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.

As key regulators of the Jasmonates (JAs) signal transduction pathway, JAZ protein, and MYC transcription factors are imperative for plant response to external environmental changes, growth, and development. In this study, 18 StJAZs and 12 StMYCs were identified in potatoes. Their chromosomal position, phylogenetic development, gene structure, and promoter cis-acting parts of the StJAZ genes were analyzed. In addition, Protein–Protein Interaction (PPI) network analysis of StJAZ and StMYC gene families and yeast two-hybrid assay demonstrated that five StMYCs can interact with 16 StJAZs, which provides new insights into the operation mechanism of StJAZs and StMYCs in JA signal response. Moreover, we explored the expression profiles of StJAZs and StMYCs genes in different tissues and during abiotic stresses by RNA-seq data. Based on the PPI network and transcriptome data, the genes StJAZ11, StJAZ16, and StMYC6 were chosen for further qRT-PCR study under salt or mannitol treatment. Under mannitol-induced drought or salinity treatment, the expression patterns of StMYC6, StJAZ11, and StJAZ16 were different, indicating that the JAZ protein and MYC transcription factor may be engaged in the response of potatoes to abiotic stress, which opened up a new research direction for the genetic improvement of potatoes in response to environmental stress.

Purple-fleshed potatoes accumulate high amounts of anthocyanins, which are beneficial to human health. Although the biosynthesis of these secondary metabolites has been well studied in plants, the mechanisms underlying anthocyanin accumulation in different tissue regions of potato tubers remain less understood. To identify genes and metabolites involved in anthocyanin accumulation, we performed comparative transcriptomic and metabolomic analyses of pith and vasculature tissues from the tubers of three different potato cultivars. Anthocyanin-targeted metabolome analysis revealed that 20 anthocyanins were key metabolites conferring purple pigmentation in the tuber. Integrated transcriptomic and metabolomic analysis identified 1,924 genes potentially involved in multiple pathways for the biosynthesis of these anthocyanins. In particular, we identified 47 genes that were specifically expressed in the tuber and highly correlated with different anthocyanins. These genes were associated with ATP-binding cassette transporters and phytohormone pathways. Additionally, a core transcription factor, StWRKY44, involved in anthocyanin accumulation in the tuber was identified; it was capable of binding to and activating the promoters of 7 anthocyanin structural genes. This study provides insights into the genes and metabolites underlying anthocyanin accumulation in potato tubers, which will be valuable for future functional studies and breeding efforts.

Family-1 UDP-glycosyltransferases (UGTs) are the most common and functional glycosyltransferases in the plant world. UGT is closely related to plant growth and the response to abiotic stress. However, despite systematic research, our understanding of potato UGT genes is still unclear. In this study, we identified 174 potato UGT proteins based on their conserved plant secondary product glycosyltransferase (PSPG) motifs. Phylogenetic analyses were used to compare these proteins with Arabidopsis UGTs and other plant UGTs, and it was found that they could be clustered into 18 distinct groups. Patterns of intron gain/loss and intron phases within potato UGTs revealed highly conserved intron insertion events. The promoter cis-elements of these 174 UGT genes were systematically investigated. The promoter regions of these UGT genes are known to contain various classes of cis-acting compounds. These include elements that are light-responsive, phytohormone-responsive, and stress-responsive. Transcriptome data analysis established that 25, 10, 6, and 4 of these 174 UGT genes were specifically expressed in leaves, roots, stolons, and young tubers, respectively. The mannitol-treated transcriptomic data showed thirty-eight UGT genes were significantly upregulated. The quantitative real-time PCR results showed that the four genes were all responsive to osmotic stress under a 10% PEG6000 treatment. The results of our study provide a basis for clarifying the molecular mechanism of potato osmotic stress resistance and better understanding its function in the future.