Comparative transcriptomic profile of two mandarin varieties during maturation reveals pectinase regulating peelability

Abstract

Peelability is an important fruit quality trait of citrus. Pectinase is a group of heterozygous enzymes that function in pectin degradation, which is implicated in fruit ripening and softening. Previously we established a method to quantify citrus peelability through two mechanical indexes (peel-pulp adherence and peel resistance of penetration), and exhibited the genetic diversity of peelability in mandarins (Citrus reticulata Blanco). With this method, the present study first confirmed that Clementine is an easy-peeling mandarin in comparison with Fremont, and both showed increasingly easy peeling as the fruits matured. A range of measurements for the two mandarins at three maturation stages demonstrated that peelability had negative correlation with pectin contents but positive with pectinase activity. Subsequently, RNA sequencing was performed for comparative transcriptomic profiling of the two varieties at three maturation stages. We identified 12322 differentially expressed genes (DEGs) in total. Through comparative time-course analysis, the gene expression patterns were displayed with 12 clusters each in albedo and flavedo. Some cell wall-related gene ontology terms were over-represented in albedo and flavedo Cluster6. We mined 153 genes encoding pectinase (pectin methylesterase, polygalacturonase, pectin lyase (PL), beta-galactanase, pectin acetylesterase and alpha-arabinofuranosidase) in silica from Clementine genome, and 78 of them were significantly expressed in the peel of Clementine or Fremont, whereas 62/60 belonged to the DEGs in albedo/flavedo. In weighted correlation network analysis, six/five out of eight/nine modules in albedo/flavedo had eigengene values that were significantly correlated with the two mechanical indexes, pectin contents and pectinase activity, and six/eight pectinase genes were present in the co-expression networks. Based on the results of multi-approach bioinformatics analysis, three PL genes (Ciclev10004783m.g, Ciclev10020423m.g and Ciclev10031429m.g) were highlighted as potential regulators for peelability. This study provides clues for understanding the molecular basis of the regulation of citrus peelability, and proposes pectinase as a target for peelability-oriented breeding of citrus.