Identification of Novel Flavonoid-Pathway Regulatory Genes using Transcriptome Correlation Network Analysis in Ripe Strawberry (Fragaria x ananassa) Fruit

The flavonoid pathway is of great interest in strawberry (Fragaria x ananassa), as it figures central to a suite of metabolites with roles in nutrition, flavor and ripening. Individual transcriptomes from progeny of a wide parental cross were analyzed for transcripts with expression patterns matching those of flavonoid pathway genes. In this genetic dataset, we have implemented a Transcriptome Co-expression Network Analysis to identify new candidates that affect specific nodes of the flavonoid pathway. The analysis revealed co-expression relationships between common flavonoid pathway genes and uncharacterized transcripts, which were considered candidates because of tightly-correlating expression patterns. We prioritized analysis of transcription factors for functional characterization in fruit-infiltration assays. A subset of the candidates was either silenced or overexpresssed in transient fruit expression assays, and demonstrated specific mechanisms of action in the regulation of discrete offshoots of the flavonoid pathway.  Analysis of co-expression networks provides a rapid means to identify new candidates related to well conserved pathways.