The Genomic Legacy of Ancient Polyploidy in Crop Domestication

Abstract Species that have an ancestry of whole-genome duplications (WGDs) are more likely to be domesticated, but the underlying mechanisms remain unclear. We tested whether paleologs—genes duplicated during ancient WGDs—are enriched in candidate domestication lists across 22 crop species spanning 17 genera. Paleologs were significantly enriched in 14 species, with single-copy paleologs showing the most consistent overrepresentation. In contrast, genes from small-scale duplications were consistently underrepresented among domestication candidates. This enrichment was independent of WGD age and degree of gene loss, indicating that constraint on copy number does not preclude selection on gene function. Several non-mutually exclusive processes could explain this pattern, including accumulated genetic diversity becoming available upon return to single-copy, selection to maintain essential functions, and greater selection efficiency on unmasked loci. Ancient WGDs thus provide a persistent genomic substrate for crop evolution millions of years later.