Graph-based pangenome provides insights into the structural variation and genetic basis of metabolic traits in potato.

Potato is the world's most important nongrain crop. Here, we report that 29 genomes from Petota and Etuberosum sections were de novo assembled, and that 248 accessions of wild potatoes, landraces and modern cultivars were re-sequenced at > 25× depth to assess genetic diversity within the Petota section. Subsequently, a graph-based pangenome was constructed by using DM8.1 as the backbone integrated 194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 accessions, and 9,321 SVs were detected to be significantly associated with 1,258 distinct metabolites via PAV-based metabolomics-GWAS analysis, including metabolites of flavonoids, phenolic acids and phospholipids. To facilitate the utilization of pangenome resources, a comprehensive platform, the potato pangenome database (PPDB, http://101.201.107.228:16666/), was developed for the potato community worldwide. Our study provides a comprehensive genomic resource that enables us to assess the genomic basis of agronomic and metabolic traits, and the genomic dataset resources will accelerate functional genomics studies and genetic improvements in potato.