The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.

AgBiome Inc Research Triangle Park NC 27709 USA

Agricultural Institute Centre for Agricultural Research ELKH Martonvásár 2462 Hungary

Alliance Management at Enko Chem 62 Maritime Dr Mystic CT 06355 USA

Blades Foundation Evanston IL USA

Center of integrated Breeding Research Department of Crop Sciences Georg August University Von Siebold Str 8 37075 Göttingen Germany

Crop Development Centre Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada

Department of Agroecology Aarhus University Forsøgsvej 1 DK 4200 Slagelse Denmark

Department of Agronomy Kansas State University Manhattan KS 66506 USA

Department of Plant Pathology University of Minnesota St Paul MN 55108 USA

German Centre for Integrative Biodiversity Research Halle Jena Leipzig Deutscher Platz 5e 04103 Leipzig Germany

Institute for Cereal Crops Improvement Tel Aviv University Tel Aviv Israel

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research 779 00 Olomouc Czech Republic

John Innes Centre Norwich Research Park Norwich NR4 7UH UK

KAUST Center for Desert Agriculture King Abdullah University of Science and Technology Thuwal 23955 6900 Saudi Arabia

Leibniz Institute of Plant Genetics and Crop Plant Research Seeland Germany

Plant Science Program Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology Thuwal 23955 6900 Saudi Arabia

School of Plant Sciences and Food Security Tel Aviv University Tel Aviv Israel

Syngenta Flowers Downers Grove IL 60515 USA

The Sainsbury Laboratory University of East Anglia Norwich NR4 7UK UK

Zobrazit více v PubMed

Peterson, P. D. Stem Rust of Wheat: From Ancient Enemy to Modern Foe. Am. Phytopathol. Soc. (APS Press, St. Paul, 2001).

Le Roux J, Rijkenberg FH. Occurrence and pathogenicity of Puccinia graminis f. sp. tritici in South Africa during the period 1981–1985. Phytophylactica. 1987;19:467–472.

Addai, D. et al Potential economic impacts of the wheat stem rust strain Ug99 in Australia, ABARES research report, prepared for the Plant Biosecurity Branch, Department of Agriculture and Water Resources, Canberra (2018).

Pretorius ZA, Singh RP, Wagoire WW, Payne TS. Detection of virulence to wheat stem rust resistance gene Sr31 in Puccinia graminis f. sp. tritici in Uganda. Plant Dis. 2000;84:203. doi: 10.1094/PDIS.2000.84.2.203B. PubMed DOI

Jin Y, et al. Detection of virulence to resistance gene Sr24 within race TTKS of Puccinia graminis f. sp. tritici. Plant Dis. 2008;92:923–926. doi: 10.1094/PDIS-92-6-0923. PubMed DOI

Jin Y, et al. Detection of virulence to resistance gene Sr36 within the TTKS race lineage of Puccinia graminis f. sp. tritici. Plant Dis. 2009;93:367–370. doi: 10.1094/PDIS-93-4-0367. PubMed DOI

Olivera P, et al. Phenotypic and genotypic characterization of race TKTTF of Puccinia graminis f. sp. tritici that caused a wheat stem rust epidemic in southern Ethiopia in 2013–14. Phytopathology. 2015;105:917–928. doi: 10.1094/PHYTO-11-14-0302-FI. PubMed DOI

Olivera Firpo PD, et al. Characterization of Puccinia graminis f. sp. tritici isolates derived from an unusual wheat stem rust outbreak in Germany in 2013. Plant Pathol. 2017;66:1258–1266. doi: 10.1111/ppa.12674. DOI

Lewis CM, et al. Potential for re-emergence of wheat stem rust in the United Kingdom. Commun. Biol. 2018;1:13. doi: 10.1038/s42003-018-0013-y. PubMed DOI PMC

Bhattacharya S. Deadly new wheat disease threatens Europe’s crops. Nature. 2017;542:145–146. doi: 10.1038/nature.2017.21424. PubMed DOI

Shamanin V, et al. Genetic diversity of spring wheat from Kazakhstan and Russia for resistance to stem rust Ug99. Euphytica. 2016;212:287–296. doi: 10.1007/s10681-016-1769-0. DOI

Prank, M., Kenaley, S. C., Bergstrom, G. C., Acevedo, M. & Mahowald, N. M. Climate change impacts the spread potential of wheat stem rust, a significant crop disease. Environ. Res. Lett.14, 124053 (2019).

Hafeez AN, et al. Creation and judicious application of a wheat resistance gene atlas. Mol. Plant. 2021;14:1053–1070. doi: 10.1016/j.molp.2021.05.014. PubMed DOI

Moore JW, et al. A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat. Genet. 2015;47:1494–1498. doi: 10.1038/ng.3439. PubMed DOI

Krattinger SG, et al. A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science. 2009;323:1360–1363. doi: 10.1126/science.1166453. PubMed DOI

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. 2017;114:E9483–E9492. PubMed PMC

Chen S, Zhang W, Bolus S, Rouse MN, Dubcovsky J. Identification and characterization of wheat stem rust resistance gene Sr21 effective against the Ug99 race group at high temperature. PLoS Genet. 2018;14:e1007287. doi: 10.1371/journal.pgen.1007287. PubMed DOI PMC

Steuernagel B, et al. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat. Biotechnol. 2016;34:652–655. doi: 10.1038/nbt.3543. PubMed DOI

Zhang J, et al. A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes. Nat. Commun. 2021;12:3378. doi: 10.1038/s41467-021-23738-0. PubMed DOI PMC

Periyannan S, et al. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science. 2013;341:786–789. doi: 10.1126/science.1239028. PubMed DOI

Saintenac C, et al. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science. 2013;341:783–786. doi: 10.1126/science.1239022. PubMed DOI PMC

Arora S, et al. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat. Biotechnol. 2019;37:139–143. doi: 10.1038/s41587-018-0007-9. PubMed DOI

Mago R, et al. The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus. Nat. Plants. 2015;1:15186. doi: 10.1038/nplants.2015.186. PubMed DOI

Chen S, et al. Wheat gene Sr60 encodes a protein with two putative kinase domains that confers resistance to stem rust. N. Phytol. 2020;225:948–959. doi: 10.1111/nph.16169. PubMed DOI

Gaurav, K. et al. Population genomic analysis of Aegilops tauschiii dentifies targets for bread wheat improvement. Nat. Biotechnol.10.1038/s41587-021-01058-4 (2021). PubMed PMC

Klymiuk V., Coaker G., Fahima T., Pozniak C. Tandem protein kinases emerge as new regulators of plant immunity. Mol. Plant Microbe. Interact.10.1094/MPMI-03-21-0073-CR (2021). PubMed PMC

Brueggeman R, et al. The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc. Natl Acad. Sci. USA. 2002;99:9328–9333. doi: 10.1073/pnas.142284999. PubMed DOI PMC

Klymiuk V, et al. Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat. Commun. 2018;9:3735. doi: 10.1038/s41467-018-06138-9. PubMed DOI PMC

Lu P, et al. A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew. Nat. Commun. 2020;11:680. doi: 10.1038/s41467-020-14294-0. PubMed DOI PMC

Olivera PD, Steffenson BJ. Aegilops sharonensis: Origin, genetics, diversity, and potential for wheat improvement. Botany. 2009;87:740–756. doi: 10.1139/B09-040. DOI

Olivera PD, Anikster Y, Kolmer JA, Steffenson BJ. Resistance of Sharon goatgrass (Aegilops sharonensis) to fungal diseases of wheat. Plant Dis. 2007;91:942–950. doi: 10.1094/PDIS-91-8-0942. PubMed DOI

Scott JC, Manisterski J, Sela H, Ben-Yehuda P, Steffenson BJ. Resistance of Aegilops species from Israel to widely virulent African and Israeli races of the wheat stem rust pathogen. Plant Dis. 2014;98:1309–1320. doi: 10.1094/PDIS-01-14-0062-RE. PubMed DOI

Tsujimoto H, Tsunewaki K. Gametocidal genes in wheat and its relatives. I. Genetic analyses in common wheat of a gametocidal gene derived from Aegilops speltoides. Can. J. Genet. Cytol. 1984;26:78–84. doi: 10.1139/g84-013. DOI

Marais GF, McCallum B, Marais AS. Leaf Rust and Stripe Rust Resistance Genes Derived from Aegilops Sharonensis. Euphytica. 2006;149:373–380. doi: 10.1007/s10681-006-9092-9. DOI

Knight E, et al. Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4Ssh of Aegilops sharonensis. Theor. Appl. Genet. 2015;128:1049–1059. doi: 10.1007/s00122-015-2489-x. PubMed DOI PMC

Millet E, et al. Introgression of leaf rust and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis Eig) into bread wheat (Triticum aestivum L.) Genome. 2014;57:309–316. doi: 10.1139/gen-2014-0004. PubMed DOI

Millet E, et al. Genome targeted introgression of resistance to African stem rust from Aegilops sharonensis into bread wheat. Plant Genome. 2017;10:1–11. doi: 10.3835/plantgenome2017.07.0061. PubMed DOI

Yu G, et al. Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis. Theor. Appl. Genet. 2017;130:1207–1222. doi: 10.1007/s00122-017-2882-8. PubMed DOI PMC

Monat C, et al. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol. 2019;20:284. doi: 10.1186/s13059-019-1899-5. PubMed DOI PMC

International Wheat Genome Sequencing Consortium (IWGSC). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science361, eaar7191 (2018). PubMed

Elshire RJ, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011;6:e19379. doi: 10.1371/journal.pone.0019379. PubMed DOI PMC

Uauy C, Wulff BBH, Dubcovsky J. Combining traditional mutagenesis with wew high-throughput sequencing and genome editing to reveal hidden variation in polyploid wheat. Annu Rev. Genet. 2017;51:435–454. doi: 10.1146/annurev-genet-120116-024533. PubMed DOI

Steuernagel B, et al. The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire. Plant Physiol. 2020;183:468–482. doi: 10.1104/pp.19.01273. PubMed DOI PMC

Kelley L, et al. The Phyre2 web portal for protein modelling, prediction and analysis. Nat. Protoc. 2015;10:845–858. doi: 10.1038/nprot.2015.053. PubMed DOI PMC

McNicholas S, Potterton E, Wilson KS, Noble MEM. Presenting your structures: the CCP4mg molecular-graphics software. Acta Cryst. 2011;D67:386–394. PubMed PMC

Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. J. Mol. Biol. 2009;390:560–577. doi: 10.1016/j.jmb.2009.05.015. PubMed DOI

Hanks SK, Quinn AM, Hunter T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science. 1988;241:42–52. doi: 10.1126/science.3291115. PubMed DOI

Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970;48:443–453. doi: 10.1016/0022-2836(70)90057-4. PubMed DOI

Lehti-Shiu MD, Shiu S-H. Diversity, classification and function of the plant protein kinase superfamily. Philos. Trans. R. Soc. B. 2012;367:2619–2639. doi: 10.1098/rstb.2012.0003. PubMed DOI PMC

Tello-Ruiz MK, et al. Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 2021;49:D1452–D1463. doi: 10.1093/nar/gkaa979. PubMed DOI PMC

Howe KL, et al. Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res. 2020;48:D689–D695. doi: 10.1093/nar/gkz890. PubMed DOI PMC

Chalupska D, et al. Acc homoeoloci and the evolution of wheat genomes. Proc. Natl Acad. Sci. USA. 2008;105:9691–9696. doi: 10.1073/pnas.0803981105. PubMed DOI PMC

Kourelis J, van der Hoorn RAL. Defended to the Nines: 25 Years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell. 2018;30:285–299. doi: 10.1105/tpc.17.00579. PubMed DOI PMC

Van der Biezen EA, Jones JDG. Plant disease-resistance proteins and the gene-for-gene concept. Trends Plant Sci. 1998;23:454–456. PubMed

Jones JDG, Dangl JL. The plant immune system. Nature. 2006;444:323–329. doi: 10.1038/nature05286. PubMed DOI

DeYoung BJ, Innes RW. Plant NBS-LRR proteins in pathogen sensing and host defense. Nat. Immunol. 2006;7:1243–1249. doi: 10.1038/ni1410. PubMed DOI PMC

Cesari S. Multiple strategies for pathogen perception by plant immune receptors. N. Phytol. 2018;219:17–24. doi: 10.1111/nph.14877. PubMed DOI

van Wersch S, Tian L, Hoy R, Li X. Plant NLRs: the whistleblowers of plant immunity. Plant Commun. 2020;1:100016. doi: 10.1016/j.xplc.2019.100016. PubMed DOI PMC

van der Hoorn RA, Kamoun S. From guard to decoy: a new model for perception of plant pathogen effectors. Plant Cell. 2008;20:2009–2017. doi: 10.1105/tpc.108.060194. PubMed DOI PMC

Mackey D, Holt BF, 3rd, Wiig A, Dangl JL. RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis. Cell. 2002;108:743–754. doi: 10.1016/S0092-8674(02)00661-X. PubMed DOI

Kim MG, et al. Two Pseudomonas syringae type III effectors inhibit RIN4-regulated basal defense in Arabidopsis. Cell. 2005;121:749–759. doi: 10.1016/j.cell.2005.03.025. PubMed DOI

Hofius D, et al. Autophagic components contribute to hypersensitive cell death in Arabidopsis. Cell. 2009;137:773–783. doi: 10.1016/j.cell.2009.02.036. PubMed DOI

Wu AJ, Andriotis VM, Durrant MC, Rathjen JP. A patch of surface-exposed residues mediates negative regulation of immune signalling by tomato Pto kinase. Plant Cell. 2004;16:2809–2821. doi: 10.1105/tpc.104.024141. PubMed DOI PMC

Mucyn TS, et al. The tomato NBARC-LRR protein Prf interacts with Pto kinase in vivo to regulate specific plant immunity. Plant Cell. 2006;18:2792–2806. doi: 10.1105/tpc.106.044016. PubMed DOI PMC

Martin GB, et al. Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science. 1993;262:1432–1435. doi: 10.1126/science.7902614. PubMed DOI

Wang G, et al. The decoy substrate of a pathogen effector and a pseudokinase specify pathogen-induced modified-self recognition and immunity in plants. Cell Host Microbe. 2015;18:285–295. doi: 10.1016/j.chom.2015.08.004. PubMed DOI

Lehti-Shiu MD, Zou C, Hanada K, Shiu SH. Evolutionary history and stress regulation of plant receptor-like kinase/Pelle genes. Plant Phys. 2009;150:12–26. doi: 10.1104/pp.108.134353. PubMed DOI PMC

Mascher M, et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544:427–433. doi: 10.1038/nature22043. PubMed DOI

Luo MC, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. 2017;551:498–502. doi: 10.1038/nature24486. PubMed DOI PMC

Maccaferri M, et al. Durum wheat genome highlights past domestication signatures and future improvement targets. Nat. Genet. 2019;51:885–895. doi: 10.1038/s41588-019-0381-3. PubMed DOI

Ouyang, S. et al The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35 (Database issue), D883–D887 (2007). PubMed PMC

Beier S, et al. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci. Data. 2017;4:170044. doi: 10.1038/sdata.2017.44. PubMed DOI PMC

Eilam T, et al. Genome size and genome evolution in diploid Triticeae species. Genome. 2007;50:1029–1037. doi: 10.1139/G07-083. PubMed DOI

International Barley Genome Sequencing Consortium (IBGSC A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711–716. doi: 10.1038/nature11543. PubMed DOI

Ling HQ, et al. Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature. 2018;557:424–428. doi: 10.1038/s41586-018-0108-0. PubMed DOI PMC

Marcussen T, et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 2014;345:1250092. doi: 10.1126/science.1250092. PubMed DOI

Miki Y, et al. Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops. DNA Res. 2019;26:171–182. doi: 10.1093/dnares/dsy047. PubMed DOI PMC

Avni, R. et al. Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement. Plant J.10.1111/tpj.15664 (2022). PubMed PMC

Tsujimoto H. Gametocidal genes in wheat and its relatives. IV. Functional relationships between six gametocidal genes. Genome. 1995;38:283–289. doi: 10.1139/g95-035. PubMed DOI

Friebe B, et al. Characterization of a knock-out mutation at the Gc2 locus in wheat. Chromosoma. 2003;111:509–517. doi: 10.1007/s00412-003-0234-8. PubMed DOI

Grewal S, et al. Comparative mapping and targeted-capture sequencing of the gametocidal loci in Aegilops sharonensis. Plant Genome. 2017;10:2. doi: 10.3835/plantgenome2016.09.0090. PubMed DOI

Sánchez-Martín J, et al. Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol. 2016;17:221. doi: 10.1186/s13059-016-1082-1. PubMed DOI PMC

Dracatos PM, et al. The coiled-coil NLR Rph1, confers leaf rust resistance in barley cultivar Sudan. Plant Physiol. 2019;179:1362–1372. doi: 10.1104/pp.18.01052. PubMed DOI PMC

Thind AK, et al. Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat. Biotechnol. 2017;35:793–796. doi: 10.1038/nbt.3877. PubMed DOI

Xing L, et al. Pm21 from Haynaldia villosa encodes a CC-NBS-LRR protein conferring powdery mildew resistance in wheat. Mol. Plant. 2018;4:874–878. doi: 10.1016/j.molp.2018.02.013. PubMed DOI

Wulff BBH, Dhugga KS. Wheat–the cereal abandoned by GM. Science. 2018;361:451–452. doi: 10.1126/science.aat5119. PubMed DOI

Argentina first to market with drought-resistant GM wheat. Nat. Biotechnol. 39, 652 (2021). PubMed

Crop Solutions Announces Regulatory Approval of Drought Tolerant HB4® Wheat by Brazil’s CTNBio, https://www.businesswire.com/news/home/20211111006003/en/Bioceres-Crop-Solutions-Announces-Regulatory-Approval-of-Drought-Tolerant-HB4%C2%AE-Wheat-by-Brazil%E2%80%99s-CTNBio (2021).

Stakman EC. Barberry eradication prevents black rust in Western Europe. U. S. Dep. Agriculture, Dep. Circular. 1923;269:1–15.

Yu G, Hatta A, Periyannan S, Lagudah E, Wulff BBH. Isolation of wheat genomic DNA for gene mapping and cloning. Methods Mol. Biol. 2017;1659:207–213. doi: 10.1007/978-1-4939-7249-4_18. PubMed DOI

Jupe, F. et al. The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS ONE10.1371/journal.pgen.1007819 (2019). PubMed PMC

Vrána J, et al. Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.) Genetics. 2000;156:2033–2041. doi: 10.1093/genetics/156.4.2033. PubMed DOI PMC

Kubaláková M, et al. Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics. 2005;170:823–829. doi: 10.1534/genetics.104.039180. PubMed DOI PMC

Giorgi D, et al. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS ONE. 2013;8:e57994. doi: 10.1371/journal.pone.0057994. PubMed DOI PMC

Kubaláková M, Macas J, Doležel J. Mapping of repeated DNA sequences in plant chromosomes by PRINS and C-PRINS. Theor. Appl Genet. 1997;94:758–763. doi: 10.1007/s001220050475. DOI

Molnár I, et al. Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat. Plant J. 2016;88:452–467. doi: 10.1111/tpj.13266. PubMed DOI

Zhang Y, Zhu M-L, Dai S-L. Analysis of karyotype diversity of 40 Chinese chrysanthemum cultivars. J Sytematics. Evolution. 2013;51:335–352.

Badaeva ED, Friebe B, Gill BS. Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species. Genome. 1996;39:293–306. doi: 10.1139/g96-040. PubMed DOI

Šimková H, et al. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genomics. 2008;9:294. doi: 10.1186/1471-2164-9-294. PubMed DOI PMC

Bushnell B, Rood J, Singer E. BBMerge—accurate paired shotgun read merging via overlap. PLoS ONE. 2017;12:e0185056. doi: 10.1371/journal.pone.0185056. PubMed DOI PMC

Li H. BFC: correcting Illumina sequencing errors. Bioinformatics. 2015;31:2885–2887. doi: 10.1093/bioinformatics/btv290. PubMed DOI PMC

Chikhi R, Limasset A, Medvedev P. Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinformatics. 2016;32:i201–i208. doi: 10.1093/bioinformatics/btw279. PubMed DOI PMC

Luo R, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:18. doi: 10.1186/2047-217X-1-18. PubMed DOI PMC

Chapman JA, et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 2015;16:26. doi: 10.1186/s13059-015-0582-8. PubMed DOI PMC

Mascher M, et al. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 2013;76:494–505. doi: 10.1111/tpj.12294. PubMed DOI PMC

Muñoz-Amatriaín M, et al. An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers. Plant Genome. 2011;4:238–249. doi: 10.3835/plantgenome2011.08.0023. DOI

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 2019;37:907–915. doi: 10.1038/s41587-019-0201-4. PubMed DOI PMC

Li H, et al. 1000 Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC

Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome. 2012;5:92–102.

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324. PubMed DOI PMC

Sim NL, et al. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012;40:W452–W457. doi: 10.1093/nar/gks539. PubMed DOI PMC

Wypij, D. In Wiley StatsRef: Statistics Reference Online (eds N. Balakrishnan et al). 10.1002/9781118445112.stat04852 (2014).

Hayta S, et al. An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.) Plant Methods. 2019;15:121. doi: 10.1186/s13007-019-0503-z. PubMed DOI PMC

Bartlett JG, et al. High-throughput Agrobacterium-mediated barley transformation. Plant Methods. 2008;4:22. doi: 10.1186/1746-4811-4-22. PubMed DOI PMC

Yu, G. et al. Reference genome-assisted identification of stem rust resistance gene Sr62 encoding a tandem kinase. Zenodo, https://zenodo.org/badge/latestdoi/394326594 (2022). PubMed PMC

A single NLR gene confers resistance to leaf and stripe rust in wheat

DArTseq genotyping facilitates the transfer of "exotic" chromatin from a Secale cereale × S. strictum hybrid into wheat

A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Chromosome genomics facilitates the marker development and selection of wheat-Aegilops biuncialis addition, substitution and translocation lines

Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9

The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

Flow karyotyping of wheat-Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62