Current status of cotton leaf curl disease and associated begomovirus complex in cotton growing areas of Northwest India
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Date
2022
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DIVISION OF PLANT PATHOLOGY INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI –110012, INDIA
Abstract
Cotton leaf curl disease (CLCuD) is caused by begomoviruses (family Geminiviridae) associated with
satellite molecules, viz. betasatellite and alphasatellite, and transmitted exclusively by whitefly
(Bemisia tabaci). Since the report of this disease, there have been several outbreaks of the CLCuD
disease in NW India. To know the current status of CLCuD, a survey to estimate CLCuD incidence
and percent disease index (PDI) was made in the cotton-growing areas of Haryana, Punjab, and
Rajasthan of NW India for two successive years, 2020 and 2021. Cotton germplasms were evaluated
for resistance against the CLCuD complex by whitefly inoculation. Genetic variation in CLCuD
begomovirus and its associated satellite molecules were studied. In Haryana, PDI of 13.8 and 16.5; in
Rajasthan, CLCuD incidence of 37.9% with PDI of 8.43 and 46.7% with PDI of 10.14; and in
Punjab, PDI of 4.12 and 5.1 were estimated in 2020 and 2021, respectively. These findings revealed
that CLCuD incidence is low during these years.
Thirteen cotton varieties and six Bt-hybrid cotton were screened for resistance against CLCuD. All the
germplasms screened were susceptible to CLCuD, indicating a lack of resistance in cotton in the
present condition. Twenty-nine CLCuD-begomovirus isolates; six isolates of the year 2020 and 23
isolates of the year 2021, were collected randomly from different cotton growing areas of Punjab,
Haryana, and Rajasthan of NW India, and the ICAR-IARI experimental field of New Delhi, and were
characterized by amplification, cloning, and sequences of complete CP gene (771nt) of the CLCuDbegomovirus isolates. All the present isolates shared 81-100% nt identity amongst themselves and 69-
100% nt identity with other CLCuD begomovirus isolates. In the phylogenetic analysis, all the isolates
of both years were segregated into three species, Cotton leaf curl Multan virus (CLCuMuV) and
Cotton leaf curl Kokhran virus (CLCuKoV), and Cotton leaf curl Multan virus- Rajasthan
(CLCuMuV-Ra). However, the population of CLCuMuV-Ra was more in both years, indicating that
the strain CLCuMuV-Ra is predominant in cotton-growing areas of NW India. In the recombination
analysis, most of the isolates were identified as recombinants, and seven recombination breakpoints
were identified amongst the present isolates. The βC1 gene of betasatellites associated with the current
eight CLCuD-begomovirus isolates was analyzed. The present study showed that the single
betasatellite species CLCuMB is associated with the CLCuD complex in NW India. In the multiple
sequence alignment using the complete CP gene, remarkable sequence variations were detected among
the isolates of CLCuMuV, CLCuMuV-Ra, and CLCuKoV. Although the disease incidence is low
compared to the previous couple of years, the cotton varieties and Bt-hybrid cotton cultivated in the
present situation are susceptible to CLCuD-begomovirus.