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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #331983

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: Non-cultivated cotton species (Gossypium spp.) act as a reservoir for cotton leaf curl begomoviruses and associated satellites

Author
item SHAKIR, SARA - University Of Agriculture - Pakistan
item ZAIDI, SYED SHAN-E-ALI - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
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 NAWAZ-UL-REHMAN, MUHAMMAD SHAH - University Of Agriculture - Pakistan
item MANSOOR, SHAHID - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item ATIQ, UR-REHMAN - National Institute Of Biotechnology And Genetic Engineering (NIBGE)

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/10/2019
Publication Date: 5/14/2019
Publication URL: http://handle.nal.usda.gov/10113/6472491
Citation: Shakir, S., Zaidi, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Nawaz-Ul-Rehman, M., Mansoor, S., Atiq, U. 2019. Non-cultivated cotton species (Gossypium spp.) act as a reservoir for cotton leaf curl begomoviruses and associated satellites. Plants. 8:127. https://doi.org/10.3390/plants8050127 .
DOI: https://doi.org/10.3390/plants8050127

Interpretive Summary: Begomoviruses are a group of viruses that have multiple plant hosts and are spread by whiteflies. They cause large crop losses worldwide and their ability to infect plants is influenced by the type and number of satellites that are found associated with the virus. Previous studies have reported that cotton can simultaneously contain multiple types of Begomoviruses. There is a new technology called next generation sequencing (NGS) that allows more efficient and inexpensive sequencing of viruses and satellites. This study used that technology to sequence the DNA of the viruses and satellites found in three species of cotton that had been growing for many years in Pakistan as part of an in situ living cotton collection. In each species, there were multiple types of viruses and satellites, proving that different Begomoviruses can co-exist in a plant. This information on the types and number of viruses and satellites present allows scientists to better understand how viruses function in plants and helps them develop more effective strategies to control viruses.

Technical Abstract: A collection of wild and cultivated species of cotton have been maintained for the last four decades at the Central Cotton Research Institute, Multan Pakistan. The availability of next generation sequencing technologies has provided new tools to evaluate the diversity of the begomovirus complex found in this historical collection. Rolling circle amplification (RCA) was used to amplify all circular DNA molecules which were used directly for sequencing using the Illumina MiSeq platform. Leaves were collected from Gossypium thurberi and G. raimondii, wild D genome diploid cotton species and G. mustelinum, an AD genome tetraploid species. All the species have a New World (NW) origin. A number of begomoviruses and betasatellites were found in G. thurberi and G. raimondii. The begomoviruses Cotton leaf curl Multan virus (Pakistan strain), Cotton leaf curl Alabad virus (Multan and Lobatum strain) and Bhendi yellow vein mosaic virus (Thanagan and Pakistan strain) were found in the diploid species evaluated. Two species of betasatellites, cotton leaf curl Multan betasatellite (Shahdadpur and Burewala strains) and okra leaf curl betasatellite were found in G. thurberi, while no alphasatellites were found in this host. This was contrasted with the presence of 5 distinct alphasatellites in tetraploid G. mustelinum. The alphasatellites identified were gossypium darwinii symptomless alphasatellite, gossypium davidsonii symptomless alphasatellite, ageratum yellow vein Singapore alphasatellite, cotton leaf curl Burewala alphasatellite and papaya leaf curl alphasatellite. Semi-quantitative analysis with Southern blot hybridization found that the comparative level of virus significantly decreased in the presence of alphasatellites. These results indicate that all these wild species were challenged by diverse begomoviruses and associated satellites via the whitefly vectors, but the host plant played a role in selectivity of begomoviruses and satellite species present. Our results provide a novel insight into understanding the diversity and spread of begomoviruses and associated satellites in NW cotton species introduced into the Old World.