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Molecular characterization and development of sequence characterized amplified region (SCAR) marker for detection of Ascochyta rabiei (Pass.) Labr., infecting chickpea

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Abstract

The Ascochyta Blight (AB) caused by Ascochyta rabiei is recognized as a major foliar disease of chickpea worldwide. The rapid detection of AB is a prerequisite for the effective and timely management of disease at an early stage to prevent the AB epidemics in chickpea. The Indian isolates of A. rabiei were characterized pathogenically and sequencing of Internal Transcribed Spacer (ITS) region. The phylogenetic analysis of ITS sequences indicated 99.97% similarity index and isolates formed two major clusters through neighbour joining analysis. The RAPD monomorphic bands were cloned and sequenced. The best set of SCAR marker pairs designated as SCAR1F/SCAR1R were validated using PCR with sensitivity of 0.30 ng of genomic DNA. The RAPD derived SCAR marker demonstrated high sensitivity and were species specific in the detection of A. rabiei. The SCAR marker could be used for quick and timely detection of the A. rabiei fungus in seed materials of quarantine importance for phytosanitary certification of chickpea.

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Acknowledgements

This research was funded by Science and Engineering Research Board (DST-SERB), Government of India under Early Career Research [Grant No. ECR/2016/000855], India.

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Authors and Affiliations

  1. Crop Protection Division, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, 208024, India

    Lakshmaiah Manjunatha, Sanjay Bandi & Shailendra Singh

  2. Regional Research Centre Cum Off-Season Nursery, ICAR-IIPR, Dharwad, Karnataka, India

    Parasappa Rajappa Saabale

  3. Division of Pl. Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India

    Nagappa Srinivasa

  4. Pandit Deendayal Upadhyay College of Horticulture and Forestry, RPCAU, Pusa, Bihar, India

    Krishna Kumar

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  1. Lakshmaiah Manjunatha
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  2. Parasappa Rajappa Saabale
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  3. Nagappa Srinivasa
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  4. Sanjay Bandi
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  5. Shailendra Singh
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  6. Krishna Kumar
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Contributions

LM, PRS, SS, perceived this work, designed the experiments, work carried out and drafted the article. SN, assisted in sample collection, LM, SB, KK, analysed the data and upgraded the manuscript.

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Correspondence to Lakshmaiah Manjunatha.

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Manjunatha, L., Saabale, P.R., Srinivasa, N. et al. Molecular characterization and development of sequence characterized amplified region (SCAR) marker for detection of Ascochyta rabiei (Pass.) Labr., infecting chickpea. Indian Phytopathology 74, 605–613 (2021). https://doi.org/10.1007/s42360-021-00345-z

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