Identification of metabolic pathways related to rough-skinned fruit formation in Korla pear

The formation of rough-skinned fruits is one of the major factors that adversely affect the Korla pear (Pyrus sinkiangensis Yü) fruit quality. However, little is known about the underlying mechanism of pericarp roughening. The aim of this study was to determine the metabolic pathways and biological processes involved in the formation of rough-skinned fruits using both the pericarp and pulp of normal and rough-skinned fruits. Morphological and physiological observations showed that stone cell, cellulose, hemicellulose, lignin and polysaccharide contents in both the pericarp and pulp of rough-skinned fruits were significantly higher than normal fruits. However, flavor substances like soluble sugar, fructose, glucose, and sucrose were abundant in the pulp of normal fruits. In addition, the total phenol, flavone and isoflavone contents were much higher in the pericarp of rough-skinned fruits than in that of normal fruits, while anthocyanin was abundant in the pericarp of normal fruits. Accordingly, in our metabolomic and transcriptomic analysis, the differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) involved in flavone and flavonol biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism pathways were further investigated. Moreover, we identified 33 DAMs and 84 DEGs that were enriched in the aforementioned pathways. Compared with normal fruits, these DAMs and DEGs were significantly upregulated in both the pericarp and pulp of rough-skinned fruits. Correlation analysis indicates that these identified genes encode enzymes that are responsible for the biosynthesis of DAMs identified in this study. Significant enrichment of these pathways in both the pericarp and pulp of rough-skinned fruits is probably responsible for pericarp roughening and lack of coloring in rough-skinned fruits.