Comparative transcriptome analyses of a late-ripening mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit ripening

Late-ripening characteristics of a fruit is a good agronomic trait for extending both the harvest period and marketing time. However, underlying molecular basis of the late-ripening mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-seq) technology was used to identify differentially expressed genes (DEGs) related to late-ripening characteristics from a late-ripening mutant ‘Huwan Wuzishatangju’ (HWWZSTJ) (Citrus reticulata Blanco) and its original line ‘Wuzishatangju’ (WZSTJ). A total of approximately 17.0 G base and 84.2 M paried-end reads were obtained. DEGs were mainly enriched in processes including photosynthesis, phenylpropanoid biosynthesis, carotenoid biosynthesis, chlorophyll and abscisic acid (ABA) metabolism. Thirteen candidate transcripts related to chlorophyll metabolism, carotenoid biosynthesis and ABA metabolism were analyzed using real-time quantitative PCR (qPCR) at all fruit maturation stages of HWWZSTJ and WZSTJ. Chlorophyllase (CLH) and divinyl reductase (DVR) from chlorophyll metabolism, phytoene synthase (PSY) and capsanthin/capsorubin synthase (CCS) from carotenoid biosynthesis, abscisic acid 8'-hydroxylase (AB) and 9-cis-epoxycarotenoid dioxygenase (NCED1) from ABA metabolism were cloned and analyzed. NCED1 is probably responsible for the formation of late-repining of HWWZSTJ based on sequence and expression analyses. The preliminary study provides new information to better understand the complex process of late-ripening in Citrus at the transcriptional level.