Transcriptional Regulation During Maturation of Somatic and Zygotic Embryos in Theobroma cacao L., The Chocolate Tree

A high degree of variability between cacao genotypes is observed in response to in vitro culture at somatic embryo (SE) initiation and later during embryo maturation steps. A whole genome microarray analysis was performed to investigate the molecular mechanisms of SE competency and maturation by comparing the development of cacao zygotic (ZE) and somatic embryos.

RNA from maturing ZEs and SEs at several developmental stages was hybridized to a whole genome NimbleGen expression microarray. Samples included 4 developmental time points for ZE and 2 time points for SE. Within the ZE time course, 10,288 genes were differentially expressed, from which 8,220 were functionally annotated. A comparison between SE and ZE revealed 10,210 differentially expressed genes.  Further analysis revealed that a group of transcription factor (TFs) genes, potentially involved in epigenetic regulation, were expressed at higher levels during SEs development compared to ZEs development. This suggests that epigenetic regulation could play an important role in SE maturation and might explain the differences between SE and ZE development. A number of other TFs were regulated during embryo maturation, some of which displayed similar expression patterns during ZE and SE. Orthologs of several of these TFs have been reported to regulate embryo maturation process in other plant species. Additionally, differences were recorded in the expression of lipid biosynthesis and seed storage proteins genes, which is consistent with the phenotypic differences between ZEs and SEs, where SE do not develop the large storage cotyledons found in ZEs.