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High-density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat

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The durable stripe rust resistance gene Yr30 was fine-mapped to a 610-kb region in which five candidate genes were identified by expression analysis and sequence polymorphisms.


The emergence of genetically diverse and more aggressive races of Puccinia striiformis f. sp. tritici (Pst) in the past twenty years has resulted in global stripe rust outbreaks and the rapid breakdown of resistance genes. Yr30 is an adult plant resistance (APR) gene with broad-spectrum effectiveness and its durability. Here, we fine-mapped the YR30 locus to a 0.52-cM interval using 1629 individuals derived from residual heterozygous F5:6 plants in a Yaco"S"/Mingxian169 recombinant inbred line population. This interval corresponded to a 610-kb region in the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 2.1 on chromosome arm 3BS harboring 30 high-confidence genes. Five genes were identified as candidate genes based on functional annotation, expression analysis by RNA-seq and sequence polymorphisms between cultivars with and without Yr30 based on resequencing. Haplotype analysis of the target region identified six haplotypes (YR30_h1–YR30_h6) in a panel of 1215 wheat accessions based on the 660K feature genotyping array. Lines with YR30_h6 displayed more resistance to stripe rust than the other five haplotypes. Near-isogenic lines (NILs) with Yr30 showed a 32.94% higher grain yield than susceptible counterparts when grown in a stripe rust nursery, whereas there was no difference in grain yield under rust-free conditions. These results lay a foundation for map-based cloning Yr30.

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Data availability

All data, models, or codes generated or used during the study are available from the corresponding authors by request.



Adult plant resistance


All-stage resistance


International maize and wheat improvement center


Chromosome segment substitution lines


Disease severity


Infection type


Kompetitive allele-specific PCR


Marker-assisted selection


Near-isogenic line


Recombinant inbred line


  • Bouvet L, Holdgate S, James L, Thomas J, Mackay IJ, Cockram J (2022) The evolving battle between yellow rust and wheat: implications for global food security. Theor Appl Genet 135:741–753

    Article  PubMed  Google Scholar 

  • Buschges R, Hollricher K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, Diergaarde P, Groenendijk J, Topsch S, Vos P, Salamini F, Schulze-Lefert P (1997) The barley Mlo gene: a novel control element of plant pathogen resistance. Cell 88:695–705

    Article  CAS  PubMed  Google Scholar 

  • Chen XM (2005) Epidemiology and control of stripe rust Puccinia striiformis f. sp. tritici on wheat. Can J Plant Pathol 27:314–337

    Article  Google Scholar 

  • Chen W, Wellings C, Chen X, Kang Z, Liu T (2014) Wheat stripe (yellow) rust caused by Puccinia striiformis f. sp. tritici. Mol Plant Pathol 15:433–446

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen YM, Song WJ, Xie XM, Wang ZH, Guan PF, Peng HR, Jiao YN, Ni ZF, Sun QX, Guo WL (2020) A collinearity-incorporating homology inference strategy for connecting emerging assemblies in the Triticeae tribe as a pilot practice in the plant pangenomic era. Mol Plant 13:1694–1708

    Article  CAS  PubMed  Google Scholar 

  • Consonni C, Humphry ME, Hartmann HA, Livaja M, Durner J, Westphal L, Vogel J, Lipka V, Kemmerling B, Schulze-Lefert P, Somerville SC, Panstruga R (2006) Conserved requirement for a plant host cell protein in powdery mildew pathogenesis. Nat Genet 38:716–720

    Article  CAS  PubMed  Google Scholar 

  • Deng Y, Zhai K, Xie Z, Yang D, Zhu X, Liu J, Wang X, Qin P, Yang Y, Zhang G, Li Q, Zhang J, Wu S, Milazzo J, Mao B, Wang E, Xie H, Tharreau D, He Z (2017) Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science 355:962–965

    Article  CAS  PubMed  Google Scholar 

  • Dong Y, Xu D, Xu X, Ren Y, Gao F, Song J, Jia A, Hao Y, He Z, Xia X (2022) Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.). Theor Appl Genet 135:1083–1099

    Article  CAS  PubMed  Google Scholar 

  • Fu D, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen X, Sela H, Fahima T, Dubcovsky J (2009) A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323:1357–1360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hare RA, McIntosh RA (1979) Genetic and cytogenetic studies of durable adult plant resistance in hope and related cultivars to wheat rust. 83:350–367

  • Huang S, Wu J, Wang X, Mu J, Xu Z, Zeng Q, Liu S, Wang Q, Kang Z, Han D (2019) Utilization of the genome-wide wheat 55K SNP array for genetic analysis of stripe rust resistance in common wheat line P9936. Phytopathology 109:819–882

    Article  CAS  PubMed  Google Scholar 

  • Huang S, Zhang Y, Ren H, Zhang X, Yu R, Liu S, Zeng Q, Wang Q, Yuan F, Singh RP, Bhavani S, Wu J, Han D, Kang Z (2023) High density mapping of wheat stripe rust resistance gene QYrXN3517-1BL using QTL mapping, BSE-Seq and candidate gene analysis. Theor Appl Genet 136:39

    Article  CAS  PubMed  Google Scholar 

  • Huerta-Espino J, Singh RP, Herrera-Foessel SA, Perez-Lopez JB, Figueroa-Lopez P (2009) First detection of virulence in Puccinia triticina to resistance genes Lr27 + Lr31 present in durum wheat in Mexico. Plant Dis 93(1):110

    Article  CAS  PubMed  Google Scholar 

  • Jia M, Yang L, Zhang W, Rosewarne G, Li J, Yang E, Chen L, Wang W, Liu Y, Tong H, He W, Zhang Y, Zhu Z, Gao C (2020) Genome-wide association analysis of stripe rust resistance in modern Chinese wheat. BMC Plant Biol 20:491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Joukhadar R, Hollaway G, Shi F, Kant S, Forrest K, Wong D, Petkowski J, Pasam R, Tibbits J, Bariana H, Bansal U, Spangenberg G, Daetwyler H, Gendall T, Hayden M (2020) Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions. Theor Appl Genet 133:2695–2712

    Article  CAS  PubMed  Google Scholar 

  • Kosambi DD (1943) The estimation of map distance from recombination values. Ann Hum Genet 12:172–175

    Google Scholar 

  • Kota R, Spielmeyer W, McIntosh RA, Lagudah ES (2006) Fine genetic mapping fails to dissociate durable stem rust resistance gene Sr2 from pseudo-black chaff in common wheat (Triticum aestivum L.). Theor Appl Genet 112:492–499

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Lagudah ES (2011) Molecular genetics of race non-specific rust resistance in wheat. Euphytica 179:81–91

    Article  Google Scholar 

  • Letunic I, Bork P (2019) Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:256–259

    Article  Google Scholar 

  • Li H, Wang Q, Xu L, Mu J, Wu J, Zeng Q, Yu S, Huang L, Han D, Kang Z (2017) Rapid identification of a major effect QTL conferring adult plant resistance to stripe rust in wheat cultivar Yaco"S". Euphytica 213:124

    Article  Google Scholar 

  • Li YJ, Xu H, Yu SN, Tang JW, Li QY, Gao Y, Zheng JZ, Dong CH, Yuan YH, Zheng TC, Yin GH (2023) Genetic analysis of elite stripe rust resistance genes of founder parent Zhou8425B in its derived varieties. Acta Agron Sin 50:16–31

    Google Scholar 

  • Line RF, Qayoum A (1992) Virulence, aggressiveness, evolution and distribution of races of Puccinia striiformis (the cause of stripe of wheat) in North America, 1968–1987. US Department of Agriculture, Washington, DC, p 74

    Google Scholar 

  • Liu S, Wang X, Zhang Y, Jin Y, Xia Z, Xiang M, Huang S, Qiao L, Zheng W, Zeng Q, Wang Q, Yu R, Singh RP, Bhavani S, Kang Z, Han D, Wang C, Wu J (2022) Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL. Theor Appl Genet 135:351–365

    Article  PubMed  Google Scholar 

  • Liu S (2022) Genetics dissection of stripe rust resistance in four wheat cultivars (lines) and map-based cloning of QYrnap.nwafu-2BS (YrNP63). PhD dissertation (In Chinese). College of Agronomy Northwest A&F University: P147.

  • Lu P, Liang Y, Li D, Wang Z, Li W, Wang G, Wang Y, Zhou S, Wu Q, Xie J, Zhang D, Chen Y, Li M, Zhang Y, Sun Q, Han C, Liu Z (2016) Fine genetic mapping of spot blotch resistance gene Sb3 in wheat (Triticum aestivum). Theor Appl Genet 129:577–589

    Article  CAS  PubMed  Google Scholar 

  • Ma S, Wang M, Wu J, Guo W, Chen Y, Li G, Wang Y, Shi W, Xia G, Fu D, Kang Z, Ni F (2021) WheatOmics: a platform combining multiple omics data to accelerate functional genomics studies in wheat. Mol Plant 14:1965–1968

    Article  CAS  PubMed  Google Scholar 

  • Mago R, Tabe L, McIntosh RA, Pretorius Z, Kota R, Paux E, Wicker T, Breen J, Lagudah ES, Ellis JG, Spielmeyer W (2011) A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew. Theor Appl Genet 123:615–623

    Article  CAS  PubMed  Google Scholar 

  • Mago R, Tabe L, Vautrin S, Simkova H, Kubalakova M, Upadhyaya N, Berges H, Kong X, Breen J, Dolezel J, Appels R, Ellis JG, Spielmeyer W (2014) Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biol 14:379

    Article  PubMed  PubMed Central  Google Scholar 

  • Mapuranga J, Zhang N, Zhang L, Liu W, Chang J, Yang W (2022) Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. Front Plant Sci 13:951095

    Article  PubMed  PubMed Central  Google Scholar 

  • McDonald BA, Linde C (2002) The population genetics of plant pathogens and breeding strategies fo durable resistance. Euphytica 124:163–180

    Article  CAS  Google Scholar 

  • Mei F, Chen B, Du L, Li S, Zhu D, Chen N, Zhang Y, Li F, Wang Z, Cheng X, Ding L, Kang Z, Mao H (2022) A gain-of-function allele of a DREB transcription factor gene ameliorates drought tolerance in wheat. Plant Cell 34:4472–4494

    Article  PubMed  PubMed Central  Google Scholar 

  • Moore JW, Herrera-Foessel S, Lan C, Schnippenkoetter W, Ayliffe M, Huerta-Espino J, Lillemo M, Viccars L, Milne R, Periyannan S, Kong X, Spielmeyer W, Talbot M, Bariana H, Patrick JW, Dodds P, Singh R, Lagudah E (2015) A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat Genet 47:1494–1498

    Article  CAS  PubMed  Google Scholar 

  • Mu J, Huang S, Liu S, Zeng Q, Dai M, Wang Q, Wu J, Yu S, Kang Z, Han D (2019) Genetic architecture of wheat stripe rust resistance revealed by combining QTL mapping using SNP-based genetic maps and bulked segregant analysis. Theor Appl Genet 132:443–455

    Article  CAS  PubMed  Google Scholar 

  • Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peterson RF, Campbell AB, Hannah AE (1948) A diagrammatic scale for estimating rust intensity on leaves and stems of cereals. Can J Res 26:496–500

    Article  Google Scholar 

  • Shiferaw B, Smale M, Braun H, 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 Secur 5:291–317

    Article  Google Scholar 

  • Singh RP, McIntosh RA (1984a) Complementary genes for reaction to Puccinia recondita tritici in Triticum aestivum I. Genetic and linkage studies. Can J Genet Cytol 26:723–735

    Article  Google Scholar 

  • Singh RP, McIntosh RA (1984b) Complementary genes for reaction to Puccinia recondite tritici in Triticum aestivum II. Cytogenet Stud Can J Genet Cytol 26:736–742

    Article  Google Scholar 

  • Singh RP, Nelson JC, Sorrells ME (2000) Mapping Yr28 and other genes for resistance to stripe rust in wheat. Crop Sci 40:1148–1155

    Article  CAS  Google Scholar 

  • Singh RP, Huerta-Espino J, Bhavani S, Herrerra-Foessel S, Singh D, Singh P et al (2011) Race non-specific resistance to rust diseases in CIMMYT spring wheats. Euphytica 179:175–186

    Article  Google Scholar 

  • Singh R, Herrera-Foessel S, Huerta-Espino J, Singh S, Bhavani S, Lan C et al (2014) Progress towards genetics and breeding for minor genes based resistance to Ug99 and other rusts in CIMMYT high-yielding spring wheat. J Integr Agric 13:255–261

    Article  CAS  Google Scholar 

  • Song W, Ko L, Henry RJ (1994) Polymorphisms in the α-amy1 gene of wild and cultivated barley revealed by the polymerase chain reaction. Theor Appl Genet 89:509–513

    Article  Google Scholar 

  • Spielmeyer W, Singh RP, McFadden H, Wellings CR, Huerta-Espino J, Kong X, Appels R, Lagudah ES (2008) Fine scale genetic and physical mapping using interstitial deletion mutants of Lr34/Yr18: a disease resistance locus effective against multiple pathogens in wheat. Theor Appl Genet 116:481–490

    Article  CAS  PubMed  Google Scholar 

  • Suenaga K, Singh RP, Huerta-Espino J, William HM (2003) Microsatellite markers for genes Lr34/Yr18 and other quantitative trait loci for leaf rust and stripe rust resistance in bread wheat. Phytopathology 93:881–890

    Article  CAS  PubMed  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 77=78

  • William M, Singh RP, Huerta-Espino J, Islas SO, Hoisington D (2003) Molecular marker mapping of leaf rust resistance gene Lr46 and its association with stripe rust resistance gene Yr29 in wheat. Phytopathology 93:153–159

    Article  CAS  PubMed  Google Scholar 

  • William HM, Singh RP, Huerta-Espino J, Palacios G, Suenaga K (2006) Characterization of genetic loci conferring adult plant resistance to leaf rust and stripe rust in spring wheat. Genome 49:977–990

    Article  CAS  PubMed  Google Scholar 

  • Wu J, Wang Q, Chen X, Wang M, Mu J, Lv X, Huang L, Han D, Kang Z (2016) Stripe rust resistance in wheat breeding lines developed for central Shaanxi, an overwintering region for Puccinia striiformis f. sp. tritici in China. Can J Plant Pathol 38:317–324

    Article  CAS  Google Scholar 

  • Xiao YG, Yin GH, Li HH, Xia XC, Yan J, Zheng TC, Ji WQ, Wu ZH (2011) Genetic diversity and genome-wide association analysis of stripe rust resistance among the core wheat parent Zhou 8425B and its derivatives. Acta Agron Sin 44:3919–3929 ((in Chinese with English abstract))

    Google Scholar 

  • Yang EN, Rosewarne GM, Herrera-Foessel SA, Huerta-Espino J, Tang ZX, Sun CF, Ren ZL, Singh RP (2013) QTL analysis of the spring wheat “Chapio” identifies stable stripe rust resistance despite inter-continental genotype×environment interactions. Theor Appl Genet 126:1721–1732

    Article  CAS  PubMed  Google Scholar 

  • Yao F, Guan F, Duan L, Long L, Tang H, Jiang Y, Li H, Jiang Q, Wang J, Qi P, Kang H, Li W, Ma J, Pu Z, Deng M, Wei Y, Zheng Y, Chen X, Chen G (2021) Genome-wide association analysis of stable stripe rust resistance loci in a Chinese wheat landrace panel using the 660K SNP array. Front Plant Sci 12:783830

    Article  PubMed  PubMed Central  Google Scholar 

  • Yuan FP, Zeng QD, Wu JH, Wang QL, Yang ZJ, Liang BP, Kang ZS, Chen XH, Han DJ (2018) QTL mapping and validation of adult plant resistance to stripe rust in Chinese wheat landrace Humai 15. Front Plant Sci 9:968

    Article  PubMed  PubMed Central  Google Scholar 

  • Zeng Q, Wu J, Huang S, Yuan F, Liu S, Wang Q, Mu J, Yu S, Chen L, Han D, Kang Z (2019) SNP-based linkage mapping for validation of adult plant stripe rust resistance QTL in common wheat cultivar Chakwal 86. Crop J 7:176–186

    Article  Google Scholar 

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The authors are grateful to Prof. R.A. McIntosh, Plant Breeding Institute, University of Sydney, for language editing and proofreading of the draft manuscript and Dr. Xueling Huang, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, for providing a genotyping platform for KASP assays. The authors thank Professors Zhiyong Liu, Caixia Lan and Evans Lagudah for their helpful suggestions and discussion.


This study was financially supported by the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant no. 31961143019), National Science Foundation for Young Scientists in China (Grant no. 32302377), National Natural Science Foundation of China (Grant no. 32272088 and 32372562), National Key Research and Development Program of China (2022YFF1001500).

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Authors and Affiliations



XT Wang, SJ Liu and DJ Han designed and conducted the experiments, analyzed the data, and wrote the manuscript. MJ Xiang, QD Zeng, JH Wu and S Huang participated in developing the genetic populations and assisted in analysis of the SNP array data. MJ Xiang, HZ Li, XX Li, KQ Mu, YB Zhang, XR Cheng, XY Yuan and SQ Yang participated in greenhouse and field experiments and contributed to genotyping. RP Singh, S Bhavani and ZS Kang participated in revision of the manuscript. DJ Han conceived and directed the project and revised the manuscript.

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Correspondence to Shengjie Liu or Dejun Han.

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Communicated by James Cockram.

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Wang, X., Xiang, M., Li, H. et al. High-density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat. Theor Appl Genet 137, 152 (2024).

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