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An SNP based genotyping assay for genes associated with drought tolerance in bread wheat

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Abstract

Background

SnRK2 plays vital role in responding to adverse abiotic stimuli. The applicability of TaSnRK2.4 and TaSnRK2.9 was investigated to leverage the potential of these genes in indigenous wheat breeding programs.

Methods

Genetic diversity was assessed using pre-existing markers for TaSnRK2.4 and TaSnRK2.9. Furthermore, new markers were also developed to enhance their broader applicability. KASP markers were designed for TaSnRK2.4, while CAPS-based markers were tailored for TaSnRK2.9.

Results

Analysis revealed lack of polymorphism in TaSnRK2.4 among Pakistani wheat germplasm under study. To validate this finding, available gel-based markers for TaSnRK2.4 were employed, producing consistent results and offering limited potential for application in marker-assisted wheat breeding with Pakistani wheat material. For TaSnRK2.9-5A, CAPS2.9-5A-1 and CAPS2.9-5A-2 markers were designed to target SNP positions at 308 nt and 1700 nt revealing four distinct haplotypes. Association analysis highlighted the significance of Hap-5A-1 of TaSnRK2.9-5A, which exhibited association with an increased number of productive tillers (NPT), grains per spike (GPS), and reduced plant height (PH) under well-watered (WW) conditions. Moreover, it showed positive influence on NPT under WW conditions, GPS under water-limited (WL) conditions, and PH under both WW and WL conditions. High selection intensity observed for Hap-5A-1 underscores the valuable role it has played in Pakistani wheat breeding programs. Gene expression studies of TaSnRK2.9-5A revealed the involvement of this gene in response to PEG, NaCl, low temperature and ABA treatments.

Conclusion

These findings propose that TaSnRK2.9 can be effectively employed for improving wheat through marker-assisted selection in wheat breeding efforts.

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Data availability

No datasets were generated or analysed during the current study.

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Acknowledgements

The authors extend their appreciation to Researchers Supporting Project number (RSP-2024 R369), King Saud University, Riyadh, Saudi Arabia. The authors are thankful to the Director of University Farms, Dr. Abdul Ghaffar and Deputy Director of University Farms, Mr. Mahmood Alam Khan, MNS University of Agriculture, Multan, for assisting in field experimentation.

Funding

This study was financially supported by the “LO21002838-National Crop Genomics and Speed Breeding Center For Agriculture Sustainability - ADP- 2021-22 to 2023-24” and 2022 ZDZX0014 Cultivation of Major New Varieties of Green and High Efficiency Wheat” projects.

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Authors and Affiliations

  1. Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan

    Abdul Rauf, Muhammad Ali Sher, Zulqurnain Khan & Shoaib Ur Rehman

  2. SINO-PAK Joint Research Laboratory, MNS University of Agriculture, Multan, Pakistan

    Abdul Rauf & Shoaib Ur Rehman

  3. Department of Food Science and Technology, MNS University of Agriculture, Multan, Pakistan

    Umar Farooq

  4. Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan

    Awais Rasheed

  5. Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan

    Muhammad Sajjad

  6. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Ruilian Jing

  7. Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Riyadh, 11451, Saudi Arabia

    KOTB A. Attia & Arif Ahmed Mohammed

  8. Department of Plant Breeding and Genetics, the University of Haripur, Haripur, 22620, Pakistan

    Sajid Fiaz

  9. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China

    Jing Chen

Authors
  1. Abdul Rauf
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  2. Muhammad Ali Sher
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  11. Jing Chen
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Contributions

Conceptualization by A.R and S.U.R; Data curation by A.R; Analysis by A.R, M.A.S, U.F, A.R (Awais Rasheed), Z.K; Original draft written by A.R; Reviewed by S.U.R, A.R (Awais Rasheed), M.S, R.J, R.M.I, J.C, Z.K; Overall supervision by J.C and S.U.R. K.A.A, A.A.M and S.F provided with technical expertise and funding acquisition. All author agreed on submission of article.

Corresponding authors

Correspondence to Jing Chen or Shoaib Ur Rehman.

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The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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Rauf, A., Sher, M.A., Farooq, U. et al. An SNP based genotyping assay for genes associated with drought tolerance in bread wheat. Mol Biol Rep 51, 527 (2024). https://doi.org/10.1007/s11033-024-09481-x

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