Utility and challenges of using whole‐genome resequencing to detect emerging insect and mite resistance in agroecosystems

Abstract

Since the advent of modern agriculture, humans have competed with other species for food and fiber. To eliminate this competition, myriad physical, chemical, and biological control measures have been applied in agricultural ecosystems (agroecosystems). Melander (1914) was the first to recognize that when these competition-reducing measures, collectively called "pest management," are applied repeatedly, some pest populations evolve resistance to their effects.Although the pest management tools used in agroecosystems have changed since Melander's original work, the propensity of pests to evolve resistance has not. Today, resistance is defined as a genetically-based decrease in the susceptibility of a population to a pest management tool that results from exposure in the field (Tabashnik et al., 2013;Walsh et al., 2022).Pesticide resistance was recently described as a "wicked problem," partly because its complex underlying biological, sociological, and economic drivers make it difficult to prevent (Gould et al., 2018).

Polygenic basis of Bt Cry resistance evolution in wildHelicoverpa zea

“…It is possible that gene duplication may be more likely to underlie rapid phenotypic evolution than other variant types, but the prevalence of structural variants is not well described as detection is difficult with current technologies (Ho et al, 2020; Mahmoud et al, 2019). As gene amplifications have frequently been linked to resistance evolution, genomic monitoring for resistance should be extended to consider a range of genomic variant types beyond SNPs (Fritz 2022).…”

“…One meta-analysis estimated that resistance evolved on average within 14 years of the release of a new chemical control measure (Brevik et al, 2018). In arthropods alone, resistance to over 300 pesticidal compounds in more than 600 species has been documented (Fritz, 2022; Mota-Sanchez & Wise, 2022). Keeping pace with pest resistance evolution is a significant challenge, as discovery and development of new control measures is time consuming and costly (Gould et al, 2018; Sparks, 2013).…”

“…One common feature of agroecosystems is the use of population suppression practices, which exert strong pressure on socalled agricultural pests to evade management through resistance evolution. High levels of resistance can evolve rapidly (Brevik et al, 2018), and in arthropods alone, resistance to over 300 pesticidal compounds in more than 600 species has been documented (Fritz, 2022;Mota-Sanchez & Wise, 2022). Rapid pesticide resistance evolution also has economic and environmental consequences, which provides incentive for its study.…”

Extended Sentinel Monitoring of Helicoverpa zea Resistance to Cry and Vip3Aa Toxins in Bt Sweet Corn: Assessing Changes in Phenotypic and Allele Frequencies of Resistance

“…More effective monitoring approaches are clearly needed to identify resistance early enough to enable proactive mitigation measures [44,46,54]. Fritz [55] reviewed the successes and limitations of genomic methods to detect and understand mechanisms of insect resistance, but further advancements are likely needed before they can provide an adequate warning of early stages of resistance to Bt toxins. Several EPA scientific advisory panels [56][57][58][59] have addressed the limitations and challenges of the diet bioassay approach used by registrants, as well as the utility of sentinel plot monitoring.…”

Evolution in agricultural systems: Moving toward the understanding of complexity

“…Second, decades of curiosity‐driven studies in agricultural fields have been contributing not only to finetune predictions, but also to develop diagnostic methods and tools to better manage agricultural fields (Mavridis et al, 2022 ). For example, Fritz ( 2022 ) discusses the possibility of using whole genome scanning, by means of genomic approaches and bioinformatic tools, to monitor, in real time, the dynamics of resistant genotypes in agroecosystems.…”