Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes

BMC Genomics

Research Article

Johan Bucher¹  Natalia Moreno-Pachon¹  Chris Maliepaard²  Guusje Bonnema²  Ram Kumar Basnet²  Richard G F Visser²  Ke Lin³ 

[1] Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands;Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands;Centre for BioSystems Genomics, PO Box 98, 6700 AB, Wageningen, the Netherlands;Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands;Wageningen UR Bioinformatics, Wageningen University and Research Center, PO Box 569, 6700 AN, Wageningen, the Netherlands;

关键词: Brassica rapa;    Leafy vegetables;    Oil-seed;    Seed development;    Microarray;    Co-expression network analysis;    Transcript abundance;    cis;   

DOI  :  10.1186/1471-2164-14-840

 received in 2013-06-25, accepted in 2013-11-13,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundBrassica 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.ResultsSeed 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Basnet et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.