Location: Tropical Pest Genetics and Molecular Biology Research Unit
Project Number: 2040-30400-003-000-D
Project Type: In-House Appropriated
Start Date: Oct 15, 2025
End Date: Oct 14, 2030
Objective:
Objective 1: Perform foundational genomic research for emerging and established invasive arthropod pests of specialty crops, especially, tephritid fruit flies, to assist in the development of novel tools and approaches for the detection of pestiferous species in support of exclusion, eradication, and integrated pest management strategies.
Sub-objective 1A: Develop emerging approaches for integration of whole genome, transcriptome, and epigenetic sequencing towards elucidating novel mechanisms in invasive species.
Sub-objective 1B: Characterize the function of genomic variants in target arthropods from historic collections for population genetic analysis to identify genes and variants associated with invasion.
Sub-objective 1C: Perform foundational genomic research for emerging and established invasive arthropod pests of specialty crops, especially tephritid fruit flies, to assist in the development of novel tools and approaches for the detection of pestiferous species in support of exclusion, eradication, and integrated pest management strategies.
Objective 2: Develop improved sterile insect technique or other genetic biocontrol methods to enhance their production and efficacy for field applications.
Sub-objective 2A: Functionally characterize genes that have applications to pest management strategies to create new SIT strains.
Sub-objective 2B: Characterize and develop microbial isolate(s) from wild fruit flies for reintroduction into rearing systems to enhance sterile male performance.
Sub-objective 2C: Assess impacts of micronutrient additions to adult diet on male fruit fly reproductive potential, survival, and microbiome composition and functioning.
Objective 3: Enhance biological control of tropical crop pests, such as fruit flies, by identifying and characterizing mechanisms by which natural enemies or infectious agents impact pest insects, improving their detection and discrimination of species, and developing improvements in biocontrol production.
Sub-objective 3A: Determine the role of endogenous and associated viruses in parasitoid wasp associated with subtropical fruit flies.
Sub-objective 3B: Evaluate and compare potential entomopathogenic agents against tropical insects.
Approach:
Goal 1A: Implement and demonstrate emerging approaches in telomere-to-telomere sequencing, high-throughput full length isoform sequencing, and nucleosome mapping/regulatory element prediction approaches on single molecule sequencing platforms towards generation of “holistic” genomes in target pest and beneficial species. Using single molecule sequencing platforms, whole genome, transcriptome, and epigenome sequencing will be performed. Bioinformatic analysis will be used to generate analysis and data visualizations. Goal 1B: Identify genomic variants associated with invasive tephritid populations to improve understanding of their geographic origin and phenotypes that are conducive to invasion. Collections of outbreak populations of tephritid fruit flies will be subjected to whole genome sequencing. Population genomic analyses will be used to characterize the outbreak dynamics. Research Goal 1C: Generate a transgenic line in an invasive arthropod pest that endogenously expresses a functional Cas9 and explore cryopreservation of tephritids or other invasive insect species embryos. Cas9 expressing plasmids will be injected into fly lines to generate flies which express Cas9 during the embryo stage. The long-term storage of these lines will be tested using liquid nitrogen cryopreservation. Research Goal 2A: Identify genes and regulatory elements that are sex-specific autosomal or on sex-linked chromosomes (X and Y in Tephritidae) that can be manipulated to induce male-sterility, sex-marking, or sex-linked conditional lethal traits. Functional genomic data will be generated to characterize novel regulatory elements and genes on the sex chromosome that can then be tested using CRISPR or transgenesis to drive novel sex conditional traits. Research Hypothesis 2B: Mass-rearing has adverse impacts on microbiome diversity and function that adversely impacts the competitiveness of fruit flies reared for SIT and systematic introductions of strain(s) can improve performance metrics. Microbiome profiling will be performed on mass reared flies and the ability to manipulate the microbiome community will be assessed along with characterization of performance metrics of flies with manipulated microbiomes. Research Hypothesis 2C: Adult diet nutritional composition impacts the production of sperm and re-mating potential of mass-reared Mediterranean fruit flies. Diet nutrition will be manipulated using a chemically defined diet and the performance metrics of flies will be measured. Research Goal 3A: Determine the role of an endogenous virus in a cryptic parasitoid complex. Competition of two related biocontrol wasp species will be evaluated across species of host fruit flies, and the role of associated viruses on success will be determined. Research Goal 3B: Evaluate putative pathogenic bacteria against larvae and adult insects to determine their pathogenic potential and sequence their reference genomes to identify potentially novel virulence factors. Whole genome sequencing will be performed on bacterial isolates cultured from host flies, and those isolates will be screened for pathogenic traits.