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Characterization and distribution of phytoplasma strains associated with temperate stone fruits and their possible natural reservoirs in the north-western Himalayan states of India

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Abstract

Symptoms of leaf yellowing, reddening, witches’ broom and declining were observed in peach, apricot, and plum orchards from two states and a union territory [Himachal Pradesh (H.P.), Uttarakhand and Jammu & Kashmir (J&K)] of India during 2019–2021. Association of three groups (16SrI, 16SrII,16SrV) of phytoplasma were confirmed in symptomatic peach, plum and apricot samples by amplifying DNA using 16S rRNA and multiple non-ribosomal primers (secA, secY, tuf). Pair wise sequence comparison, phylogenetic analysis and virtual RFLP analysis using multiple non-ribosomal gene sequences confirmed the presence of ‘Candidatus Phytoplasma asteris’ (16SrI-B), ‘Ca. Phytoplasma australasia' (16SrII-D), elm yellows (new subgroup variant of 16SrV) and ‘Ca. Phytoplasma ziziphi' (16SrV-B) related strains in peach, plum and apricot trees. Besides, other suspected symptomatic plant hosts and weeds in and around stone fruit orchards were also identified positive with phytoplasma strains belonging to 16SrI-B and 16Sr II-D subgroups by amplifying 16SrRNA and secA genes and sequence analysis. Association of similar strains of phytoplasma was identified in leafhopper species, Hishimonus phycitis from J&K and Empoasca sp. from Uttarakhand by utilizing the same set of primer pairs and 16S rRNA and secA gene sequence comparison. The presence of ‘Ca. P. asteris’ (16SrI-B) and ‘Ca. P. australasia’ (16SrII-D) related strains detected in peach are new host records from India and the association of elm yellows (a variant of 16SrV subgroup) related strain in plum is the first report in the world.

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Acknowledgements

The authors are thankful to the Director, ICAR-Indian Agricultural Research Institute, New Delhi, India, for providing financial assistance. Also, wish to express sincere thanks to the Head, Division of Plant Pathology, Indian Agricultural Research Institute, for providing laboratory facilities.

Funding

Consumables funding provided by Indian Agricultural Research Institute, New Delhi, India.

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Authors and Affiliations

  1. Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India

    Yapalahalli Sathyanarayanappa Shreenath, Pasumarthi Venkata Dinesh Kumar & Govind Pratap Rao

  2. Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Chatha, Jammu, 180009, India

    Ashok Kumar Singh

  3. ICAR-Indian Agricultural Research Institute, Regional Station (CHC), Shimla, Himachal Pradesh, 171004, India

    Santosh Watpade

  4. Department of Plant Pathology, G. B. Pant University of Agriculture and Technology, Uttarakhand, Pantnagar, 263153, India

    Krishna Pratap Singh

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  1. Yapalahalli Sathyanarayanappa Shreenath
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  3. Pasumarthi Venkata Dinesh Kumar
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Correspondence to Govind Pratap Rao.

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The paper has not been submitted elsewhere for publication, in whole or in part. Y.S.S. collected the samples and recorded field data and analyses the samples for PCR assays. PVDK analysed the data. AKS, SW and KPS helped in survey of stone fruit crops in different states, GPR drafted the first manuscript and made corrections. All authors contributed to improve the manuscript, reviewed and approved the manuscript.

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Shreenath, Y.S., Singh, A.K., Kumar, P.V.D. et al. Characterization and distribution of phytoplasma strains associated with temperate stone fruits and their possible natural reservoirs in the north-western Himalayan states of India. Eur J Plant Pathol 164, 93–108 (2022). https://doi.org/10.1007/s10658-022-02541-7

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