Location: Genomics and Bioinformatics Research2011 Annual Report
1a. Objectives (from AD-416)
The vulnerability of the cotton crop to near complete failure owing to infection by whitefly-transmitted geminiviruses has been of concern for some time, both before and since the release of Bt varieties. The cotton crop has limited genetic variability and therefore low versatility in traits. Plant viruses are capable of rapid diversification to pressures imposed by a static genetic structure of the host, a type of pathogen that is referred to as ‘emergent.’ In the major cotton producing regions of Pakistan and India (Punjab region), enormous yield losses have been associated with twelve or more emergent begomovirus species (and additional strains). Additional strains likely exist within the population that have not been discovered but that could emerge under changing selection pressures, including the continued increase of Bt cotton cultivation. A recent example is the emergence in Pakistan of the Burewala strain of Cotton leaf curl virus (CLCuV), which overcame the genetic resistance in newly released cotton lines in less than two years. Stable and durable resistance to these highly virulent viruses has become essential. To develop durable resistant varieties, new tools will be needed to assess the genetic diversity within the virus population and to understand how selection pressure influences population structure. In addition the adaptation of high throughput sequencing methods will be needed to assess virus population composition and dynamics, and new approaches will be required to quantify the viral load in germplasm assessed for susceptibility and resistance to the cotton leaf curl complex. Optimized virus detection methods will allow monitoring of virus population dynamics in relation to the performance of cotton germplasm lines and cultivars under natural field conditions where selection pressures are unknown and dynamic from year to year.
1b. Approach (from AD-416)
To preserve the effectiveness of resistant cotton lines, it is essential to be able to identify, characterize and monitor the different strains of CLCuV. New tools (predominately based on molecular biology approaches) will be needed to determine the range of different viral strains, track their changes and study how these changes affect virulence. Assessing the range of CLCuV strains, rates of change, and the effect on virulence will require the expertise of a virologist(s) well versed in the area of molecular biology.
3. Progress Report
Project startup included hiring of a postdoctoral researcher and a student worker to assist with routine lab support activities, and acquisition of necessary equipment and supplies for the lab at the University of Arizona. Researchers from the University of Arizona were instrumental in identifying collaborators in Pakistan and developing a set of objectives and general plan of work for characterizing the cotton leaf curl virus population, monitoring changes in the severity of cotton leaf curl disease on cotton, and finding links between specific sequences within the virus DNA and the level of disease in the plant. In anticipation of virus DNA samples that will be received during the 2011 crop season, a procedure for amplifying and sequencing virus DNA was successfully optimized. Methods to characterize whiteflies, which transfer cotton leaf curl virus from plant to plant, based on DNA sequence information were developed. Together, these methods will allow researchers to track changes in the virus and concurrent changes in the insect that transmits the virus. The research activities during this reporting period were monitored by the ADODR through email communications with the cooperator and through in-person discussions with the cooperator at professional society meetings and during a site visit to the USDA ARS research facility at Stoneville, MS.