Identification of Gene and Metabolite Regulatory Networks During Early Fruit Development in Tomato (Solanum lycopersicum): the Effect of SUN on Early Fruit Development

SUN is a tomato fruit shape gene controlling fruit elongation.  The mutation arose from a retrotransposon-mediated duplication of a 24.7 kb locus from chromosome 10 to chromosome 7 in which SUN was placed under control the promoter of DEFL1, causing SUN to be highly expressed in the developing tomato fruit.  Currently, it is not fully known how SUN controls fruit elongation at the molecular level.  We used metabolite and gene profiling during early fruit development to identify metabolite and gene regulatory networks and to infer the relationship of these networks in round and elongated fruit.  Fruit from Near Isogenic Lines (NILs) isogenic for SUN in the cultivated background were harvested at 4, 7, and 10 days post anthesis (dpa) and septum, seed, and pericarp tissue were isolated and analyzed for primary metabolites and gene expression.  Metabolite and gene expression values were normalized using their z score. Metabolite profiles were clustered using an unsupervised Bayesian algorithm. Expression profiles were clustered based on log fold difference in expression and k-means clustering.  Clusters were verified using Pearson’s correlation coefficient.  Three separate analyses were performed: metabolite accumulation, gene expression, and the combined interactome between wild type and SUN fruit.  We identified distinct metabolite and gene expression regulatory networks, and found that new associations were made in elongated fruit.  Analysis of gene expression networks revealed a complex interaction between hormone homeostasis and secondary metabolism.  These data provide new insights into how SUN might regulate fruit elongation.