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Multilocus gene-based characterization of peanut witches’ broom related phytoplasma strain associated with flower malformation of papaya in India

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Abstract

Papaya (Carica papaya L.) is an important fruit crop which significantly contributed to fulfill the national fruit requirement of India. Papaya plant is affected by many diseases that greatly effect on the growth and fruit yield. Flower malformation symptoms (PFM) were reported in papaya plantations in university campus at Faizabad, Uttar Pradesh during 2019. Flower samples from symptomatic and asymptomatic papaya trees were collected and analysed with nested and semi-nested PCR assays for the 16S rRNA, secA, tuf, and imp genes, in order to identify the relevant phytoplasma strain associated with the disease. Amplicons of  ~ 1.2 kb DNA products were consistently amplified in five symptomatic flower samples of papaya using universal phytoplasma specific nested primer pairs P1/P7 and R16F2n/R2, but not from flowers collected from any asymptomatic plants. Pair wise sequence comparison, phylogeny and virtual RFLP analysis of 16S rRNA gene sequences confirmed the identification and taxonomic assignment of papaya flower malformation strain into ‘Candidatus Phytoplasma australasia’ strain subgroup D (16SrII-D). Phytoplasma association was further established and validated by amplifying phytoplasma specific multilocus candidate genes in all the symptomatic flower malformed samples by utilizing multilocus gene specific primers of secA, secY and tuf genes. The BLAST sequence comparison of secA (600 bp), tuf (1067 bp), and imp (727 bp) genes revealed  that the PFM phytoplasma strain associated with symptomatic papaya tress belonged to Ca. P. australasia related strain. In phylogeny analysis, the 16Sr RNA, secA, secY and tuf genes sequences showed clustering of PFM isolate with the strains of peanut witches’ broom group. Our results confirmed association of Ca. P. australasia strain (16SrII-D subgroup) with papapa showing flower malformation symptoms in Eastern Uttar Pradesh, India.

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Acknowledgements

The authors would like to express their gratitude to the Head, Division of Plant Pathology and to the Director, Indian Agricultural Research Institute for providing laboratory facilities.

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Authors and Affiliations

  1. Discipline of Life Sciences, Indira Gandhi National Open University, New Delhi, 110068, India

    Priyam Panda

  2. Department of Plant Pathology, A. N. D. University of Agriculture and Technology, Kumarganj, Ayodhya, 224229, Uttar Pradesh, India

    Sushil Kumar Singh

  3. Departmant of Botany, DDU Gorakhpur University, Gorakhpur, 273009, Uttar Pradesh, India

    Smriti Mall

  4. Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Govind Pratap Rao

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  1. Priyam Panda
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  2. Sushil Kumar Singh
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Correspondence to Govind Pratap Rao.

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Panda, P., Singh, S.K., Mall, S. et al. Multilocus gene-based characterization of peanut witches’ broom related phytoplasma strain associated with flower malformation of papaya in India. Indian Phytopathology 75, 1211–1216 (2022). https://doi.org/10.1007/s42360-022-00547-z

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