title: Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis.
abstract: Embryogenesis is central to the life cycle of most plant species. Despite its importance, because of the difficulty associated with embryo isolation, global gene expression programs involved in plant embryogenesis, especially the early events following fertilization, are largely unknown. To address this gap, we have developed methods to isolate whole live Arabidopsis (Arabidopsis thaliana) embryos as young as zygote and performed genome-wide profiling of gene expression. These studies revealed insights into patterns of gene expression relating to: maternal and paternal contributions to zygote development, chromosomal level clustering of temporal expression in embryogenesis, and embryo-specific functions. Functional analysis of some of the modulated transcription factor encoding genes from our data sets confirmed that they are critical for embryogenesis. Furthermore, we constructed stage-specific metabolic networks mapped with differentially regulated genes by combining the microarray data with the available Kyoto Encyclopedia of Genes and Genomes metabolic data sets. Comparative analysis of these networks revealed the network-associated structural and topological features, pathway interactions, and gene expression with reference to the metabolic activities during embryogenesis. Together, these studies have generated comprehensive gene expression data sets for embryo development in Arabidopsis and may serve as an important foundational resource for other seed plants.
authors.affiliation: Plant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, Canada S7N 0W9.
authors.forename: Daoquan
authors.initials: D
authors.lastname: Xiang
authors.forename: Prakash
authors.initials: P
authors.lastname: Venglat
authors.forename: Chabane
authors.initials: C
authors.lastname: Tibiche
authors.forename: Hui
authors.initials: H
authors.lastname: Yang
authors.forename: Eddy
authors.initials: E
authors.lastname: Risseeuw
authors.forename: Yongguo
authors.initials: Y
authors.lastname: Cao
authors.forename: Vivijan
authors.initials: V
authors.lastname: Babic
authors.forename: Mathieu
authors.initials: M
authors.lastname: Cloutier
authors.forename: Wilf
authors.initials: W
authors.lastname: Keller
authors.forename: Edwin
authors.initials: E
authors.lastname: Wang
authors.forename: Gopalan
authors.initials: G
authors.lastname: Selvaraj
authors.forename: Raju
authors.initials: R
authors.lastname: Datla
mesh_terms: D017360:Arabidopsis / Q000196:embryology / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D053858:Metabolic Networks and Pathways; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D012639:Seeds / Q000196:embryology / Q000235:genetics / Q000378:metabolism