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Development of PCR based SSR markers for Wilsonomyces carpophilus and a PCR based diagnosis protocol for the early detection of shot hole disease in stone fruit crops

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Abstract

Background

The conidial Ascomycota fungus Wilsonomyces carpophilus causing shot hole in stone fruits is a major constraint in the production of stone fruits worldwide. Shothole disease symptoms appear on leaves, fruits, and twigs. Successful isolation of the pathogen from different hosts on synthetic culture medium is a time consuming and tedious procedure for identification of the pathogen based on morpho-cultural characterization.

Methods and results

The present research was carried out to develop a successful PCR based early detection protocol for the shot hole disease of stone fruits, viz., peach, plum, apricot, cherry, and almond using the pathogen specific SSR markers developed from the Wilsonomyces carpophilus genome using Genome-wide Microsatellite Analysing Tool package (GMATA) software. Diseased leaf samples of different stone fruits were collected from the SKUAST-K orchard and the pathogen was isolated on potato dextrose agar (PDA) medium and maintained on Asthana and Hawkers’ medium with a total of 50 pathogen isolates comprised of 10 isolates each from peach, plum, apricot, cherry and almond. The DNA was extracted from both healthy and infected leaf samples of different stone fruits. The DNA was also extracted from the isolated pathogen cultures (50 isolates). Out of 2851 SSR markers developed, 30 SSRs were used for the successful amplification of DNA extracted from all the 50 pathogen isolates. These SSRs were used for the amplification DNA from shot hole infected leaf samples of different stone fruits, but the amplification was not observed in the control samples (DNA from healthy leaves), thus confirming the detection of this disease directly from the shot hole infected samples using PCR based SSR markers. To our knowledge, this forms the first report of SSR development for the Wilsonomyces carpophilus and their validation for the detection of shot hole disease directly from infected leaves.

Conclusion

PCR based SSR makers were successfully developed and used for the detection of Wilsonomyces carpophilus causing shot hole disease in stone fruits including almond in nuts for the first time. These SSR markers could successfully detect the pathogen directly from the infected leaves of stone fruits namely peach, plum, apricot and cherry including almond from the nuts.

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Data availability statement

There is no data associated with this manuscript.

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Acknowledgements

The authors are thankful to Professor and Head, Division of Plant Pathology, SKUAST-Kashmir for providing necessary help and support.

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Authors and Affiliations

  1. Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India

    Sehla Khursheed, Mahiya Farooq, Bilal A. Padder, Asha Nabi, Sana B. Surma, Sumaira Hamid & Mehraj D. Shah

  2. Division of Agricultural Statistics, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India

    Imran Khan

  3. Division of Floriculture and Landscape Architecture, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India

    F. U. Khan

  4. Division of Vegetable Science, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India

    Rizwan Rashid

  5. Department of Biosciences (Microbiology), Integral University, Lucknow, U.P., India

    Sumaira Hamid

Authors
  1. Sehla Khursheed
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  2. Mahiya Farooq
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  3. Bilal A. Padder
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  4. Imran Khan
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  5. F. U. Khan
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  6. Asha Nabi
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  7. Rizwan Rashid
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  8. Sana B. Surma
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  9. Sumaira Hamid
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  10. Mehraj D. Shah
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Correspondence to Mehraj D. Shah.

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Khursheed, S., Farooq, M., Padder, B.A. et al. Development of PCR based SSR markers for Wilsonomyces carpophilus and a PCR based diagnosis protocol for the early detection of shot hole disease in stone fruit crops. Mol Biol Rep 50, 7173–7182 (2023). https://doi.org/10.1007/s11033-023-08636-6

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