A supergene controls facultative diapause in the crop pest Helicoverpa armigera.

Many insect species, including the economically important pest Helicoverpa armigera, avoid unfavorable conditions by suspending development. This form of phenotypic plasticity-facultative diapause-is a complex trait, though its evolution and intricate genetic architecture remain poorly understood. To investigate how such a polygenic trait could be locally adapted, we explore its genetic architecture. We map a large-effect diapause-associated locus to the Z chromosome by crossing high- and low-latitude populations. By generating multiple chromosome-scale assemblies, we identify an ∼5.93-Mb chromosomal inversion that constitutes the locus. Within this inversion, 33 genes harbor divergent non-synonymous mutations, notably including three circadian rhythm genes: Period, Clock, and Cycle. CRISPR-Cas9 knockout experiments confirm that each gene is independently essential for pupal diapause. Thus, a diapause supergene arose within H. armigera via a Z chromosome inversion, enabling local climatic adaptation in this economically important crop pest.