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High density mapping of wheat stripe rust resistance gene QYrXN3517-1BL using QTL mapping, BSE-Seq and candidate gene analysis

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Abstract

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Fine mapping of a major stripe rust resistance locus QYrXN3517-1BL to a 336 kb region that includes 12 candidate genes.

Abstract

Utilization of genetic resistance is an effective strategy to control stripe rust disease in wheat. Cultivar XINONG-3517 (XN3517) has remained highly resistant to stripe rust since its release in 2008. To understand the genetic architecture of stripe rust resistance, Avocet S (AvS) × XN3517 F6 RIL population was assessed for stripe rust severity in five field environments. The parents and RILs were genotyped by using the GenoBaits Wheat 16 K Panel. Four stable QTL from XINONG-3517 were detected on chromosome arms 1BL, 2AL, 2BL, and 6BS, named as QYrXN3517-1BL, QYrXN3517-2AL, QYrXN3517-2BL, and QYrXN3517-6BS, respectively. Based on the Wheat 660 K array and bulked segregant exome sequencing (BSE-Seq), the most effective QTL on chromosome 1BL is most likely different from the known adult plant resistance gene Yr29 and was mapped to a 1.7 cM region [336 kb, including twelve candidate genes in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0]. The 6BS QTL was identified as Yr78, and the 2AL QTL was probably same as QYr.caas-2AL or QYrqin.nwafu-2AL. The novel QTL on 2BL was effective in seedling stage against the races used in phenotyping. In addition, allele-specifc quantitative PCR (AQP) marker nwafu.a5 was developed for QYrXN3517-1BL to assist marker-assisted breeding.

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Data availability

Data, analysis codes and wheat material used in this study are available from the corresponding author upon request.

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Acknowledgements

The authors are grateful to Prof. R.A. McIntosh, Plant Breeding Institute, University of Sydney, for language editing and proofreading of the draft manuscript. This study was financially supported by National Key R&D Program of China (2021YFD1200600 and 2021YFD1401000), the Key R&D Program of Shaanxi Province in China (2021ZDLNY0-01), China Postdoctoral Science Foundation funding (2021M702698), Key R&D Program of Yangling Seed Industry Innovation Center, National Natural Science Foundation of China (2022T150538), and State Key Laboratory of North China Crop Improvement and Regulation (NCCIR2021KF-4).

Funding

This study was funded by the Department of Plant Protection at the University of Northwest A&F.

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Author notes

  1. Shuo Huang, Yibo Zhang, and Hui Ren contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Shuo Huang, Qingdong Zeng, Qilin Wang & Zhensheng Kang

  2. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Yibo Zhang, Hui Ren, Xin Zhang, Rui Yu, Shengjie Liu, Fengping Yuan, Jianhui Wu & Dejun Han

  3. International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, Estado de Mexico, Mexico

    Ravi P. Singh & Sridhar Bhavani

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  1. Shuo Huang
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Contributions

S Huang designed and conducted the experiments, analyzed the data, and wrote the manuscript. YBZ, HR, XZ, RY, QDZ, and QLW participated in creation of the genetic populations and assisted in analysis of the SNP array data. YBZ, HR, SJL, and FPY participated in greenhouse and field experiments and contributed to genotyping. RPS, SB, and ZSK participated in revision of the manuscript. JHW, DJH and ZSK conceived and directed the project.

Corresponding authors

Correspondence to Jianhui Wu, Dejun Han or Zhensheng Kang.

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Communicated by Hermann Buerstmayr.

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Supplementary Information

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122_2023_4282_MOESM1_ESM.pptx

Supplementary file1: Fig. S1.Frequency distributions of stripe rust infection type (IT) and disease severity(DS) recorded in different field experiments for the wheat mapping populations AvS ×XN3517 during 2017 2018 (A, B) and 2018 2019 cropping season (C, D). Fig. S2.Collinearity analysis of QYrXN3517 1BL candidate genes using the 10+genomic website.

Supplementary file2 (XLSX 116 KB)

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Huang, S., Zhang, Y., Ren, H. et al. 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 (2023). https://doi.org/10.1007/s00122-023-04282-5

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