GSE61040
Apple russeting as seen through the RNA-seq lens: strong alterations in the exocarp cell wall
Russeting is a commercially important defect in apple (Malus x domestica) fruit production. Apple russeting is mainly characterized by the accumulation of suberin on the inner part of the cell wall. However, knowledge on the underlying genetic components triggering this trait remains sketchy. A bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties using RNA sequencing. This experimental design was chosen to lower the specificities of each genotype. A qPCR validation was carried out on representative genes and additional contrasting varieties. Gene ontology enrichment revealed a repression of the lignin and cuticle biosynthesis genes in the russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R2=0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of the cuticle layer biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. In addition, the large number of candidate genes highlighted in this study provides a solid platform for further functional investigations. Overall design: In order to draw a consistent picture of the gene expression profiles specific to both russeted and waxy apples and at the same time to highlight and interpret the mechanism leading to the russeted phenotype, a bulk RNA-sequencing was performed on the exocarp of a group of three distinct fully-russeted apple varieties ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') and a second one including 3 fully waxy varieties ('Gala', 'CRAW/Ma/AF42', and 'CRAW/Ma/AG94').