Wheat and its close relatives have large and complex genomes, making gene cloning difficult. Nevertheless, developments in genomics over the past decade have made it more feasible. The large and complex genomes of cereals, especially bread wheat, have always been a challenge for gene mapping and cloning. Nevertheless, recent advances in genomics have led to significant progress in this field. Currently, high-quality reference sequences are available for major wheat species and their relatives. New high-throughput genotyping platforms and next-generation sequencing technologies combined with genome complexity reduction techniques and mutagenesis have opened new avenues for gene cloning. In this review, we provide a comprehensive overview of the genes cloned in wheat so far and discuss the strategies used for cloning these genes. We highlight the advantages and drawbacks of individual approaches and show how particular genomic progress contributed to wheat gene cloning. A wide range of new resources and approaches have led to a significant increase in the number of successful cloning projects over the past decade, demonstrating that it is now feasible to perform rapid gene cloning of agronomically important genes, even in a genome as large and complex as that of wheat.

Centre of Plant Structural and Functional Genomics Institute of Experimental Botany of the Czech Academy of Sciences 77900 Olomouc Czech Republic

Department of Botany Faculty of Natural Sciences Comenius University in Bratislava Bratislava 84104 Slovakia

Department of Cell Biology and Genetics Faculty of Science Palacký University 77900 Olomouc Czech Republic

Zobrazit více v PubMed

Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30(2):174–178. 10.1038/nbt.2095 PubMed DOI

Abrouk M, Wang Y, Cavalet-Giorsa E, Troukhan M, Kravchuk M, Krattinger SG (2023) Chromosome-scale assembly of the wild wheat relative PubMed DOI PMC

Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BB, Uauy C (2020) A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. Elife 9:e55646. 10.7554/elife.55646 PubMed DOI PMC

Ahmed HI, Heuberger M, Schoen A, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Lazo GR, Kathiresan N, Sharma PK, Moot I, Yadav IS, Singh L, Saripalli G, Rawat N, Datla R, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Tiwari VK, Abrouk M, Poland J, Krattinger SG (2023) Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 620(7975):830–838. 10.1038/s41586-023-06389-7 PubMed DOI PMC

Akpinar B, Leroy P, Watson-Haigh N, Baumann U, Barbe V, Budak H (2022) The complete genome sequence of elite bread wheat cultivar, “Sonmez.” F1000Research 11:614. 10.12688/f1000research.121637.1 PubMed DOI PMC

Allouis S, Moore G, Bellec A, Sharp R, Faivre Rampant P, Mortimer K, Pateyron S, Foote TN, Griffiths S, Caboche M, Chalhoub B (2003) Construction and characterisation of a hexaploid wheat ( DOI

Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Wulff BB (2019) Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat Biotechnol 37(2):139–143. 10.1038/s41587-018-0007-9 PubMed DOI

Athiyannan N, Abrouk M, Boshoff WH, Cauet S, Rodde N, Kudrna D, Mohammed N, Bettgenhaeuser J, Botha KS, Derman SS, Wing RA, Prins R, Krattinger SG (2022) Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat Genet 54(3):227–231. 10.1038/s41588-022-01022-1 PubMed DOI PMC

Aury J, Engelen S, Istace B, Monat C, Lasserre-Zuber P, Belser C, Cruaud C, Rimbert H, Leroy P, Arribat S, Dufau I, Bellec A, Grimbichler D, Papon N, Paux E, Ranoux M, Alberti A, Wincker P, Choulet F (2022) Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. GigaScience 11:giac034. 10.1093/gigascience/giac034 PubMed DOI PMC

Avni R, Lux T, Minz-Dub A, Millet E, Sela H, Distelfeld A, Deek J, Yu G, Steuernagel B, Pozniak C, Ens J, Gundlach H, Mayer KFX, Himmelbach A, Stein N, Mascher M, Spannagl M, Wulff BBH, Sharon A (2022) Genome sequences of three PubMed DOI PMC

Barillot E, Lacroix B, Cohen D (1995) Theoretical analysis of library screening using a N-dimensional pooling strategy. Nucleic Acids Res 19(22):6241–6247. 10.1093/nar/19.22.6241 PubMed DOI PMC

Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81(5):1084–1097. 10.1086/521987 PubMed DOI PMC

Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J (2003) Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 107(5):931–939. 10.1007/s00122-003-1331-z PubMed DOI

Chen S, Zhang W, Bolus S, Rouse MN, Dubcovsky J (2018) Identification and characterization of wheat stem rust resistance gene PubMed DOI PMC

Chen S, Rouse MN, Zhang W, Zhang X, Guo Y, Briggs J, Dubcovsky J (2020) Wheat gene PubMed DOI

Debernardi J, Tricoli D, Ercoli M, Hayta S, Ronald P, Palatnik J, Dubcovsky J (2020) A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nat Biotechnol 38(11):1274–1279. 10.1038/s41587-020-0703-0 PubMed DOI PMC

Delseny M (2004) Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr Opin Plant Biol 7(2):126–131. 10.1016/j.pbi.2004.01.005 PubMed DOI

Distelfeld A, Uauy C, Olmos S, Schlatter AR, Dubcovsky J, Fahima T (2004) Microcolinearity between a 2-cM region encompassing the grain protein content locus PubMed DOI

Doudna J, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science. 10.1126/science.1258096 PubMed DOI

Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379. 10.1371/journal.pone.0019379 PubMed DOI PMC

Faris J, Fellers J, Brooks S, Gill B (2003) A bacterial artificial chromosome contig spanning the major domestication locus PubMed DOI PMC

Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ (2014) Whole genome profiling of spontaneous and chemically induced mutations in PubMed DOI PMC

Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, Sharma S, Sharma S, Kanzaki H, Matsumura H, Saitoh H, Mitsuoka C, Utsushi H, Uemura A, Kanzaki E, Kosugi S, Yoshida K, Cano L, Kamoun S, Terauchi R (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS ONE 8(7):e68529. 10.1371/journal.pone.0068529 PubMed DOI PMC

Feldman M (1995) Wheats. In: Smartt J, Simmonds NW (eds) Evolution of crop plants. Longman Scientific and Technical, Harlow, pp 185–192

Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B (2003) Map-based isolation of the leaf rust disease resistance gene PubMed DOI PMC

Ford BA, Foo E, Sharwood R, Karafiatova M, Vrána J, MacMillan C, Nichols DS, Steuernagel B, Uauy C, Doležel J, Chandler PM, Spielmeyer W (2018) PubMed DOI PMC

Gale MD, Youssefian S (1985) Dwarfing genes in wheat. In: Russell GE (ed) Progress in plant breeding. Trumpington, Cambridge, pp 1–35

Gaurav K, Arora S, Silva P, Sánchez-Martín J, Horsnell R, Gao L, Brar GS, Widrig V, John Raupp W, Singh N, Wu S, Kale SM, Chinoy C, Nicholson P, Quiroz-Chávez J, Simmonds J, Hayta S, Smedley MA, Harwood W, Pearce S, Gilbert D, Kangara N, Gardener C, Forner-Martínez M, Liu J, Yu G, Boden SA, Pascucci A, Ghosh S, Hafeez AN, O’Hara T, Waites J, Cheema J, Steuernagel B, Patpour M, Justesen AF, Liu S, Rudd JC, Avni R, Sharon A, Steiner B, Kirana RP, Buerstmayr H, Mehrabi AA, Nasyrova FY, Chayut N, Matny O, Steffenson BJ, Sandhu N, Chhuneja P, Lagudah E, Elkot AF, Tyrrell S, Bian X, Davey RP, Simonsen M, Schauser L, Tiwari VK, Randy Kutcher H, Hucl P, Li A, Liu DC, Mao L, Xu S, Brown-Guedira G, Faris J, Dvorak J, Luo MC, Krasileva K, Lux T, Artmeier S, Mayer KFX, Uauy C, Mascher M, Bentley AR, Keller B, Poland J, Wulff BBH (2022) Population genomic analysis of PubMed DOI PMC

Giorgi D, Farina A, Grosso V, Gennaro A, Ceoloni C, Lucretti S (2013) FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS ONE 8(2):e57994. 10.1371/journal.pone.0057994 PubMed DOI PMC

Grewal S, Yang CY, Scholefield D, Ashling S, Ghosh S, Swarbreck D, Collins J, Yao E, Sen TZ, Wilson M, Yant L, King IP, King J (2024) Chromosome-scale genome assembly of bread wheat’s wild relative PubMed DOI PMC

Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M, Reader S, Colas I, Moore G (2006) Molecular characterization of PubMed DOI

Hayta S, Smedley M, Demir S, Blundell R, Hinchliffe A, Atkinson N, Harwood W (2019) An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.). Plant Methods. 10.1186/s13007-019-0503-z PubMed DOI PMC

Heffelfinger C, Fragoso CA, Lorieux M (2017) Constructing linkage maps in the genomics era with MapDisto 2.0. Bioinformatics 33:2224–2225. 10.1093/bioinformatics/btx177 PubMed DOI PMC

Henry IM, Nagalakshmi U, Lieberman MC, Ngo KJ, Krasileva KV, Vasquez-Gross H, Akhunova A, Akhunov E, Dubcovsky J, Tai TH, Comai L (2014) Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell 26(4):1382–1397. 10.1105/tpc.113.121590 PubMed DOI PMC

Hewitt T, Müller MC, Molnár I, Mascher M, Holušová K, Šimková H, Kunz L, Zhang J, Li J, Bhatt D, Sharma R, Schudel S, Yu G, Steuernagel B, Periyannan S, Wulff B, Ayliffe M, McIntosh R, Keller B, Lagudah E, Zhang P (2021a) A highly differentiated region of wheat chromosome 7AL encodes a PubMed DOI PMC

Hewitt T, Zhang J, Huang L, Upadhyaya N, Li J, Park R, Hoxha S, McIntosh R, Lagudah E, Zhang P (2021b) Wheat leaf rust resistance gene PubMed DOI

Hockemeyer D, Wang H, Kiani S, Lai C, Gao Q, Cassady J, Cost G, Zhang L, Santiago Y, Miller J, Zeitler B, Cherone J, Meng X, Hinkley S, Rebar E, Gregory P, Urnov F, Jaenisch R (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29(8):731–734. 10.1038/nbt.1927 PubMed DOI PMC

Huai B, Yuan P, Ma X, Zhang X, Jiang L, Zheng P, Yao M, Chen Z, Chen L, Shen Q, Kang Z, Liu J (2022) Sugar transporter PubMed DOI

Hurni S, Brunner S, Buchmann G, Herren G, Jordan T, Krukowski P, Wicker T, Yahiaoui N, Mago R, Keller B (2013) Rye PubMed DOI

International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome-based draft sequence of the hexaploid bread wheat ( PubMed DOI

Janáková E, Jakobson I, Peusha H, Abrouk M, Škopová M, Šimková H, Šafář J, Vrána J, Doležel J, Järve K, Valárik M (2019) Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene. Theor Appl Genet 132(4):1061–1072. 10.1007/s00122-018-3259-3 PubMed DOI PMC

Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z (2016) A sorghum mutant resource as an efficient platform for gene discovery in grasses. Plant Cell 28(7):1551–1562. 10.1105/tpc.16.00373 PubMed DOI PMC

Jiao C, Xie X, Hao C, Chen L, Xie Y, Garg V, Zhao L, Wang Z, Zhang Y, Li T, Fu J, Chitikineni A, Hou J, Liu H, Dwivedi G, Liu X, Jia J, Mao L, Wang X, Appels R, Varshney R, Guo W, Zhang X (2025) Pan-genome bridges wheat structural variations with habitat and breeding. Nature 637(8045):384–393. 10.1038/s41586-024-08277-0 PubMed DOI

Jupe F, Witek K, Verweij W, Śliwka J, Pritchard L, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Cardle L, Hein I, Jones JDG (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the PubMed DOI PMC

Kale S, Schulthess A, Padmarasu S, Boeven P, Schacht J, Himmelbach A, Steuernagel B, Wulff B, Reif J, Stein N, Mascher M (2022) A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat. Plant Biotechnol J 20(9):1730–1742. 10.1111/pbi.13843 PubMed DOI PMC

Keller B, Feuillet C, Yahiaoui N (2005) Map-based isolation of disease resistance genes from bread wheat: cloning in a supersize genome. Genet Res 85(2):93–100. 10.1017/S0016672305007391 PubMed DOI

Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89. 10.1007/978-1-61779-870-2_5 PubMed DOI

Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T (2018) Cloning of the wheat PubMed DOI PMC

Kolodziej MC, Singla J, Sánchez-Martín J, Zbinden H, Šimková H, Karafiátová M, Doležel J, Gronnier J, Poretti M, Glauser G, Zhu W, Köster P, Zipfel C, Wicker T, Krattinger S, Keller B (2021) A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat. Nat Commun 12(1):956. 10.1038/s41467-020-20777-x PubMed DOI PMC

Korchanová Z, Švec M, Janáková E, Lampar A, Majka M, Holušová K, Bonchev G, Juračka J, Cápal P, Valárik M (2022) Identification, high-density mapping, and characterization of new major powdery mildew resistance loci from the emmer wheat landrace GZ1. Front Plant Sci 13:897697. 10.3389/fpls.2022.897697 PubMed DOI PMC

Kourelis J, van der Hoorn RAL (2018) Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell 30(2):285–299. 10.1105/tpc.17.00579 PubMed DOI PMC

Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J (2017) Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci U S A 114(6):E913–E921. 10.1073/pnas.1619268114 PubMed DOI PMC

Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363. 10.1126/science.1166453 PubMed DOI

Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg LA (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1(2):174–181. 10.1016/0888-7543(87)90010-3 PubMed DOI

Lee WS, Rudd JJ, Kanyuka K (2015) Virus induced gene silencing (VIGS) for functional analysis of wheat genes involved in PubMed DOI PMC

Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M, Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H, Feuillet C (2012) TriAnnot: A versatile and high performance pipeline for the automated annotation of plant genomes. Front Plant Sci 3:5. 10.3389/fpls.2012.00005 PubMed DOI PMC

Li M, Dong L, Li B, Wang Z, Xie J, Qiu D, Li Y, Shi W, Yang L, Wu Q, Chen Y, Lu P, Guo G, Zhang H, Zhang P, Zhu K, Li Y, Zhang Y, Wang R, Yuan C, Liu W, Yu D, Luo MC, Fahima T, Nevo E, Li H, Liu Z (2020) A CNL protein in wild emmer wheat confers powdery mildew resistance. New Phytol 228(3):1027–1037. 10.1111/nph.16761 PubMed DOI

Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S (2023a) Cloning of the wheat leaf rust resistance gene PubMed DOI PMC

Li Y, Wei ZZ, Sela H, Govta L, Klymiuk V, Roychowdhury R, Chawla HS, Ens J, Wiebe K, Bocharova V, Ben-David R, Pawar PB, Zhang Y, Jaiwar S, Molnár I, Doležel J, Coaker G, Pozniak CJ, Fahima T (2023b) Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of PubMed DOI PMC

Lijavetzky D, Muzzi G, Wicker T, Keller B, Wing R, Dubcovsky J (1999) Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42(6):1176–1182. 10.1139/g99-076 PubMed DOI

Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C (2018) Genome sequence of the progenitor of wheat A subgenome PubMed DOI PMC

Liu S, Sehgal SK, Li J, Lin M, Trick HN, Yu J, Gill BS, Bai G (2013) Cloning and characterization of a critical regulator for preharvest sprouting in wheat. Genetics 195:263–273. 10.1534/genetics.113.152330 PubMed DOI PMC

Lowe K, Wu E, Wang N, Hoerster G, Hastings C, Cho M, Scelonge C, Lenderts B, Chamberlin M, Cushatt J, Wang L, Ryan L, Khan T, Chow-Yiu J, Hua W, Yu M, Banh J, Bao Z, Brink K, Igo E, Rudrappa B, Shamseer P, Bruce W, Newman L, Shen B, Zheng P, Bidney D, Falco C, Register J, Zhao Z, Xu D, Jones T, Gordon-Kamm W (2016) Morphogenic Regulators PubMed DOI PMC

Maccaferri M, Harris NS, Twardziok SO, Pasam RK, Gundlach H, Spannagl M, Ormanbekova D, Lux T, Prade VM, Milner SG, Himmelbach A, Mascher M, Bagnaresi P, Faccioli P, Cozzi P, Lauria M, Lazzari B, Stella A, Manconi A, Gnocchi M, Moscatelli M, Avni R, Deek J, Biyiklioglu S, Frascaroli E, Corneti S, Salvi S, Sonnante G, Desiderio F, Marè C, Crosatti C, Mica E, Özkan H, Kilian B, De Vita P, Marone D, Joukhadar R, Mazzucotelli E, Nigro D, Gadaleta A, Chao S, Faris JD, Melo ATO, Pumphrey M, Pecchioni N, Milanesi L, Wiebe K, Ens J, MacLachlan RP, Clarke JM, Sharpe AG, Koh CS, LiangKYH, Taylor GJ, Knox R, Budak H, Mastrangelo AM, Xu SS, Stein N, Hale I, Distelfeld A, Hayden MJ, Tuberosa R, Walkowiak S, Mayer KFX, Ceriotti A, Pozniak CJ, Cattivelli L. (2019) Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet 51(5):885–895. 10.1038/s41588-019-0381-3 PubMed

Mago R, Zhang P, Vautrin S, Šimková H, Bansal U, Luo MC, Rouse M, Karaoglu H, Periyannan S, Kolmer J, Jin Y, Ayliffe MA, Bariana H, Park RF, McIntosh R, Doležel J, Bergès H, Spielmeyer W, Lagudah ES, Ellis JG, Dodds PN (2015) The wheat PubMed DOI

Marchal C, Zhang J, Zhang P, Fenwick P, Steuernagel B, Adamski NM, Boyd L, McIntosh R, Wulff BB, Berry S, Lagudah E, Uauy C (2018) BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust. Nat Plants 4:662–668. 10.1038/s41477-018-0236-4 PubMed DOI

Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17(2):240–248. 10.1101/gr.5681207 PubMed DOI PMC

Moullet O, Zhang HB, Lagudah ES (1999) Construction and characterisation of a large DNA insert library from the D genome of wheat. Theor Appl Genet 99(1):305–313. 10.1007/s001220051237 DOI

Ni F, Qi J, Hao Q, Lyu B, Luo MC, Wang Y, Chen F, Wang S, Zhang C, Epstein L, Zhao X, Wang H, Zhang X, Chen C, Sun L, Fu D (2017) Wheat PubMed DOI PMC

Ni F, Zheng Y, Liu X, Yu Y, Zhang G, Epstein L, Mao X, Wu J, Yuan C, Lv B, Yu H, Li J, Zhao Q, Yang Q, Liu J, Qi J, Fu D, Wu J (2023) Sequencing trait-associated mutations to clone wheat rust-resistance gene PubMed DOI PMC

Nilmalgoda SD, Cloutier S, Walichnowski AZ (2003) Construction and characterization of a bacterial artificial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers. Genome 46(5):870–878. 10.1139/g03-067 PubMed DOI

Olson EL, Rouse MN, Pumphrey MO, Bowden RL, Gill BS, Poland JA (2013) Introgression of stem rust resistance genes PubMed DOI

Pan X, Nie X, Gao W, Yan S, Feng H, Cao J, Lu J, Shao H, Ma C, Chang C, Zhang H (2024) Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings. Theor Appl Genet 137(3):57. 10.1007/s00122-024-04564-6 PubMed DOI

Paux E, Legeai F, Guilhot N, Adam-Blondon AF, Alaux M, Salse J, Sourdille P, Leroy P, Feuillet C (2008) Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics 8(1):29–32. 10.1007/s10142-007-0068-1 PubMed DOI

Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H, Mago R, Mcintosh R, Dodds P, Dvorak J, Lagudah E (2013) The gene PubMed DOI

Raman V, Rojas C, Vasudevan B, Dunning K, Kolape J, Oh S, Yun J, Yang L, Li G, Pant B, Jiang Q, Mysore K (2022) Agrobacterium expressing a type III secretion system delivers PubMed DOI PMC

Rawat N, Pumphrey MO, Liu S, Zhang X, Tiwari VK, Ando K, Trick HN, Bockus WW, Akhunov E, Anderson JA, Gill BS (2016) Wheat PubMed DOI

Ronin YI, Mester DI, Minkov DG, Akhunov E, Korol AB (2017) Building ultra-high-density linkage maps based on efficient filtering of trustable markers. Genetics 206(3):1285–1295. 10.1534/genetics.116.197491 PubMed DOI PMC

Saintenac C, Zhang W, Salcedo A, Rouse MN, Trick HN, Akhunov E, Dubcovsky J (2013) Identification of wheat gene PubMed DOI PMC

Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH (2016) Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 17:1–7. 10.1186/s13059-016-1082-1 PubMed DOI PMC

Sánchez-Martín J, Widrig V, Herren G, Wicker T, Zbinden H, Gronnier J, Spörri L, Praz CR, Heuberger M, Kolodziej MC, Isaksson J, Steuernagel B, Karafiátová M, Doležel J, Zipfel C, Keller B (2021) Wheat PubMed DOI PMC

Sato K, Abe F, Mascher M, Haberer G, Gundlach H, Spannagl M, Shirasawa K, Isobe S (2021) Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder.’ DNA Res 28(3):dasb008. 10.1093/dnares/dsab008 PubMed DOI PMC

Schweizer P, Pokorny J, Abderhalden O, Dudler R (1999) A transient assay system for the functional assessment of defense-related genes in wheat. Mol Plant-Microbe Inter 12(8):647–654. 10.1094/MPMI.1999.12.8.647 DOI

Sharma D, Avni R, Gutierrez-Gonzalez J, Kumar R, Sela H, Prusty MR, Shatil-Cohen A, Molnár I, Holušová K, Said M, Doležel J, Millet E, Khazan-Kost S, Landau U, Bethke G, Sharon O, Ezrati S, Ronen M, Maatuk O, Eilam T, Manisterski J, Ben-Yehuda P, Anikster Y, Matny O, Steffenson BJ, Mascher M, Brabham HJ, Moscou MJ, Liang Y, Yu G, Wulff BBH, Muehlbauer G, Minz-Dub A, Sharon A (2024) A single NLR gene confers resistance to leaf and stripe rust in wheat. Nat Commun 15(1):9925. 10.1038/s41467-024-54068-6 PubMed DOI PMC

Shiferaw B, Smale M, Braun HJ, Duveiller E, Reynolds M, Muricho G (2013) Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security. Food Security 5:291–317. 10.1007/s12571-013-0263-y DOI

Shirasawa K, Hirakawa H, Nunome T, Tabata S, Isobe S (2016) Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato. Plant Biotechnol J 14(1):51–60. 10.1111/pbi.12348 PubMed DOI PMC

Šimková H, Safář J, Kubaláková M, Suchánková P, Čihalíková J, Robert-Quatre H, Azhaguvel P, Weng Y, Peng J, Lapitan NL, Ma Y, You FM, Luo MC, Bartoš J, Doležel J (2011) BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes. J Biomed Biotechnol 46(5):870–878. 10.1155/2011/302543 PubMed DOI PMC

Singh SP, Hurni S, Ruinelli M, Brunner S, Sanchez-Martin J, Krukowski P, Peditto D, Buchmann G, Zbinden H, Keller B (2018) Evolutionary divergence of the rye PubMed DOI

Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23(1):75–81. 10.1038/nbt1043 PubMed DOI

Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 1:1–12. 10.1186/gb-2006-7-s1-s10 PubMed DOI PMC

Srichumpa P, Brunner S, Keller B, Yahiaoui N (2005) Allelic series of four powdery mildew resistance genes at the PubMed DOI PMC

Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: join Map. Plant J 3(5):739–744. 10.1111/j.1365-313X.1993.00739.x DOI

Steuernagel B, Periyannan SK, Hernández-Pinzón I, Witek K, Rouse MN, Yu G, Hatta A, Ayliffe M, Bariana H, Jones JD, Lagudah ES, Wulff BBH (2016) Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat Biotechnol 34:652–655. 10.1038/nbt.3543 PubMed DOI

Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314(5803):1298–12301. 10.1126/science.1133649 PubMed DOI PMC

Uauy C, Paraiso F, Colasuonno P, Tran RK, Tsai H, Berardi S, Comai L, Dubcovsky J (2009) A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol 9:115. 10.1186/1471-2229-9-115 PubMed DOI PMC

Upadhyaya NM, Mago R, Panwar V, Hewitt T, Luo M, Chen J, Sperschneider J, Nguyen-Phuc H, Wang A, Ortiz D, Hac L, Bhatt D, Li F, Zhang J, Ayliffe M, Figueroa M, Kanyuka K, Ellis JG, Dodds PN (2021) Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair. Nat Plants 7(9):1220–1228. 10.1038/s41477-021-00971-5 PubMed DOI

Valárik M, Linkiewicz AM, Dubcovsky J (2006) A microcolinearity study at the earliness PubMed DOI

Vrána J, Kubaláková M, Simková H, Číhalíkovái J, Lysák MA, Dolezel J (2000) Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156(4):2033–2041. 10.1093/genetics/156.4.2033 PubMed DOI PMC

Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo DH, Ens J, Wiebe K, N’Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnère G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, Pozniak CJ (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature 588(7837):277–283. 10.1038/s41586-020-2961-x PubMed DOI PMC

Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu J (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32(9):947–951. 10.1038/nbt.2969 PubMed DOI

Wang H, Zou S, Li Y, Lin F, Tang D (2020) An ankyrin-repeat and WRKY-domain-containing immune receptor confers stripe rust resistance in wheat. Nat Commun 11(1):1353. 10.1038/s41467-020-15139-6 PubMed DOI PMC

Wang L, Zhu T, Rodriguez JC, Deal KR, Dubcovsky J, McGuire PE, Lux T, Spannagl M, Mayer KFX, Baldrich P, Meyers BC, Huo N, Gu YQ, Zhou H, Devos KM, Bennetzen JL, Unver T, Budak H, Gulick PJ, Galiba G, Kalapos B, Nelson DR, Li P, You FM, Luo MC, Dvorak J (2021) Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 (Bethesda) 11(12):325. 10.1093/g3journal/jkab325 PubMed DOI PMC

Wang Y, Abrouk M, Gourdoupis S, Koo DH, Karafiátová M, Molnár I, Holušová K, Doležel J, Athiyannan N, Cavalet-Giorsa E, Jaremko Ł, Poland J, Krattinger SG (2023) An unusual tandem kinase fusion protein confers leaf rust resistance in wheat. Nat Genet 55(6):914–920. 10.1038/s41588-023-01401-2 PubMed DOI PMC

Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene PubMed DOI

Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene PubMed DOI PMC

Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat PubMed DOI PMC

Yu G, Zhang Q, Friesen TL, Rouse MN, Jin Y, Zhong S, Rasmussen JB, Lagudah ES, Xu SS. (2015) Identification and mapping of Sr46 from Aegilops tauschii accession CIae 25 conferring resistance to race TTKSK (Ug99) of wheat stem rust pathogen. Theor Appl Genet 128(3):431–43. 10.1007/s00122-014-2442-4 PubMed

Yu G, Matny O, Champouret N, Steuernagel B, Moscou MJ, Hernández-Pinzón I, Green P, Hayta S, Smedley M, Harwood W, Kangara N, Yue Y, Gardener C, Banfield MJ, Olivera PD, Welchin C, Simmons J, Millet E, Minz-Dub A, Ronen M, Avni R, Sharon A, Patpour M, Justesen AF, Jayakodi M, Himmelbach A, Stein N, Wu S, Poland J, Ens J, Pozniak C, Karafiátová M, Molnár I, Doležel J, Ward ER, Reuber TL, Jones JDG, Mascher M, Steffenson BJ, Wulff BBH (2022) PubMed DOI PMC

Yu G, Matny O, Gourdoupis S, Rayapuram N, Aljedaani FR, Wang YL, Nürnberger T, Johnson R, Crean EE, Saur IM, Gardener C, Yue Y, Kangara N, Steuernagel B, Hayta S, Smedley M, Harwood W, Patpour M, Wu S, Poland J, Jones JDG, Reuber TL, Ronen M, Sharon A, Rouse MN, Xu S, Holušová K, Bartoš J, Molnár I, Karafiátová M, Hirt H, Blilou I, Jaremko Ł, Doležel J, Steffenson BJ, Wulff BBH (2023) The wheat stem rust resistance gene PubMed DOI PMC

Zhang J, Hewitt TC, Boshoff WH, Dundas I, Upadhyaya N, Li J, Patpour M, Chandramohan S, Pretorius ZA, Hovmøller M, Schnippenkoetter W, Park RF, Mago R, Periyannan S, Bhatt D, Hoxha S, Chakraborty S, Luo M, Dodds P, Steuernagel B, Wulff BBH, Ayliffe M, McIntosh RA, Zhang P, Lagudah ES (2021) A recombined PubMed DOI PMC

Zhang J, Nirmala J, Chen S, Jost M, Steuernagel B, Karafiatova M, Hewitt T, Li H, Edae E, Sharma K, Hoxha S, Bhatt D, Antoniou-Kourounioti R, Dodds P, Wulff BBH, Dolezel J, Ayliffe M, Hiebert C, McIntosh R, Dubcovsky J, Zhang P, Rouse MN, Lagudah E (2023) Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus PubMed DOI PMC

Zhou Y, Bai S, Li H, Sun G, Zhang D, Ma F, Zhao X, Nie F, Li J, Chen L, Lv L, Zhu L, Fan R, Ge Y, Shaheen A, Guo G, Zhang Z, Ma J, Liang H, Qiu X, Hu J, Sun T, Hou J, Xu H, Xue S, Jiang W, Huang J, Li S, Zou C, Song C (2021) Introgressing the PubMed DOI

Zhu T, Wang L, Rodriguez JC, Deal KR, Avni R, Distelfeld A, McGuire PE, Dvorak J, Luo MC (2019) Improved genome sequence of wild emmer wheat zavitan with the aid of optical maps. G3 (Bethesda) 9(3):619–624. 10.1534/g3.118.200902 PubMed DOI PMC

Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble-Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Mascher M, Dvorak J, Luo MC (2021) Optical maps refine the bread wheat PubMed DOI PMC

Zou S, Wang H, Li Y, Kong Z, Tang D (2018) The NB-LRR gene PubMed DOI