Potato is the most important tuber crop. However, the complexity of tetrasomic inheritance and clonal propagation limit the genetic gain of potato breeding. To reinvent the potato into an inbred line-based diploid on the basis of true seeds, the research team of Sanwen Huang initiated the Upotato Plan, which aims to transform potato breeding from a slow, non-accumulative mode into a fast-iterative one.

In order to accelerate the hybrid potato breeding, this study constructed the pan-genome of wild and cultivated potatoes. The researchers observed pervasive intra- and inter- group discordance, suggesting a complex history of potato evolution, including extensive hybridization and incomplete lineage sorting. The expansion of NLR genes in potato may contribute to protecting stolon or tuber from pathogen infection. The researchers applied a multi-omics comparative analysis and identified a TCP transcription factor that plays a pivotal role in tuber initiation, therefore it was named Identity of Tuber1 (IT1).

Taken together, this study provides critical insights into the tuber evolution, and lays a solid foundation for genome design of hybrid potato that will revolutionize the genetic improvement of this globally important crop, as well as builds a feasible framework of pan-genome studies that can be followed by other crops.