Solanum tuberosum Raw sequence reads. Solanum tuberosum

Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. Here, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the rewiring of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja, and identified a jasmonic acid biosynthetic gene possibly affecting tuber dormancy period. Genome-wide association studies revealed a novel UDP-glycosyltransferase gene for biosynthesis of antinutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated tetraploid potatoes originated from the diploid S. tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato breeding practices.