A Systems Biology Approach to Identifying Genes Associated with Strawberry (Fragaria x ananassa) Flavor and Aroma

Strawberry fruit is recognized for its sweet flavors and appealing aromas, resulting from the interaction of sugars, acids and 360 volatile compounds. However, we have limited understanding of fruit flavor biosynthetic pathways. We have employed RNA sequencing, genetics and analytical chemistry to investigate the structure of this complex problem with a systems biology approach.  Breeding populations were used based on two parental cultivars, varying in volatile compounds profiles. We analyzed volatile compositions in the different fruits using GC/MS and gene expression profiles using RNA sequencing. A weighted gene co-expression network analysis (WGCNA) was applied to the RNA sequencing dataset and compared to volatile composition profiles. Several volatile compound profiles correlate with some module eigengene expression profiles. Some of the fruit flavors like methoxyfuraneol shared a correlation with other flavors and the same eigengene. This could be interpretated as a link in the biosynthetic or regulatory pathways of those volatile compounds. Gene network analysis of the most significant genes in the module correlated to methyl anthranilate accumulation showed that this volatile compound is sensitive to temperature and led to the identification of candidate genes involved in its biosynthetic pathway such as a methyl transferase gene. The systems biology approach gave us new insights into suites of co-regulated genes and even identified candidates that may be validated in transient and transgenic assays.