Ancient hybridization underlies tuberization and radiation of the potato lineage

Interspecific hybridization may trigger species radiation by creating novel allele combinations and new traits. Cultivated potato and its 107 wild species from the Petota lineage all share the distinctive tuber organ, but the underlying mechanisms for tuberization and extensive species diversification remain unclear. Through analyses of 128 genomes, including 58 novel haplotype-resolved genomes, we revealed that Petota is of ancient hybrid origin, with all members exhibiting stable mixed genomic ancestry, derived from the Etuberosum and Tomato lineages ca. 8–9 million years ago. Our functional experiments further validated the crucial roles of parental genes in tuberization, indicating that interspecific hybridization is a key driver of this innovative trait. This trait, along with the sorting and recombination of hybridization-derived polymorphisms, likely triggered the explosive species diversification of Petota by enabling the occupation of broader ecological niches. These findings highlight how ancient hybridization fosters key innovation and drives subsequent species radiation.