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Three variants of cotton leaf curl begomoviruses with their satellite molecules are associated with cotton leaf curl disease aggravation in New Delhi

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Abstract

Cotton leaf curl disease (CLCuD), caused by monopartite begomoviruses and its satellite molecules, is one of the serious constrains in cultivation of cotton in India. In the present study, five CLCuD-begomovirus and its associated satellite molecules were characterized based on rolling circle amplification and sequencing of complete genome. Sequence analysis showed 82–99 % nucleotide identity among them. The phylogenetic analysis and nt identity matrix determined that of the five CLCuD-begomovirus isolates, three IARI-34, IARI-42 and IARI-50 were members of Cotton leaf curl Multan virus (CLCuMuV)-Rajasthan isolates, designated as CLCuMuV-Rajasthan-34 and two, IARI-30 and IARI-45 of Cotton leaf curl Kokhran virus (CLCuKoV)-Burewala isolates, designated as CLCuKoV-Burewala-45. The present CLCuMuV-Rajasthan-34 is recombinant isolate showing recombination events in IR, C1 and C4 regions of its genome with high probality (P = 9.9 × 10−10–3.2 × 10−6). Same species of betasatellite (1371 nt) molecules obtained from both the present isolates was related with cotton leaf curl Multan betasatellite by 89–97 % nt identity. Three alphasatellites (1366–1396 nt) related to Cotton leaf curl Burewala alphasatellite and Gossypium darwinii symptomless alphasatellite by 86 % nt identity were also obtained. This is the first report of appearance of CLCuKoV-Burewala isolate and CLCuD associated alphasatellites in New Delhi. The present study demonstrated that CLCuD in New Delhi is caused by three kinds of variants, two are strains of CLCuMuV and one of CLCuKoV, either by single or mixed infection along with beta- and alpha-satellite molecues.

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Abbreviations

CLCuD:

Cotton leaf curl disease

IARI:

Indian Agricultural Research Institute

CLCuMuV:

Cotton leaf curl Multan virus

CLCuKoV:

Cotton leaf curl Kokhran virus

CLCuMB:

Cotton leaf curl Multan betasatellite

RDP4:

Recombination detection program

nt:

Nucleotide

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Acknowledgments

First author is grateful to DST for financial assistantship as JRF. The authors are grateful to Dr. R.K.Jain, Dean, IARI and Dr. Baranwal, In-charge Plant Virology Unit, IARI, Head, Div of Plant Pathology; Director IARI for providing laboratory facilities. Authors are also grateful to Prof. Anupam Varma, Ex-National Professor, IARI; Dr. V.G Malathi, Ex-Principal Scientist, IARI for their valuable suggestions during this research work.

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Authors and Affiliations

  1. Division of Plant Pathology, Advanced Centre of Plant Virology, Indian Agricultural Research Institute, New Delhi, India

    Shruti Godara & K. K. Biswas

  2. Amity University, Manesar, Haryana, India

    S. M. Paul Khurana

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  1. Shruti Godara
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  2. S. M. Paul Khurana
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  3. K. K. Biswas
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Correspondence to K. K. Biswas.

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Godara, S., Paul Khurana, S.M. & Biswas, K.K. Three variants of cotton leaf curl begomoviruses with their satellite molecules are associated with cotton leaf curl disease aggravation in New Delhi. J. Plant Biochem. Biotechnol. 26, 97–105 (2017). https://doi.org/10.1007/s13562-016-0370-x

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