Linkage drag can hinder the integration of resistance genes from wild crop relatives into breeding programs. We used a chromosome-scale Nicotiana alata genome assembly and a segregating population exceeding 160,000 plants to dissect the complex genetic architecture and overcome the tight linkage between resistance and deleterious loci to produce plants free from linkage drag. We cloned N. alata RTSW , encoding an immune receptor that confers broad-spectrum resistance to orthotospoviruses through the interaction of its carboxyl-terminal domain with an orthotospovirus-encoded protein. Notably, despite recognizing the same avirulence factor, RTSW genes from N. alata and Sw-5b from Solanum peruvianum have evolved independently of adjacent nonorthologous ancestral loci. Our work illustrates the potential of wild relative genomes as resources from which to precisely introduce disease resistance into cultivated crops.