Allopolyploids are known to have superior advantages such as high growth speed. Triploids have even greater heterozygosity, explaining more phenotypic variance than 2n hybrid F1 and have therefore become new resources in breeding. To date, the metabolomic basis underlying polyploidization vigor remains unclear. Here, we identified and compared 235 metabolites in the shoot apical buds between multiple allo-triploid populations and parental 2n hybrid F1 in Populus via metabolome profiling using liquid chromatography–mass spectrometry (LC–MS) assays. Associations with growth vigor in three types of allo-triploid populations, namely first division restitution (FDR), second division restitution (SDR) and postmeiotic restitution (PMR) generated from doubled 2n female gametes and male gametes of 2n hybrid, were also investigated. Each allo-triploid population has different sub-genome duplicated. Major metabolomes were amino acids, secondary metabolism associated, and carbohydrates. We mapped 181 metabolites into known metabolism pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Ten compounds, i.e. fructose 1,6-diphosphate and xylulose, were more abundant in all allo-triploids than the 2n hybrid. Principal component analysis revealed the abundance of metabolites fell into distinct clusters corresponding to ploidy composition. Heterozygosity in triploids mainly effected the contents of carbohydrates and secondary metabolites rather than lipids. Comparisons between subgroups with different growth rates revealed some carbohydrates and secondary metabolites of flavonoids were positively associated with gene expression and the high growth vigor. The results provided an informative metabolomic basis for factors conferring growth vigor in polyploid Populus.
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