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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #335578

Research Project: Phase 2 Enhancing Cotton Germplasm, Improving Resistance to Cotton Leaf Curl Virus and Supporting Cotton Best Management Practices for Small Farmers

Location: Genomics and Bioinformatics Research

Title: Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton

Author
item ZUBAIR, MUHAMMAD - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item ZAIDI, SYED SHAN-E-ALI - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item SHAKIR, SARA - Ayub Agricultural Research Institute
item FAROOQ, MUHAMMAD - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item AMIN, IMRAN - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item Scheffler, Jodi
item Scheffler, Brian
item MANSOOR, SHAHID - National Institute Of Biotechnology And Genetic Engineering (NIBGE)

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2017
Publication Date: 4/6/2017
Citation: Zubair, M., Zaidi, S., Shakir, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Mansoor, S. 2017. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Scientific Reports. 7:article number 680. doi:10.1038/s41598-017-00727-2.

Interpretive Summary: Cotton leaf curl disease (CLCuD) is a devastating virus in Pakistan and is spreading to other countries. Millions of bales of cotton are lost each year due to this virus. Although there are currently no resistant varieties available, elite lines have been developed and should be available as varieties within a few years. CLCuD can be caused by different strains of the same virus, much like influenza in humans. Monitoring of the strains found in cotton grown in Pakistan, indicated that in the Vehari area of the country, the strains present in cultivated cotton may be changing and require the stacking of multiple resistance genes to develop varieties with sustainable resistance to the CLCuD complex. In Response to these findings, the stacking of multiple types of resistance genes has already begun. These lines should give the plant breeder more weapons to use in mitigating the effects of cotton leaf curl virus disease.

Technical Abstract: The first epidemic of cotton leaf curl disease (CLCuD) in the early 1990’s on the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in the late 1990’s, but resistance was broken in early 2000. There only a single recombinant begomovirus named Burewala strain of cotton leaf curl Khokhran virus (CLCuKoV-Bu) was found in cultivated cotton. This strain lacks the full complement of a gene encoding a transcription activator protein (TrAP). However, we recently found isolates of CLCuKoV-Bu with a full complement of TrAP. Symptomatic plants from a cotton field at Vehari were collected and next generation sequencing (NGS) as well as cloning and Sanger 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, as well as several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These cloned viruses possess a full complement of TrAP gene. A new strain of betasatellites was also identified and named CLCuMuBVeh. Stacking of multiple sources of resistance is needed to provide varieties with sustainable resistance to CLCuD.