Development of molecular markers for early detection of insecticide resistance in Spodoptera frugiperda and Euschistus heros using transcriptome and whole genome sequencing analyses

Abstract

The continued exposure to insecticides imposes a strong selective pressure upon target site mutations and almost invariably leads to resistance evolution. The development of means to reliably monitor resistance can be of great advantage to pest and resistance management helping the decision-makers to implement better and more sustainable strategies to delay chemical control failure in the field. Yet, the challenge resides on the fact that resistance to insecticide can be the product of multiple mechanisms and interconnected physiological pathways that make the recognition of its factors rather challenging. Unfortunately, the currently used methodologies such as the phenotypic and the genotypic methods still suffers from major hurdles involving cost and the laboriousness of laboratory colony maintenance and large-scale cross assays to detect rare alleles. The development of high-throughput DNA and RNA sequencing technologies are now powerful tools that can be used to detect mutations associated with the resistance phenotype allowing the development of reliable markers and the elucidation of complex physiological mechanisms involving gene expression and gene regulation. Our main goal with this project is to develop molecular tools for the detection and genotyping of resistant variant alleles present in field populations. Such tools can be used in the insect resistance monitoring effort of Spodoptera frugiperda and Euschistus heros also offering prospects for mechanism elucidation and new forms of control. In the case of S. frugiperda we propose to use the reference genome to map RNA- (i.e. transcriptome) and DNA-based (GBS) markers and to use GWAS and TWAS approaches to detect putative markers associated with resistance to the insecticide spinosad. For E. heros, we propose the whole sequence of the genome (WGS) to be later use in mapping or the association studies of resistance genes in populations this emerging species.