Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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

ORGANISM(S): Theobroma cacao

SUBMITTER: Mark Guiltinan

PROVIDER: E-GEOD-55476 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Inoculation of endophyte-free (E-) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant foliar fungal endophyte in healthy T. cacao, induced significant changes in the expression of hundreds of host genes. Further, E+ leaves exhibit enhanced pathogen resistance, increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes that all correspond to the changes in expression of specific functional genes in related pathways. Moreover, a cacao gene highly up-regulated in E+ leaves increases pathogen resistance apart from any direct endophyte effects. Thus, benefits of increased pathogen resistance in E+ plants are partially due to enhanced induction of intrinsic host defense pathways, and potential costs include reduced photosynthetic capacity and endophyte metabolism of host tissues. Similar effects are likely to be properties of most plant-endophyte interactions, suggesting general relevance to the design and interpretation of studies of genetic and phenotypic expression in plants. The objective of this experiment was to identify Theobroma cacao genes that are differentially expressed between leaves inoculated with fungal endophyte Colletotrichum tropicale (E+ leaves) and control un-inoculated leaves (E- leaves) 3 days post endophyte inoculation. The experiment was conducted in a Percival growth chamber (model I35LL, 115 volts, 1/4 Hp, series: 8503122.16, Percival Scientific, Inc., Perry IA) with 12/12 h light/dark photoperiod and temperatures of 30M-BM-:C and 26M-BM-:C respectively. Inoculation was done by aspersion of endophyte spores (2X10^6 spore/ml) to a group of T. cacao seedlings and a second group of seedlings were maintained as control un-inoculated (E- leaves). Then three biological replicates (each one consisting of one leaf from different plants) per treatment E+ and four leaves per treatment E- leaves) were collected and processed for a two color oligo microarray analysis.

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

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