Rebound of Cotton leaf curl Multan virus and its exclusive detection in cotton leaf curl disease outbreak, Punjab (India), 2015

Sibnarayan Datta,Soumya Chatterjee,Sonika Sharma,P Srinivas Raju,Vijay Veer,Raghvendra Budhauliya,Vanlalhmuaka Vanlalhmuaka,Bidisha Das,Reji Gopalakrishnan

doi:10.1038/s41598-017-17680-9

Sibnarayan Datta, Soumya Chatterjee + Show 7 more

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https://doi.org/10.1038/s41598-017-17680-9

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Abstract

Cotton leaf curl disease (CLCuD) outbreaks caused by CLCuD associated begomoviruses (CABs) significantly constrain cotton production in India and Pakistan. In comparison to the CABs circulating in Pakistan, molecular epidemiology, evolution and recombination patterns of CABs circulating in India are less studied. In this work, we characterized CAB complex sequences obtained from the most recent outbreak (Punjab, India, 2015), and rigorously analyzed them with reference to GenBank sequences, submitted from India, Pakistan and other neighbouring countries, using contemporary bioinformatics approaches. In this manuscript, we illustrate the detection of a recombinant, phylogenetically distinct clade of Cotton leaf curl Multan virus (CLCuMuV), suggesting rebound of CLCuMuV in this region. Interestingly, we could not detect Cotton leaf curl Kokhran virus-Burewala strain (CLCuKoV-Bu), which was prevalent in this region, until now. Our study thus indicates substitution of the ‘virulent resistance breaking’ CLCuKoV-Bu by the re-emerging CLCuMuV recombinants. Our findings corroborate with that of a very recent study from Pakistan and we here discuss epidemiological links between the CAB complexes reported in these two studies. Taken together, these observations signify a shifting epidemiology of CABs, and seem to correlate with the recent prediction of the ‘third epidemic’ of CLCuD in the Indian subcontinent.

Highlights

Worldwide, cotton is considered as the most important non-food agricultural commodity and is one of the major economic crops of the Indian and the African subcontinents
We report very important and interesting findings of this study, which endows with an exciting insight into the ongoing changing molecular epidemiology of the CLCuD associated begomoviruses (CABs) in the Indian subcontinent
Results of this study demonstrated the exclusive detection of Cotton leaf curl Multan virus (CLCuMuV) in plant samples collected from the most recent Cotton leaf curl disease (CLCuD) outbreak in Punjab (India)

Summary

Introduction

Cotton is considered as the most important non-food agricultural commodity and is one of the major economic crops of the Indian and the African subcontinents. The first outbreak of CLCuD in the Indian subcontinent, the ‘Multan epidemic’ occurred in Multan, Khanewal and Vehari districts of Punjab province of Pakistan during the 1990s which was later found to be associated with a begomovirus-betasatellite complex comprised of CLCuMuV, CLCuKoV, CLCuAlV, PaLCuV along with a single betasatellite, the CLCuMuB1,3,6. This outbreak was controlled by large scale adoption of CLCuD resistant cotton varieties[3,6,8]. Apart from shattering the economy from farmer house-hold to the national level, this devastating outbreak claimed lives of at least 15 cotton farmers, who committed suicide due to heavy losses, triggering serious socio-political turmoil in the state[28]

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