Population Genomics of Agricultural Insect Pests

Population genomics offers a transformative lens on the genetic variation, evolutionary dynamics and adaptive potential of insect pests that imperil global agriculture. By surveying genome-wide patterns of polymorphism across individuals and populations, researchers can reconstruct invasion pathways, assess gene flow among fragmented habitats and detect signatures of selection underlying resistance to pesticides or novel environmental pressures. High-throughput sequencing approaches—ranging from reduced-representation techniques to whole-genome resequencing—yield dense single-nucleotide polymorphism datasets that underpin analyses of population structure, demographic history and local adaptation. These insights inform integrated pest management by pinpointing source populations for targeted eradication, anticipating the spread of resistance alleles and guiding landscape interventions such as crop rotation or refugia design. Studies to date have revealed marked genetic differentiation in pests such as the Colorado potato beetle, boll weevil and brown stink bug, alongside genomic regions swept to fixation by decades of insecticide use. By linking ecological context with genomic data, the field is maturing into a predictive science capable of safeguarding crop yields, enhancing biosecurity and sustainably managing evolving pest populations worldwide.

Research from Nature Portfolio

A novel panel of X-linked microsatellite markers has been applied to the Colorado potato beetle, revealing extensive haplotype diversity and regional migration corridors that inform on dispersal routes and local adaptation. Analyses of over a thousand individuals identified discrete clusters of X-haplotypes, uncovering both east–west barriers and north–south corridors aligned with river systems, and quantifying frequent polyandry in discrete families. In a complementary study, a copy-number variation assay for sex determination in the same species was developed using quantitative PCR. By contrasting an X-linked voltage-gated sodium channel gene with an autosomal reference, researchers achieved 100% accuracy in sexing adults and larvae, providing a rapid tool for population monitoring and experimental studies of sex-biased dispersal and fitness.

Population Genomics of Agricultural Insect Pests publication trend

The graph below shows the total number of articles in population genomics of agricultural insect pests across all publications each year (not limited to Nature Index journals).

Technical terms

Single-nucleotide polymorphism (SNP): A genome position at which individuals differ by a single base, used as a marker of genetic variation.

Genotyping-by-sequencing (GBS): A reduced-representation approach that sequences a subset of the genome to identify SNPs across many individuals.

Double-digest restriction site-associated DNA sequencing (ddRADseq): A method for sampling consistent genomic fragments via enzyme digestion, enabling population-level SNP discovery.

Selective sweep: The process by which a favourable mutation increases in frequency, reducing genetic variation at linked loci.

Haplotype: A set of alleles at adjacent loci on a chromosome that are inherited together, useful for tracing lineage and migration.

References

1. Investigation of genetic diversity and polyandry of Leptinotarsa decemlineata using X-linked microsatellite markers. Scientific Reports (2023).
2. Detection of sex in adults and larvae of Leptinotarsa decemlineata on principle of copy number variation. Scientific Reports (2022).
3. Population Genomics of the Neotropical Brown Stink Bug, Euschistus heros: The Most Important Emerging Insect Pest to Soybean in Brazil. Frontiers in Genetics (2019).
4. Population genomics and phylogeography of the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), in the United States, northern Mexico, and Argentina. Evolutionary Applications (2021).
5. Selective Sweeps in a Nutshell: The Genomic Footprint of Rapid Insecticide Resistance Evolution in the Almond Agroecosystem. Genome Biology and Evolution (2020).