Genome-Wide Analysis Reveals Divergent Patterns of Gene Expression During Zygotic and Somatic Embryo Maturation of Theobroma cacao L., The Chocolate Tree

With the goal to better understand somatic embryogenesis (SE) development and improve the efficiency of SE conversion in Theobroma cacao L. we examined the differences between zygotic and somatic embryo at gene expression level using a whole genome microarray. A gene expression microarray representing 28,752 genes was used to compare the expression profiles at 4 developmental time points during zygotic embryogenesis (ZE) and 2 time points during somatic embryogenesis (SE). Within the ZE time course, 10,288 differentially expressed genes were identified which were enriched for functions related to responses to abiotic and biotic stimulus, metabolic and cellular processes. A comparison of expression profiles of ZE and SE identified 10,175 differentially expressed genes. 463 and 714 transcription factor (TF) genes are differentially expressed during ZE and SE maturation respectively, of which, an overlapping set of 128 genes were regulated during both processes. Large numbers of TFs, putatively involved in ethylene metabolism and ethylene response, were expressed at higher levels during SE as compared to ZE. Expression levels of genes involved in fatty acid metabolism, flavonoid biosynthesis and seed storage protein genes were also differentially expressed in the two types of embryos. A 12-plex Nimblegen expression microarray representing 28,752 genes was manufactured on which only 46 of the predicted cacao genes were not represented with at least one probe. Total RNA was isolated from four biological replicates of six different types and stages of embryo development: zygotic embryo tissues: torpedo (T-ZE), early-full (EF-ZE), late-full (LF-ZE) and mature (M-ZE) embryos; and somatic embryos: late torpedo (LT-SE) and mature (M-SE) stages