title: Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.
abstract: BACKGROUND
  Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed.
  
  
  RESULTS
  Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways.
  
  
  CONCLUSIONS
  This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of seed quality traits.
authors.forename: Ram Kumar
authors.initials: RK
authors.lastname: Basnet
authors.forename: Natalia
authors.initials: N
authors.lastname: Moreno-Pachon
authors.forename: Ke
authors.initials: K
authors.lastname: Lin
authors.forename: Johan
authors.initials: J
authors.lastname: Bucher
authors.forename: Richard G F
authors.initials: RG
authors.lastname: Visser
authors.forename: Chris
authors.initials: C
authors.lastname: Maliepaard
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. guusje.bonnema@wur.nl.
authors.forename: Guusje
authors.initials: G
authors.lastname: Bonnema
mesh_terms: D001665:Binding Sites; D001937:Brassica / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D050356:Lipid Metabolism; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D010641:Phenotype; D012045:Regulatory Sequences, Nucleic Acid; D012639:Seeds / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors