Potato is the world’s most important nongrain crop.In this study,to assess genetic diversity within the Petota section,29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of...Potato is the world’s most important nongrain crop.In this study,to assess genetic diversity within the Petota section,29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes,landraces,and modern cultivars were re-sequenced at>253 depth.Subsequently,a graph-based pangenome was constructed using DM8.1 as the backbone,integrating194,330 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 structural variants(SVs)were detected to be significantly associated with 1,258 distinct metabolites via PAV(presence and absence variations)-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),was developed.Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato,which will accelerate functional genomics studies and genetic improvements in potato.展开更多
基金supported by the National Natural Science Foundation of China(31972969)the Science and Technology Department of Yunnan Province(2019FY003015)+4 种基金Research Startup Funding of Yunnan University in China(C176220100033)the Science and Technology Major Project of the Department of Science and Technology of Yunnan(K204204210017)Yunnan Fundamental Research Projects(202301BF070001-026)the Project of Central Guiding Local Technology Development(202407AB110005)the Yunnan Talent Support Plan(C619300A036)。
文摘Potato is the world’s most important nongrain crop.In this study,to assess genetic diversity within the Petota section,29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes,landraces,and modern cultivars were re-sequenced at>253 depth.Subsequently,a graph-based pangenome was constructed using DM8.1 as the backbone,integrating194,330 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 structural variants(SVs)were detected to be significantly associated with 1,258 distinct metabolites via PAV(presence and absence variations)-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),was developed.Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato,which will accelerate functional genomics studies and genetic improvements in potato.
