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Diversity analysis of different Diaporthe (Phomopsis) species and development of molecular marker to identify quarantine important species Phomopsis phaseolorum

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Abstract

The genus Diaporthe Nitschke (Phomopsis Sacc. & Harter) infect various agricultural and horticultural important crops and cause diseases such as damping off, leaf spots, blights, canker, dieback, wilt, root and fruit rots. P. vexans, P. helianthi and P. phaseolorum are the important species within genus causing huge yield and economic loss. Being primarily seed borne it also hinders import and export of germplasm and seeds. Therefore, extensive characterization is required to diagnose and manage the disease. Seventeen isolates collected from ITCC, IARI and ICAR-NBPGR belonging to eight species were morphological and molecularly characterized and diversity was analyzed. Several morphological and cultural characters were studied and analyzed. Due to lack of sufficient morphological variation to identify/differentiate species, molecular characterization using house-keeping genes, internal transcriber spacer (ITS) was carried out. ITS produced amplicon of ~ 600 bp in the isolates of Phomopsis and phylogenetic tree obtained revealed that isolates of a species belonging same geographic region had more sequence similarity than isolates belonging to different geographic regions this might be due to population adaption under varied environments. Development of EF-1alpha-based marker specific to P. phaseolorum helps in easily detection of pathogen in quarantine stations. In addition, species of Phomopsis were previously named based on host association which has led to misidentification and proliferation of species. Cross pathogenicity of isolates on three important hosts, brinjal, soybean and chilli revealed its broad host range and naming only basis of host association is unjustified.

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Acknowledgements

The authors are thankful to ITCC, ICAR-IARI, New Delhi and ICAR-NBPGR, New Delhi for providing Phomopsis cultures and also thank Division of vegetable science, ICAR-IARI and ICAR-NBPGR, New Delhi for proving seeds. The first author thanks ICAR for providing junior research fellowship.

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Authors and Affiliations

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

    Nishmitha K & Deeba Kamil

  2. Indian Council of Agricultural Research, New Delhi, 110001, India

    Sunil Chandra Dubey

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  1. Nishmitha K
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  2. Sunil Chandra Dubey
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  3. Deeba Kamil
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Contributions

NK, SCD and DK were involved in designing objectives and experiment. NK did experimental work and data analysis. DK was involved in designing primers. NK and SCD wrote the paper.

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Correspondence to Sunil Chandra Dubey.

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There was no conflict of interest among authors, co-authors and the institute where the work has been carried out.

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K, N., Dubey, S.C. & Kamil, D. Diversity analysis of different Diaporthe (Phomopsis) species and development of molecular marker to identify quarantine important species Phomopsis phaseolorum. 3 Biotech 12, 31 (2022). https://doi.org/10.1007/s13205-021-03075-1

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