Pear is a kind of common temperate fruit, whose metabolite composition that contributes to the difference in fruit quality is unclear. This study identified and quantified the metabolites using a widely targeted LC-MS/MS approach in three pear species, including Pyrus bretschneideri (PB), Pyrus usssuriensis (PU) and Pyrus pyrifolia (PP). A total of 493 metabolites were identified, consisting of 68 carbohydrates, 47 organic acids, 50 polyphenols, 21 amino acids, 20 vitamins, etc. The results of PCA and OPLS-DA demonstrated that the metabolite compositions differed distinctly with cultivar variability. Our results also involved some metabolic pathways that may link to the fruit quality based on KEGG pathway analysis, the pathway of phenylalanine metabolism revealed significant differences between PB and PP (p < 0.05). Furthermore, the study selected D-xylose, formononetin, procyanidin A1 and β-nicotinamide mononucleotide as the major differentially expressed metabolites in the three species. The present study can open new avenues for explaining the differences in fruit quality of the major commercial pear cultivars in China.
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