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.

种间杂交（interspecific hybridization）可通过产生全新的等位基因（allele）组合与新颖性状（trait），触发物种辐射演化（species radiation）。栽培马铃薯（cultivated potato）及其源自Petota谱系（Petota lineage）的107个野生种均具有独特的块茎器官，但块茎形成（tuberization）的内在机制以及该类群广泛的物种分化（species diversification）过程仍不明晰。本研究通过对128个基因组（genome）进行分析，其中包含58个全新的单倍型解析基因组（haplotype-resolved genome），揭示出Petota谱系起源于古老杂交事件，所有类群均呈现稳定的混合基因组祖先遗传组分，其祖先源自约800万至900万年前的Etuberosum类群与番茄谱系（Tomato lineage）。本研究的功能实验（functional experiment）进一步验证了亲本基因（parental gene）在块茎形成过程中的关键作用，表明种间杂交是该创新性状形成的核心驱动因素。该性状连同杂交衍生多态性位点（polymorphism）的分选与重组过程，通过促使类群占据更广泛的生态位（ecological niche），极有可能引发了Petota谱系的爆发式物种分化。本研究结果阐明了古老杂交如何推动关键性状创新，并进而驱动后续的物种辐射演化。