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Understanding how pests rapidly adapt can help develop sustainable strategies for their management and improve agroecosystem health. Pest adaptation involves stable variations in DNA sequence, as well as dynamic shifts in gene expression, often mediated by non\u2010coding regulatory elements. We examined adaptation to plant defences in the soybean aphid,\n                    <jats:italic>Aphis glycines<\/jats:italic>\n                    , in which virulent aphids have overcome plant defences and avirulent aphids have not. Previous data with laboratory colonies suggested that virulent aphids have higher overall gene expression, including transposable elements, some of which influence gene regulation. However, we lack information on how genetic variation in natural populations impacts adaptation and potentially gene regulation. We integrated population genome scans of field\u2010collected, soybean aphid populations with gene expression profiles of virulent and avirulent laboratory colonies to uncover connections between genetic differentiation and gene regulation for virulence. Genome scan methods found 2144 single nucleotide polymorphisms (SNPs) with significant genetic differentiation (i.e., outliers) in field\u2010collected populations. These SNPs were near 1004 genes, representing 5.16% of the effective number of genes. Based on previous RNA\u2010Seq data with laboratory colonies, we found 3160 genes and 147 long non\u2010coding RNAs (lncRNAs) with differential expression among virulent and avirulent biotypes. By integrating both data sets, we identified 16 genes and 5 long non\u2010coding RNAs with differential expression and that were associated with an outlier SNP (within 10\u2009kbp). We validated SNPs with additional field collected aphids and found an aphid clone with stronger virulence than our laboratory virulent colony, surviving on 2 different aphid\u2010resistant soybean varieties. This new virulent clone had fixed allele differences at 9 SNPs compared to our avirulent and other virulent colony. Field collected soybean aphids matching the phenotype of this new virulent clone had significant genetic differentiation with 3 outlier SNPs near genes related to zinc transport and lachesin compared to field collected avirulent aphids. Our entire data reinforced the importance of a potential multi\u2010genetic response to overcome plant defence and generates new insights into complex genetic and regulatory mechanisms involved in insect\u2010plant interactions.\n                  <\/jats:p>","DOI":"10.1111\/mec.70536","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T09:21:27Z","timestamp":1788772887000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Adaptation to Plant Defence in an Agricultural Insect Pest: Integrating Genome Scans and Gene Expression in the Soybean Aphid Reveals Multi\u2010Genic Pathways"],"prefix":"10.1111","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2483-1207","authenticated-orcid":false,"given":"Vitor A. C.","family":"Pavinato","sequence":"first","affiliation":[{"name":"Department of Entomology, College of Food, Agricultural and Environmental Sciences The Ohio State University  Wooster Ohio USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin H.","family":"Penton\u2010Michel","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Food, Agricultural and Environmental Sciences The Ohio State University  Wooster Ohio USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9385-0925","authenticated-orcid":false,"given":"Saima","family":"Shahid","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics, College of Arts &amp; Science The Ohio State University  Columbus Ohio USA"},{"name":"Donald Danforth Plant Science Center  St. Louis Missouri USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5653-6996","authenticated-orcid":false,"given":"Jacob A.","family":"Wenger","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Food, Agricultural and Environmental Sciences The Ohio State University  Wooster Ohio USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9582-3533","authenticated-orcid":false,"given":"R. Keith","family":"Slotkin","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics, College of Arts &amp; Science The Ohio State University  Columbus Ohio USA"},{"name":"Donald Danforth Plant Science Center  St. Louis Missouri USA"},{"name":"Division of Biological Sciences University of Missouri\u2010Columbia  Columbia Missouri USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2953-9187","authenticated-orcid":false,"given":"Andy","family":"Michel","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Food, Agricultural and Environmental Sciences The Ohio State University  Wooster Ohio USA"},{"name":"The Center for Applied Plant Sciences The Ohio State University  Columbus Ohio USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"e_1_2_12_2_1","unstructured":"Alexa A. andJ.Rahnenfuhrer.2023.\u201ctopGO: Enrichment Analysis for Gene Ontology.\u201d(Version 2.54.0). 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