Mapping of a Major Locus for Resistance to Yellow Rust in Wheat
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials and Growing Environment
2.2. Phenotyping
2.3. Genotyping and QTL Mapping
2.4. Diagnostic Marker Developing
2.5. Expression Pattern of Annotated Genes Within QTL
2.6. Statistical Analysis
3. Results
3.1. Phenotypic Differences Among Parents
3.2. Resistance Segregation in YN999 × C855 F2 Population
3.3. Mapping for YR-Resistant Loci
3.4. Verification of QYr.sxau-2A.1
3.5. Assessment of the Two Alleles of QYr.sxau-2A.1
3.6. Annotated Genes Within QYr.sxau-2A.1
4. Discussion
4.1. QYr.sxau-2A.1 Is a Novel Yr Locus
4.2. Prediction of Candidate Genes for QYr.sxau-2A.1
4.3. QYr.sxau-2A.1 Can Be Used for Wheat Breeding
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
- Hellemans, T.; Landschoot, S.; Dewitte, K.; Van Bockstaele, F.; Vermeir, P.; Eeckhout, M.; Haesaert, G. Impact of Crop Husbandry Practices and Environmental Conditions on Wheat Composition and Quality: A Review. J. Agric. Food Chem. 2018, 66, 2491–2509. [Google Scholar] [CrossRef]
- Bouvet, L.; Holdgate, S.; James, L.; Thomas, J.; Mackay, I.J.; Cockram, J. The Evolving Battle Between Yellow Rust and Wheat: Implications for Global Food Security. Theor. Appl. Genet. 2022, 135, 741–753. [Google Scholar] [CrossRef]
- Schwessinger, B. Fundamental Wheat Stripe Rust Research in the 21st Century. New Phytol. 2017, 213, 1625–1631. [Google Scholar] [CrossRef] [PubMed]
- Kaur, S.; Kaur, J.; Mavi, G.S.; Dhillon, G.S.; Sharma, A.; Singh, R.; Devi, U.; Chhuneja, P. Pyramiding of High Grain Weight with Stripe Rust and Leaf Rust Resistance in Elite Indian Wheat Cultivar Using a Combination of Marker Assisted and Phenotypic Selection. Front. Genet. 2020, 11, 593426. [Google Scholar] [CrossRef] [PubMed]
- Zhou, X.; Fang, T.; Li, K.; Huang, K.; Ma, C.; Zhang, M.; Li, X.; Yang, S.; Ren, R.; Zhang, P. Yield Losses Associated with Different Levels of Stripe Rust Resistance of Commercial Wheat Cultivars in China. Phytopathology 2022, 112, 1244–1254. [Google Scholar] [CrossRef] [PubMed]
- Hovmller, M.S.; Henriksen, K.E. Application of Pathogen Surveys, Disease Nurseries and Varietal Resistance Characteristics in an IPM Approach for the Control of Wheat Yellow Rust. Eur. J. Plant Pathol. 2008, 121, 377–385. [Google Scholar] [CrossRef]
- Wu, J.; Ma, S.; Niu, J.; Sun, W.; Dong, H.; Zheng, S.; Zhao, J.; Liu, S.; Yu, R.; Li, Y.; et al. Genomics-driven Discovery of Superior Alleles and Genes for Yellow Rust Resistance in Wheat. Nat. Genet. 2025, 57, 2017–2027. [Google Scholar] [CrossRef]
- Chen, X. Pathogens Which Threaten Food Security: Puccinia striiformis, the Wheat Stripe Rust Pathogen. Food Secur. 2020, 12, 239–251. [Google Scholar] [CrossRef]
- Mcintosh, R.A.; Dubcovsky, J.; Rogers, W.J.; Xia, X.C.; Raupp, W.J. Catalogue of Gene Symbols for Wheat: 2021 Supplement. Annu. Wheat Newsl. 2021, 67, 104–113. [Google Scholar]
- Klymiuk, V.; Chawla, H.S.; Wiebe, K.; Ens, J.; Fatiukha, A.; Govta, L.; Fahima, T.; Pozniak, C.J. Discovery of Stripe Rust Resistance with Incomplete Dominance in Wild Emmer Wheat Using Bulked Segregant Analysis Sequencing. Commun. Biol. 2022, 5, 826. [Google Scholar] [CrossRef]
- Liu, Z.Y.; Zhang, H.Z.; Bai, B.; Li, J.; Huang, L.; Xu, Z.B.; Chen, Y.X.; Liu, X.; Cao, T.J.; Li, M.M.; et al. Current Status and Strategies for Utilization of Stripe Rust Resistance Genes in Wheat Breeding Program of China. Sci. Agric. Sin. 2024, 57, 34–51. [Google Scholar]
- Klymiuk, V.; Wiebe, K.; Chawla, H.S.; Ens, J.; Subramaniam, R.; Pozniak, C.J. Coordinated Function of Paired NLRs Confers Yr84-Mediated Stripe Rust Resistance in Wheat. Nat. Genet. 2025, 57, 1535–1542. [Google Scholar] [CrossRef]
- Feng, J.; Yao, F.; Wang, M.; See, D.R.; Chen, X. Molecular Mapping of Yr85 and Comparison with Other Genes for Resistance to Stripe Rust on Wheat Chromosome 1B. Plant Dis. 2023, 107, 3585–3591. [Google Scholar] [CrossRef] [PubMed]
- Li, H.; Bariana, H.; Singh, D.; Zhang, L.Q.; Dillon, S.; Whan, A.; Bansal, U.; Ayliffe, M. A Durum Wheat Adult Plant Stripe Rust Resistance QTL and Its Relationship with The Bread Wheat Yr80 Locus. Theor. Appl. Genet. 2020, 133, 3049–3066. [Google Scholar] [CrossRef] [PubMed]
- Zhu, Z.; Cao, Q.; Han, D.; Wu, J.; Wu, L.; Tong, J.; Xu, X.; Yan, J.; Zhang, Y.; Xu, K.; et al. Molecular Characterization and Validation of Adult-Plant Stripe Rust Resistance Gene Yr86 in Chinese Wheat Cultivar Zhongmai 895. Theor. Appl. Genet. 2023, 136, 142. [Google Scholar] [CrossRef] [PubMed]
- Hu, Y.; Li, M.; Li, Y.; Du, L.; Xie, R.; Ni, F.; Xia, C.; Wang, K.; Huang, Y.; Xu, B.; et al. A Head-to-Head NLR Gene Pair from Wild Emmer Confers Stripe Rust Resistance in Wheat. Nat. Genet. 2025, 57, 1543–1552. [Google Scholar] [CrossRef]
- Nazarov, T.; Liu, Y.; Chen, X.; See, D.R. Molecular Mechanisms of the Stripe Rust Interaction with Resistant and Susceptible Wheat Genotypes. Int. J. Mol. Sci. 2024, 25, 2930. [Google Scholar] [CrossRef]
- Qiao, L.; Gao, X.; Jia, Z.; Liu, X.; Wang, H.; Kong, Y.; Qin, P.; Yang, B. Identification of Adult Resistant Genes to Stripe Rust in Wheat from Southwestern China Based on GWAS and WGCNA Analysis. Plant Cell Rep. 2024, 43, 67. [Google Scholar] [CrossRef]
- Tao, F.; Wang, J.; Guo, Z.; Hu, J.; Xu, X.; Yang, J.; Chen, X.; Hu, X. Transcriptomic Analysis Reveal the Molecular Mechanisms of Wheat Higher-Temperature Seedling-Plant Resistance to Puccinia striiformis f. sp. tritici. Front. Plant Sci. 2018, 9, 240. [Google Scholar] [CrossRef]
- Gao, F.; Zhu, J.; Xue, X.; Chen, H.; Nong, X.; Yang, C.; Shen, W.; Gan, P. Transcriptome Analysis Reveals Mechanisms of Stripe Rust Response in Wheat Cultivar Anmai1350. Int. J. Mol. Sci. 2025, 26, 5538. [Google Scholar] [CrossRef]
- Zeng, Q.; Zhao, J.; Wu, J.; Zhan, G.; Han, D.; Kang, Z. Wheat Stripe Rust and Integration of Sustainable Control Strategies in China. Front. Agric. Sci. Eng. 2022, 1, 37–51. [Google Scholar] [CrossRef]
- Zhao, J.; Kang, Z. Fighting Wheat Rusts in China: A Look Back and into the Future. Phytopathol. Res. 2023, 5, 6. [Google Scholar] [CrossRef]
- Wu, J.; Wang, X.; Chen, N.; Yu, R.; Yu, S.; Wang, Q.; Huang, S.; Wang, H.; Singh, R.P.; Bhavani, S.; et al. Association Analysis Identifies New Loci for Resistance to Chinese Yr26-Virulent Races of the Stripe Rust Pathogen in a Diverse Panel of Wheat Germplasm. Plant Dis. 2020, 104, 1751–1762. [Google Scholar] [CrossRef]
- Liu, N.; Lei, Y.; Zhang, M.; Zheng, W.M.; Shi, Y.C.; Qi, X.B.; Chen, H.B.; Zhou, Y.; Gong, G.S. Latent Infection of Powdery Mildew on Volunteer Wheat in Sichuan Province, China. Plant Dis. 2019, 103, 1084–1091. [Google Scholar] [CrossRef]
- McIntosh, R.; Mu, J.; Han, D.; Kang, Z. Wheat Stripe Rust Resistance Gene Yr24/Yr26: A Retrospective Review. Crop J. 2018, 4, 321–329. [Google Scholar] [CrossRef]
- Chen, J.; Zhang, L.; Liu, Y.; Shen, X.; Guo, Y.; Ma, X.; Zhang, X.; Li, X.; Cheng, T.; Wen, H.; et al. RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots. Plants 2024, 13, 274. [Google Scholar] [CrossRef] [PubMed]
- Line, R.F.; Qayoum, A. Virulence, Aggressiveness, Evolution, and Distribution of Races of Puccinia striiformis (the Cause of Stripe Rust of Wheat) in North America 1968–87; Technical Bulletin Number 1788; United States Department of Agriculture: Washington, DC, USA, 1992.
- Qiao, L.; Li, T.; Liu, S.; Zhang, X.; Fan, M.; Zhang, X.; Li, X.; Yang, Z.; Jia, J.; Qiao, L.; et al. Ali-A1 and TPL1 Proteins Interactively Modulate Awn Development in Wheat. Crop J. 2025, 13, 468–479. [Google Scholar] [CrossRef]
- Qiao, L.; Zhang, X.; Li, X.; Zhang, L.; Zheng, J.; Chang, Z. Development of NBS-Related Microsatellite (NRM) Markers in Hexaploid Wheat. Euphytica 2017, 213, 256. [Google Scholar] [CrossRef]
- Qiao, L.; Zhang, X.; Li, X.; Yang, Z.; Li, R.; Jia, J.; Yan, L.; Chang, Z. Genetic Incorporation of Genes for the Optimal Plant Architecture in Common Wheat. Mol. Breed. 2022, 42, 66. [Google Scholar] [CrossRef]
- Zhang, H.; Yang, Y.; Wang, C.; Liu, M.; Li, H.; Fu, Y.; Wang, Y.; Nie, Y.; Liu, X.; Ji, W. Large-Scale Transcriptome Comparison Reveals Distinct Gene Activations in Wheat Responding to Stripe Rust and Powdery Mildew. BMC Genom. 2014, 15, 898. [Google Scholar] [CrossRef]
- Qiao, L.; Li, Y.; Wang, L.; Gu, C.; Luo, S.; Li, X.; Yan, J.; Lu, C.; Chang, Z.; Gao, W.; et al. Identification of Salt-Stress-Responding Genes by Weighted Gene Correlation Network Analysis and Association Analysis in Wheat Leaves. Plants 2024, 13, 2642. [Google Scholar] [CrossRef]
- Bariana, H.S.; McIntosh, R.A. Cytogenetic Studies in Wheat. XV. Location of Rust Resistance Genes in VPM1 and Their Genetic Linkage with Other Disease Resistance Genes in Chromosome 2A. Genome 1993, 36, 476–482. [Google Scholar] [CrossRef]
- Eriksen, L.; Afshari, F.; Christiansen, M.J.; McIntosh, R.A.; Jahoor, A.; Wellings, C.R. Yr32 for Resistance to Stripe (Yellow) Rust Present in the Wheat Cultivar Carstens V. Theor. Appl. Genet. 2004, 108, 567–575. [Google Scholar] [CrossRef] [PubMed]
- Bansal, U.K.; Hayden, M.J.; Keller, B.; Wellings, C.R.; Park, R.F.; Bariana, H.S. Relationship Between Wheat Rust Resistance Genes Yr1 and Sr48 and a Microsatellite Marker. Plant Pathol. 2009, 58, 1039–1043. [Google Scholar] [CrossRef]
- Feng, J.; Wang, M.; See, D.R.; Chao, S.; Zheng, Y.; Chen, X. Characterization of Novel Gene Yr79 and Four Additional Quantitative Trait Loci for All-Stage and High-Temperature Adult-Plant Resistance to Stripe Rust in Spring Wheat PI 182103. Phytopathology 2018, 108, 737–747. [Google Scholar] [CrossRef] [PubMed]
- Milus, E.A.; Lee, K.D.; Brown-Guedira, G. Characterization of Stripe Rust Resistance in Wheat Lines with Resistance Gene Yr17 and Implications for Evaluating Resistance and Virulence. Phytopathology 2015, 105, 1123–1130. [Google Scholar] [CrossRef]
- Wang, Y.; Hu, Y.; Gong, F.; Jin, Y.; Xia, Y.; He, Y.; Jiang, Y.; Zhou, Q.; He, J.; Feng, L.; et al. Identification and Mapping of QTL for Stripe Rust Resistance in the Chinese Wheat Cultivar Shumai126. Plant Dis. 2022, 106, 1278–1285. [Google Scholar] [CrossRef]
- Farzand, M.; Dhariwal, R.; Hiebert, C.W.; Spaner, D.; Randhawa, H.S. QTL Mapping for Adult Plant Field Resistance to Stripe Rust in the AAC Cameron/P2711 Spring Wheat Population. Crop Sci. 2022, 62, 1088–1106. [Google Scholar] [CrossRef]
- Liu, D.; Yuan, C.; Singh, R.P.; Randhawa, M.S.; Bhavani, S.; Kumar, U.; Huerta-Espino, J.; Lagudah, E.; Lan, C. Stripe Rust and Leaf Rust Resistance in CIMMYT Wheat Line “Mucuy” is Conferred by Combinations of Race-Specific and Adult-Plant Resistance Loci. Front. Plant Sci. 2022, 13, 880138. [Google Scholar] [CrossRef]
- Gebrewahid, T.W.; Zhang, P.; Zhou, Y.; Yan, X.; Xia, X.; He, Z.; Liu, D.; Li, Z. QTL Mapping of Adult Plant Resistance to Stripe Rust and Leaf Rust in a Fuyu3/Zhengzhou 5389 Wheat Population. Crop J. 2020, 8, 655–665. [Google Scholar] [CrossRef]
- Huang, S.; Liu, S.; Zhang, Y.; Xie, Y.; Wang, X.; Jiao, H.; Wu, S.; Zeng, Q.; Wang, Q.; Singh, R.P.; et al. Genome-Wide Wheat 55K SNP-Based Mapping of Stripe Rust Resistance Loci in Wheat Cultivar Shaannong 33 and Their Alleles Frequencies in Current Chinese Wheat Cultivars and Breeding Lines. Plant Dis. 2021, 105, 1048–1156. [Google Scholar] [CrossRef] [PubMed]
- Thompson, M.D.; Jacks, C.M.; Lenvik, T.R.; Gantt, J.S. Characterization of Rps17, Rp19 and Rpl15: Three Nucleus-Encoded Plastid Ribosomal Protein Genes. Plant Mol. Biol. 1992, 18, 931–944. [Google Scholar] [CrossRef] [PubMed]
- Kopriva, S.; Koprivova, A. Plant Adenosine 5′-Phosphosulphate Reductase: The Past, the Present, and the Future. J. Exp. Bot. 2004, 55, 1775–1783. [Google Scholar] [CrossRef] [PubMed]
- Lee, J.; Amasino, R.M. Two FLX Family Members are Non-Redundantly Required to Establish the Vernalization Requirement in Arabidopsis. Nat. Commun. 2013, 4, 2186. [Google Scholar] [CrossRef]
- Nandakumar, M.; Malathi, P.; Sundar, A.R.; Rajadurai, C.P.; Philip, M.; Viswanathan, R. Role of MiRNAs in the Host-Pathogen Interaction Between Sugarcane and Colletotrichum falcatum, the Red Rot Pathogen. Plant Cell Rep. 2021, 40, 851–870. [Google Scholar] [CrossRef]
- Vasudevan, D.; Gopalan, G.; Kumar, A.; Garcia, V.J.; Luan, S.; Swaminathan, K. Plant Immunophilins: A Review of Their Structure-Function Relationship. Biochim. Biophys. Acta 2015, 1850, 2145–2158. [Google Scholar] [CrossRef]
- Cui, X.; Wei, Y.; Wang, Y.H.; Li, J.; Wong, F.L.; Zheng, Y.J.; Yan, H.; Liu, S.S.; Liu, J.L.; Jia, B.L.; et al. Proteins Interacting with Mitochondrial ATP-Dependent Lon Protease (MAP1) in Magnaporthe oryzae are Involved in Rice Blast Disease. Mol. Plant Pathol. 2015, 16, 847–859. [Google Scholar] [CrossRef]
- Xiao, L.; Jin, Y.; Liu, W.; Liu, J.; Song, H.; Li, D.; Zheng, J.; Wang, D.; Yin, Y.; Liu, Y.; et al. Genetic Basis Analysis of Key Loci in 23 Yannong Series Wheat Cultivars/Lines. Front. Plant Sci. 2022, 13, 1037027. [Google Scholar] [CrossRef]







| Marker | Position | Forward Primer Sequence (5′-3′) | Reverse Primer Sequence (5′-3′) |
|---|---|---|---|
| SSR2A-11 | 2A:227444516 | CATAGAGAGATGCTGACACG | TAGAGAGAGATTTGTGGGCC |
| SSR2A-14 | 2A:228004971 | TTACTCTGCTTTGACGCACCT | ATATAGGGGGCGTCGTGATT |
| SSR2A-17 | 2A:230800650 | GTAGAAAACCTCGTCAGTCCAAT | GTTATTCATGTTATGATAGAAATATTTAC |
| SSR2A-20 | 2A:242006358 | CATGGCGCTGTTCACGCA | GCTATCTTGCTTCCACACTG |
| NRM2A-16 | 2A:227622447 | GAGAAGGGAAGCTACGGGCTA | GATGTATATAACAGTCCAACCCG |
| Trait | Parents | F2 Population | ||||
|---|---|---|---|---|---|---|
| C855 | YN999 | Min | Max | Mean | CV | |
| IT | 0 | 8 | 1 | 9 | 6.34 | 0.50 |
| TGW (g) | 46.97 | 19.91 *** | 10.32 | 60.23 | 31.23 | 0.39 |
| GL (mm) | 9.13 | 6.39 *** | 4.04 | 10.07 | 8.14 | 0.11 |
| GW (mm) | 4.10 | 2.90 *** | 1.80 | 4.89 | 3.60 | 0.17 |
| GD (mm) | 6.04 | 4.22*** | 2.68 | 6.77 | 5.31 | 0.14 |
| QTL | Chr. | Position (cM) | Left Marker | Right Marker | LOD | PVE (%) | Add |
|---|---|---|---|---|---|---|---|
| QYr.sxau-1B | 1B | 51 | 1B668939708 | 1B668980065 | 2.52 | 9.09 | 1.96 |
| QYr.sxau-2A.1 | 2A | 288 | 2A228025139 | 2A241581399 | 6.63 | 15.62 | −1.44 |
| QYr.sxau-2A.2 | 2A | 199 | 2A555830493 | 2A550206683 | 2.51 | 8.34 | −1.10 |
| QYr.sxau-2B | 2B | 54 | 2B754789255 | 2B754657245 | 2.65 | 8.67 | −0.99 |
| QYr.sxau-2D | 2D | 133 | 2D12479990 | 2D10311517 | 3.19 | 9.49 | 2.09 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Guo, H.; Wang, L.; Bai, X.; Wu, L.; Zhang, X.; Zhang, S.; Yang, Z.; Yang, E.; Chang, Z.; Li, X.; et al. Mapping of a Major Locus for Resistance to Yellow Rust in Wheat. Agronomy 2025, 15, 2511. https://doi.org/10.3390/agronomy15112511
Guo H, Wang L, Bai X, Wu L, Zhang X, Zhang S, Yang Z, Yang E, Chang Z, Li X, et al. Mapping of a Major Locus for Resistance to Yellow Rust in Wheat. Agronomy. 2025; 15(11):2511. https://doi.org/10.3390/agronomy15112511
Chicago/Turabian StyleGuo, Huijuan, Liujie Wang, Xin Bai, Lijuan Wu, Xiaojun Zhang, Shuwei Zhang, Zujun Yang, Ennian Yang, Zhijian Chang, Xin Li, and et al. 2025. "Mapping of a Major Locus for Resistance to Yellow Rust in Wheat" Agronomy 15, no. 11: 2511. https://doi.org/10.3390/agronomy15112511
APA StyleGuo, H., Wang, L., Bai, X., Wu, L., Zhang, X., Zhang, S., Yang, Z., Yang, E., Chang, Z., Li, X., & Qiao, L. (2025). Mapping of a Major Locus for Resistance to Yellow Rust in Wheat. Agronomy, 15(11), 2511. https://doi.org/10.3390/agronomy15112511

