Abstract

The first epidemic of cotton leaf curl disease (CLCuD) in early 1990’s in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990’s but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.

Highlights

  • Cotton is the largest fiber producing and important cash crop in Pakistan and India[1]

  • The Cotton leaf curl Kokhran virus (CLCuKoV)-Bu strain, with a truncated transcriptional activator protein (TrAP), is the only begomovirus strain associated with the resistance breaking of cotton leaf curl disease (CLCuD) currently found throughout Pakistan, with the occasional identification of other strains (Table S3)[9, 43]

  • We have found that some recent isolates of CLCuKoV-Bu encode a full length TrAP (Hassan et al, unpublished data)

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Summary

Introduction

Cotton is the largest fiber producing and important cash crop in Pakistan and India[1]. Following the appearance of the second CLCuD epidemic in cotton, to present time, a predominant single recombinant begomovirus named as Cotton leaf curl Kokhran virus- Burewala (CLCuKoV-Bu), previously known as Cotton leaf curl Burewala virus (CLCuBuV), was associated with CLCuD in Pakistan and India[9]. Tomato leaf curl New Delhi virus (ToLCNDV) was identified associated with CLCuD in Pakistan[18, 19]. Another study identified Chickpea chlorotic dwarf virus (CpCDV), a Mastrevirus in cotton showing leaf curl virus disease symptoms[20] These results suggest that CLCuD complex has captured viruses that may have contributed to complete breakdown of resistance

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