Widely targeted metabolome combined with transcriptome analysis unravels metabolic and molecular pathways related to red flush and browning of peels in cold-stored ‘Yali’ pear fruit

Abstract Red flush and browning disorders develop on the peel of ‘Yali’ pears after prolonged cold storage, but their underlying mechanisms remain unclear. In this study, peel samples were collected from healthy (HP), red flush (with normal tissue NP-R and red tissue RP-R), and browning peel (with normal tissue NP-B and browning tissue BP-B) fruits, and the corresponding metabolic profiles and gene expression patterns were quantified using widely targeted metabolomics and transcriptomics. The results revealed significant accumulation of flavonoids, phenolic acids, and terpenoids in the tissues of red flush and browning peels. Kyoto Encyclopedia of Genes and Genomes enrichment analysis of differentially accumulated metabolites and differentially expressed genes demonstrated that the phenylpropanoid and flavonoid biosynthesis pathways were strongly correlated with the development of red flush and browning peels. Specifically, p-coumaryl alcohol, sinapaldehyde, coniferin, eugenol, naringin, dihydrokaempferol, dihydroquercetin, catechin, and epicatechin exhibited markedly higher levels, while the expression of phenylalanine ammonia lyase (PAL), 4-coumarate-CoA ligase (4CL), laccase (LAC), polyphenol oxidase (PPO), leucoanthocyanidin reductase (LAR), and anthocyanidin reductase (ANR) was significantly upregulated in red flush and browning tissues compared with healthy fruit. Weighted gene co-expression network analysis further revealed that the accumulation of key metabolites (naringnin, coniferin, dihydrokaempferol, and dihydroquercetin) and the expression of associated genes (chalcone synthase (CHS) and chalcone isomerase (CHI)) and transcription factors (WRKY71, MYB1/7, NAC8, etc.) were closely associated with the development of red flush. Concurrently, elevated levels of key metabolites (catechin, epicatechin, and sinapaldehyde) and upregulated expression of genes (flavanone-3-hydroxylase (F3H), cinnamyl alcohol dehydrogenase 1 (CAD1), peroxidase 73 (POD73), etc.) and transcription factors (WRKY51/53, MYB44, NAC2, etc.) were linked to browning peel. These findings suggest that the distinct metabolic and transcriptional pathways of phenylpropanoid and flavonoid biosynthesis are involved in the red flush and browning of peels, revealing disorder-specific regulatory networks in cold-stored ‘Yali’ pears.