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This project addresses the development of a disease management solution by deepening our understanding of interactions between the U.S. cotton crop and its new viral pathogen. TheCotton Leafroll Dwarf Virus(CLRDV; genusPolerovirus, familyLuteoviridae),which causes Cotton Blue Disease,is regarded as the second most damaging viral disease to commercial cotton production worldwide. This viruswas first described in African and has since spread to major cotton-producing countries in South America and Asia. In 2018, numerous cotton fields across the Southeastern states were observed to have symptomatic plants resembling a viral disease, which was later confirmed to be infected with an RNA virus resembling CLRDV. Phylogenetic analyses have nowshown that the CLRDV isolates collected from the across U.S. cotton-belt are monophyletic and form a different clade from CLRDVisolatesfrom South America, suggesting that the U.S. virus is a novel genotype resulting from a single introduction that likely occurred recently. This newly introduced virus may pose a significant threat to U.S. cotton and highlight the need to identify management strategies to avert or mitigate the economic impact on cotton production. Deployment of resistant cultivars has been shown to be the most efficacious strategy for managing CLRDV in South America. However, resistance lines from Brazil were found to be susceptible to the U.S. isolate, suggesting that breeding for host-plant resistance will necessitate additional screening to identify new sources of resistance and DNA markers linked to the resistance genes. The goals of the project are to identify and release newly identified sources of resistance to CLRDVand todevelop an understanding of thegenetic mechanisms of host-plant resistanceand use breeding approaches to deliver grower-improved solutions (biomarkers) in the short and medium time scale.Identification of germplasm resistant to the virus will have an immediate impact on U.S. cotton breeding programs across the public and private sectors, while the knowledge generated on the genetics of resistance and the molecular breeding tools developed to expedite the development of resistant cultivars will ensure the economic and environmental viability of the cotton industry. The specific objectives of this project are to: 1) identify sources of resistance to CLRDV in Upland cotton, 2) genetic mapping to identify diagnostic markers for the resistant gene(s), and 3) elucidate and characterize putative defense genes against the reddening and leaf downward cupping symptoms that are commonly associated with CLRDV.Objective 1:Identify sources of resistance to CLRDV in Upland cotton.Preliminary screening conducted at two Alabama locations in 2019 showed that six percent of the 800 public germplasm accessions including wild race stocks, obsolete varieties, and elite breeding lines to be a non-host for the CLRDV virus via the presence or absence of symptoms and RT-PCR diagnostic assay. As a foundation for the project, we will validate the putative resistant lines to confirm the phenotype observed as well as evaluate for productivity and fiber quality. Additionally, we will screen an additional 200 elite breeding lines not tested in 2019.Objective 2:Genetic mapping to identify diagnostic markers for the resistant gene(s).Two complementary approaches will be utilized for marker-trait association analysis. First, a GWAS analysis will be conducted on approximately 1,000 lines currently being screened in Activity 1. Second, marker-trait association analysis will be conducted using already developed F2:3populations developed by crossing two resistant lines from diverse origins to a common susceptible parent from an elite background. Additionally, we will draw on populations that are segregating for a specific symptomology described in activity 3 (below).Objective 3:Elucidate and characterize putative defense genes against the reddening and leaf downward cupping symptoms that are commonly associated with CLRDV.In Alabama and Georgia, the most commonly observed symptoms of infected plants are the reddening and downward cupping/weathering of leaves in seedlings with mature plants also exhibiting leaf rolling and shortening of internodes. We have observed several F2populations in a breeding nursery segregating for these symptoms and have identified parents that are contributing to these phenotypes. We will conduct a comparative transcriptome profiling study via RNA sequencing on the three parental lines of populations segregating for leaf reddening and downward cupping symptoms as described in Objective 2 to identify differentially expressed genes in symptomatic and asymptomatic plants during CLRDV infection.By focusing on genes in the genomic region identified in Activity 2, we seek to identify putative candidates for the causal gene.

Chee, P.
University of Georgia
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