Comprehensive analysis of transcriptome and metabolome to reveal potential mechanism of the development of peel browning in ‘Yali’ pear at shelf life

1. There exhibited obvious peel browning and significant changes on the related genes and metabolites during shelf-life at 20°C. 2. Phenylpropanoid and flavonoid biosynthesis were the key pathways involved in the development of peel browning. 3. The ‘transcription factor-gene-metabolite’ regulatory network related to peel browning was constructed by WGCNA. The peel of ‘Yali’ pear is prone to browning during shelf-life following long-term cold storage, but the mechanism behind this physiological disorder remains unclear. In this study, changes in fruit quality, peel browning index, gene expression, and metabolite profiles were analyzed in ‘Yali’ fruit after 180 days of cold storage at 0°C, followed by shelf-life at 20°C and 0°C (as control), using transcriptome and widely-targeted metabolome analyses. The results showed that compared with low temperature storage, the peel a value and peel browning index increased, while the titratable acid content (TAC) decreased during shelf-life at 20°C; however, no significant difference was observed in fruit firmness, soluble solids content (SSC), and L and b values of peel color. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) and differential metabolites (DEMs), it was found that phenylpropanoid and flavonoid biosynthesis were key pathways involved in the development of peel browning. Among them, the expression of phenylalanine ammonia-lyase ( PAL ), caffeic acid 3-O-methyltransferase ( COMT ), coumarate 3-hydroxylase ( C3H ), cinnamoyl-CoA reductase ( CCR ), laccase ( LAC ), bifunctional dihydroflavonol 4-reductase ( DFR ), and polyphenol oxidase ( PPO ) were significantly up-regulated, and metabolites including chlorogenic acid (CGA), 5-O-p-coumaroylquinic acid (5-CQA), dihydrokaempferol (DHA), catechin (CAT) and epiafzelechin (EAF) accumulated, but the content of phenylalanine and caffeic acid decreased significantly during shelf-life. Transcription factors (TFs), including ERF, WRKY, NAC, bHLH, and bZIP, were also associated with the peel browning. Furthermore, weighted gene co-expression network analysis (WGCNA) showed that CGA, 5-CQA, and DHA, together with their associated genes ( DFR, CCR, COMT, cytochrome P450 84A1 (CYP84A1) , and UDP-glucuronosyltransferases ( UGT )) and TFs (WRKY17/61, ERF2/11/23/73, ATHB12, MYB6, and NAC7) were closely linked to the development of peel browning. This study provides new insights into the potential molecular and metabolic mechanisms underlying the development of peel browning during shelf-life after cold storage in ‘Yali’ pear.