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Identification of a stripe rust resistance gene in Chinese wheat line Shaannong69 using bulked-segregant sequencing

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Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease, leading to huge yield losses in wheat production. Identification of resistance genes and closely linked molecular markers can greatly facilitate breeding resistant wheat cultivars. Shaannong69 conferred high resistance to stripe rust both at the seedling and adult-plant stages. The Pst race CYR31 was used to infect Shaannong69, Huixianhong, F1 and F2 plants and F2:3 lines at the seedling stage in the greenhouse. Genetic analysis identified a single dominant gene, designated as YrSN69, conferring resistance to Pst race CYR31 in Shaannong69. Seventy-four of 176 SNPs with the absolute value of ∆SNP-index more than 0.85 were identified in 753.33–766.18 Mb on chromosome 2BL based on bulked segregant RNA sequencing. Fifteen kompetitive allele-specific PCR markers were developed to genotype susceptible F2 plants derived from the Shaannong69/Huixianhong cross. YrSN69 was mapped on chromosome arm 2BL in a 2.0 cM genetic interval, with genetic distances of 0.2 cM and 1.8 cM to markers 2BC17 and 2BA20, respectively, corresponding to a 3.16 Mb physical region based on the IWGSC RefSeq v1.1 with 44 high-confidence annotated genes. The YrSN69 is likely to be a new allele of Yr72 in comparison with known Yr genes on chromosome 2BL. These results provide a solid foundation for map-based cloning of YrSN69 and marker-assisted selection for pyramiding stripe rust resistance genes.

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Data availability

The datasets generated during the current study are available from the corresponding author on reasonable request.

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Funding

This work was funded by the National Natural Science Foundation of China (32360503), National Key Research and Development Program of China (2022YFD1201500), Science and Technology Partnership Program, Ministry of Science and Technology of China (KY202201001), Key Research and Development Program of Ningxia (2023BCF01011), and Natural Science Foundation of Ningxia Province (2023AAC05050).

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Author notes

  1. Yan Dong and Yachao Dong have contributed equally to this work.

Authors and Affiliations

  1. Crop Research Institute, Ningxia Academy of Agricultural and Forestry Sciences, 490 Huanghe Road, Yinchuan, 750002, Ningxia, China

    Yan Dong & Dongsheng Chen

  2. Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China

    Yan Dong, Yachao Dong, Yuying Wu, Fengju Wang, Jingchun Wu, Yuanfeng Hao, Zhonghu He & Xianchun Xia

  3. College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Ürümqi, 830052, Xinjiang, China

    Yachao Dong & Yukun Cheng

  4. Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610011, Sichuan, China

    Ling Wu

  5. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China

    Jianhui Wu

  6. College of Agronomy, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China

    Dengan Xu

  7. Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730030, Gansu, China

    Bin Bai

  8. College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan, China

    Yan Ren

  9. International Maize and Wheat Improvement Centre (CIMMYT) China Office, C/O CAAS, Beijing, 100081, China

    Zhonghu He

Authors
  1. Yan Dong
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Contributions

Yan Dong performed the experiment and data analysis, and wrote the paper. Yachao Dong, Yuying Wu, Jingchun Wu contributed to scoring stripe rust in greenhouse. Ling Wu and Bin Bai participated in field trials. Dengan Xu contributed to BSR-Seq analysis. Fengju Wang constructed the mapping population. Jianhui Wu provided Pst races. Yukun Cheng, Yuanfeng Hao, Zhonghu He, Xianchun Xia and Dongsheng Chen designed the experiment and/or assisted in writing the paper. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Dongsheng Chen or Xianchun Xia.

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These experiments complied with the ethical standards in China.

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Dong, Y., Dong, Y., Wu, L. et al. Identification of a stripe rust resistance gene in Chinese wheat line Shaannong69 using bulked-segregant sequencing. Euphytica 220, 88 (2024). https://doi.org/10.1007/s10681-024-03340-3

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