A short-chain dehydrogenase/reductase gene confers resistance to Verticillium wilt in cotton and reveals adaptive selection during domestication

• The cotton gene GhSDR500 regulates defense against Verticillium dahliae A G>C mutation in the NAD domain of GhSDR500 was identified, with the G allele strongly selected in modern cultivars. • GhSDR500 is upregulated in resistant cotton during early infection. • Silencing GhSDR500 increases susceptibility to V. dahliae . Cotton is a globally important fiber crop that faces significant yield losses due to Verticillium wilt caused by Verticillium dahliae . Short-chain dehydrogenase/reductases (SDRs) are NAD(P)(H)-dependent enzymes involved in metabolic pathways and stress responses, but their role in disease resistance is not well understood in cotton. The objective of this study was to investigate the function of GhSDR500 in cotton defense against V. dahliae . A combination of population genetics, pangenome analysis, gene expression profiling, transcription factor binding analysis, and functional validation through Virus-Induced Gene Silencing (VIGS) was employed. Population genetic analysis revealed a favorable GhSDR500 allele selected during cotton domestication. A G>C mutation causing a glycine-to-alanine substitution in the NAD domain was identified, with the G allele strongly favored in modern cultivars due to its association with enhanced resistance. Pangenome analysis further highlighted presence–absence variations and transposable elements around GhSDR500 . Expression studies showed strong upregulation of GhSDR500 in resistant cotton varieties during early infection stages. VIGS confirmed its role in disease resistance, as silencing GhSDR500 increased susceptibility to V. dahliae and reduced expression of pathogenesis-related genes. Transcription factor binding analysis identified WRKY genes as key regulators. These results demonstrate that GhSDR500 plays a key role in resistance to V. dahliae and represents a potential target for breeding Verticillium wilt-resistant cotton varieties.