Population genomics reveals population structure and local adaptation of the Helicoverpa armigera lineage in Xinjiang, China

Abstract BACKGROUND The cotton bollworm, Helicoverpa armigera , is a global pest of many crops, particularly cotton. Populations in Xinjiang (north‐western China) are distinct from other major lineages in eastern China and elsewhere. Cotton is grown in Xinjiang in a wide range of climatic conditions but little is known about H. armigera population structure and gene exchange, either within Xinjiang or between it and the eastern China populations. RESULTS Population structure analyses showed significant gene flow throughout Xinjiang but the western‐most collections, Kashi and Shawan, were the most divergent, both from each other and from the other collections. Demographic history dynamics revealed a peak in ancestral population size for Xinjiang populations during a relatively warm and humid period about 5000–10 000 years ago. Selective sweep analyses found local adaptation of genes in Kashi including several CYP9A genes and two trehalose transport 1 ( Tret1 ) genes, and genes in Shawan including several CYP6AE genes plus the basic juvenile hormone‐suppressible protein 1 gene ( BJSP‐1 ) and two Methuselah genes. Spikes of introgression including the cyc , tim and per genes related to circadian rhythm were also detected between Kashi and/or Shawan and other Xinjiang populations. CONCLUSION Helicoverpa armigera from Shawan and Kashi are genetically differentiated from each other and from other Xinjiang populations at the whole‐genome level. Despite some evidence of introgression, they also show evidence for local adaptation in genes related to detoxification, various stress tolerances and development. Management strategies against H. armigera in Xinjiang should consider these regional differences. © 2025 Society of Chemical Industry.