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ARS Home » Southeast Area » Auburn, Alabama » Soil Dynamics Research » Research » Research Project #445380

Research Project: Integrated Crop Disease Mitigation through Improved Understanding of Relationships between Genetics, Environment, and Management

Location: Soil Dynamics Research

Project Number: 6010-21600-001-000-D
Project Type: In-House Appropriated

Start Date: Nov 2, 2023
End Date: Nov 1, 2028

1. Determine biological, ecological, and molecular characteristics of cotton leaf roll dwarf virus (CLRDV) and other pathogens to prevent and mitigate diseases that may negatively impact agronomic crop production. 1.A. Develop molecular and serological methods to improve CLRDV detection in the vector, the cotton host, and alternate hosts. 1.B. Perform high throughput sequencing to characterize the virome of cotton and cotton infesting aphids to generate knowledge about potential mixed infections with other viruses. 1.C. Monitor variants of CLRDV and other introduced diseases that have potential to reduce yield. 2. Mitigate negative impacts of CLRDV through improved understanding of pathogen epidemiology, including insect vectors, alternative plant hosts, and climate conditions. 2.A. Quantify CLRDV incidence, symptomology, and vector dynamics to identify soil and environmental factors correlated with at-risk production areas. 2.B. Characterize progression and titers of CLRDV over time. 2.C. Measure cotton plant physiological response (i.e., photosynthetic activity, stomatal conductance) to CLRDV infection under ambient and elevated CO2 levels over time. 3. Develop agronomic practices for diverse cotton germplasm in large- and small-scale production systems to minimize yield loss from CLRDV and other diseases. 3.A. Develop agronomic and weed management practices to reduce CLRDV incidence. 3.B. Define CLRDV symptoms and differentiate them from nutrient deficiency symptoms in cotton.

Recent increases in temperature, drought, and extreme weather events create additional stresses on key commodity crops. These stresses have a number of impacts, but one is that they can lower the plant’s immune response which can increase disease incidence and severity and insect infestations, ultimately reducing yields. One pathogen, present in other parts of the world for many years but first discovered in the United States (U.S.), (Alabama) in 2017, is the cotton aphid-transmitted cotton leafroll dwarf virus (CLRDV). Since that time, the virus has been found across 10 states of the U.S. Cotton Belt, but the U.S. CLRDV strain is genetically different from previously identified ‘typical’ and ‘atypical’ strains that cause cotton blue disease in Asia and South America. This research will investigate how to mitigate infection, spread, and yield loss caused by CLRDV using molecular, genetic, and management techniques to understand host-virus-vector dynamics and symptomology that will complement and enhance agronomic practices. In objective 1, we will improve detection techniques to confirm presence of CLRDV, characterize the virome of both host and aphid vectors, and monitor for variants of the virus. These aspects are important because cotton plants may appear asymptomatic, although growth is inhibited, which can result in yield losses. In objective 2, we will focus on how the vector transmits and spreads CLRDV, characterize the symptomology of the disease, and monitor how cotton plant physiology is affected over time following infection. Management practices may be one factor that could influence observed variability in CLRDV yield losses, but these effects are currently unknown. In objective 3, we will examine interactions between CLRDV and management practices that include stalk destruction methods, conservation tillage and non-host high residue cover crops, as well as soil nutrient levels to better define yield loss variability. This interdisciplinary project will benefit the U.S. cotton industry by providing better assessment tools for the disease as well as applied solutions to minimize negative impacts of CLRDV in the U.S.