2009/835608 (2009).
Yeo, F. K. et al. Golden SusPtrit: a genetically well transformable barley line for studies on the resistance to rust fungi. Theor. Appl. Genet. 127, 325–337 (2014). PubMed DOI
Bartlett, J. G., Alves, S. C., Smedley, M., Snape, J. W. & Harwood, W. A. High-throughput Agrobacterium-mediated barley transformation. Plant Methods 4, 22 (2008). PubMed DOI PMC
Close, T. J. et al. Development and implementation of high-throughput SNP genotyping in barley. BMC Genom. 10, 582 (2009). DOI
Dreiseitl, A. A novel resistance against powdery mildew found in winter barley cultivars. Plant Breed. 138, 840–845 (2019). DOI
Kølster, P., Munk, L., Stølen, O. & Løhde, J. Near-isogenic barley lines with genes for resistance to powdery mildew. Crop Sci. 26, 903–907 (1986). DOI
Kølster, P. & Stølen, O. Barley isolines with genes for resistance to Erysiphe graminis f. sp. hordei in the recurrent parent ‘Siri’. Plant Breed. 98, 79–82 (1987). DOI
Dreiseitl, A. Postulation of specific disease resistance genes in cereals: a widely used method and its detailed description. Pathogens 11, 284 (2022). PubMed DOI PMC
Torp, J., Jensen, H. P. & Jørgensen, J. H. Powdery mildew resistance genes in 106 northwest European spring barley cultivars. Kongelige Veterinaer- Og Landbohoejskole, 75–102 (1978).
Andrews, S. FastQC. Babraham Informatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. https://doi.org/10.1038/nbt.1883 (2011).
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016). PubMed DOI
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. https://doi.org/10.1186/1471-2105-10-421 (2009).
Witek, K. et al. Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nat. Biotechnol. 34, 656–660 (2016). PubMed DOI
Foster, S. J. et al. Rpi-vnt1.1, a Tm-22 homolog from Solanum venturii, confers resistance to potato late blight. Mol. Plant Microbe Interact. 22, 589–600 (2009). PubMed DOI
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods https://doi.org/10.1038/nmeth.2019 (2012).
Posit Team RStudio: Integrated Development Environment for R (Posit Software, 2025).
Haas, B. J. TransDecoder. GitHub https://github.com/TransDecoder/TransDecoder (2024).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014). PubMed DOI PMC
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. https://doi.org/10.1093/nar/gkh340 (2004).
Afrasiabi, C., Samad, B., Dineen, D., Meacham, C. & Sjölander, K. The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. Nucleic Acids Res. 41, W242–W248 (2013). PubMed DOI PMC
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics https://doi.org/10.1093/bioinformatics/btl158 (2006).
Huang, L. et al. Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics https://doi.org/10.1093/genetics/164.2.655 (2003).
Liu, W. et al. The stripe rust resistance gene Yr10 encodes an evolutionary-conserved and unique CC-NBS-LRR sequence in wheat. Mol. Plant 7, 1740–1755 (2014). PubMed DOI
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). PubMed DOI PMC
Yahiaoui, N., Srichumpa, P., Dudler, R. & Keller, B. Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J. 37, 528–538 (2004). PubMed DOI
Halterman, D. A. & Wise, R. P. A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. Plant J. 38, 215–226 (2004). PubMed DOI
Yarbrough, D., Wachter, R. M., Kallio, K., Matz, M. V. & Remington, S. J. Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-Å resolution. Proc. Natl Acad. Sci. USA 98, 462–467 (2001). PubMed DOI PMC
Huang, S., Steffenson, B. J., Sela, H. & Stinebaugh, K. Resistance of Aegilops longissima to the rusts of wheat. Plant Dis. 102, 1124–1135 (2018). PubMed DOI
Scott, J. C., Manisterski, J., Sela, H., Ben-Yehuda, P. & Steffenson, B. J. Resistance of Aegilops species from Israel to widely virulent African and Israeli races of the wheat stem rust pathogen. Plant Dis. 98, 1309–1320 (2014). PubMed DOI
Roelfs, A. P. & Martens, J. An international system of nomenclature for Puccinia graminis f. sp. tritici. Phytopathology 78, 526–533 (1988). DOI
Stakman, E. C., Stewart, D. & Loegering, W. Q. Identification of Physiologic Races of Puccinia graminis var. tritici (USDA, 1962).
Zhang, D., Bowden, R. L., Yu, J., Carver, B. F. & Bai, G. Association analysis of stem rust resistance in U.S. winter wheat. PLoS ONE 9, e103747 (2014). PubMed DOI PMC
Kolmer, J. Leaf rust of wheat: pathogen biology, variation and host resistance. Forests 4, 70–84 (2013). DOI
Zadoks, J. C., Chang, T. T. & Konzak, C. F. A decimal code for the growth stages of cereals. Weed Res. 14, 415–421 (1974). DOI
Peterson, R., Campbell, A. & Hannah, A. A diagrammatic scale for estimating rust severity on leaves and stem of cereals. Can. J. Res. 26, 490–500 (1948).
Mascher, M. et al. Long-read sequence assembly: a technical evaluation in barley. Plant Cell 33, 1888–1906 (2021). PubMed DOI PMC
Zhu, T. et al. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J. 107, 303–314 (2021). PubMed DOI PMC
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics https://doi.org/10.1093/bioinformatics/btu033 (2014).
Tegenfeldt F. et al. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Res. https://doi.org/10.1093/nar/gkae987 (2025).
Löytynoja, A. Phylogeny-aware alignment with PRANK. Methods Mol. Biol. https://doi.org/10.1007/978-1-62703-646-7_10 (2014).
Moscou, M. & Brabham, H. Source data for Brabham et al. 2024 bioRxiv. figshare https://doi.org/10.6084/m9.figshare.28680800.v1 (2025).
Kourelis, J., Sakai, T., Adachi, H. & Kamoun, S. RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLoS Biol. 19, e3001124 (2021). PubMed DOI PMC