Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)

Authors: DOELLMAN, MEREDITH - University Of Notre Dame; HOOD, GLEN - Wayne State University; GERSFELD, JACOB - University Of Notre Dame; DRISCOE, AMANDA - University Of Notre Dame; XU, CHARLES C.Y. - McGill University - Canada; SHEEHY, RYAN - University Of Notre Dame; HOLMES, NOAH - University Of Notre Dame; Yee, Wee; FEDER, JEFF - University Of Notre Dame

Submitted to: Annals of the Entomological Society of America
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2019
Publication Date: 3/1/2020
Citation: Doellman, M.M., Hood, G.R., Gersfeld, J., Driscoe, A., Xu, C., Sheehy, R., Holmes, N., Yee, W.L., Feder, J. 2020. Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae). Annals of the Entomological Society of America. 113(4):246-256. https://doi.org/10.1093/aesa/saz069.
DOI: https://doi.org/10.1093/aesa/saz069

Interpretive Summary: The apple maggot fly is an important quarantine pest of apples in the Pacific Northwest of the U.S. that is monitored using traps. The similar-looking snowberry maggot fly is frequently caught on these traps and can be mistaken for apple fly, which could lead to unjustified quarantines. Personnel at the University of Notre Dame, IN, Wayne State University, Detroit, MI, McGill University, Canada, and USDA-ARS in Wapato, WA, determined cheap, quick and reliable methods for discriminating the two fly species. A simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers was developed. In addition, a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products was able to distinguish the fly species. Results are important in that they present an effective strategy for apple maggot and are transferable to many cryptic pests.

Technical Abstract: Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.