Date of Award

5-2022

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Plant and Environmental Science

Committee Chair/Advisor

Dr. Christopher A. Saski

Committee Member

Dr. Matthew Cutulle

Committee Member

Dr. Nishanth Tharayil

Abstract

Weed and insect pests cost the agricultural sector billions in losses each year across the world, despite distributing over 1 billion pounds of potentially harmful chemicals into agroecosystems to manage these pests. Two major agricultural pests that are rapidly adapting to multiple xenobiotics are Amaranthus palmeri and Musca domestica. A. palmeri, or Palmer amaranth, is highly productive in terms of vegetative structures and reproductive propagules. Palmer amaranth has evolved multiple resistance mechanisms to several herbicidal modes of action. House fly (M. domestica) presents issues as a vector for pathogenic microbes among livestock, poultry, and humans. This insect pest has evolved resistance to almost all forms of common insecticides. The frequency, distribution, and strength of pesticide resistance in agricultural pests is increasing while we rapidly attempt to prevent further crop losses, harm to livestock or poultry, and contamination of human environments.

This research presented herein explores extrachromosomal circular DNA (eccDNA) as a dynamic genomic mechanism underlying directed pesticide resistance and as an innate component of the cell that enables rapid adaptation to general environmental stresses in agricultural pests. EccDNA are loops of DNA separate and derived from linear chromosomes that are heterogenous in size and genetic content. EccDNAs are ubiquitous across kingdoms and have been described in yeast, plants, Drosophila, humans, and many other eukaryotic organisms. Stressed organisms or cells appear to have increased amounts of eccDNA, while eccDNA encoded genes are often highly expressed during these episodes.

Circular DNA enrichment sequencing (CIDER-Seq) detected thousands of eccDNA sequences in both A. palmeri and M. domestica. Genetic characterization of eccDNAs discovered genes found on eccDNAs were often related to protein synthesis, and most notably, herbicide resistant Palmer amaranth eccDNA contained the EPSPS gene for glyphosate resistance and insecticide resistant house fly eccDNA had an abundance of cytochrome P450 domains likely to endow insecticide resistance. Various structural components of eccDNA contribute to genetic heterogeneity in these agricultural pests and are likely important for maintaining homeostasis under harsh conditions.

The discoveries of eccDNA and their role in agricultural pests provides a foundation for new research avenues to fully understand their genesis, function, and maintenance in the cell. The resulting information from these studies can also be used to develop advanced biotechnology approaches that target eccDNA for improved integrated pest management strategies.

Available for download on Saturday, April 22, 2023

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