RNA-SEQ Analysis of Fruit Ripening in 3 Clementine Varieties

RNA-Seq technology has been used to analyze the evolution of the transcriptome of 3 C. clementina varieties differing in their ripening date: Clemenules (standard), Arrufatina (early) and Hernandina (late). Samples were collected at 126, 154, 189, 240, and 275 days post-anthesis, including pulp and peel, with 2 biological replicas per sample.

A time-course expression study carried out in Clemenules with MaSIGPro, showed that 6868 genes had differential expression along fruit ripening, that were grouped in 6 clusters based on their expression profile. A total of 412 genes showed differential expression profile in Arrufatina with respect the other varieties, 2410 genes showed a differential expression profile in Hernandina and, 1700 genes showed a differential profile in each variety. Differentially expressed genes were grouped in 12 clusters with different expression patterns: early, late and late/early.

Functional annotation of these genes was carried out with BLAST2GO, and the molecular pathways with a role in fruit ripening were identified with KEGG. 5600 genes were annotated with GO terms, and 1471 could be assigned to known metabolic pathways. The identification of 370 transcription factors (TFs), differentially expressed during ripening indicates that ripening is a tightly regulated process. Interestingly 14 TFs were found in the Early clusters, 108 TFs were in Late clusters, and 101 TFs were in Late/Early clusters, indicating that the genes controlling harvesting period could be some of these TFs that have different expression in the late or early varieties with respect the control one.