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

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17 Citations (Scopus)

Abstract

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.
Original languageEnglish
Article number840
JournalBMC Genomics
Volume14
DOIs
Publication statusPublished - 2013

Fingerprint

Brassica rapa
Seeds
Genome
Plant Oils
Haploidy
Brassica
Genomics
Oils
Gene Expression
Growth
Genes

Keywords

  • gene-expression profiles
  • false discovery rate
  • arabidopsis-thaliana
  • network analysis
  • prolamin-box
  • napus
  • germination
  • embryo
  • maize
  • plant

Cite this

@article{6d40c9d5f10a4a65a363df3e21e7c51c,
title = "Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes",
abstract = "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.",
keywords = "gene-expression profiles, false discovery rate, arabidopsis-thaliana, network analysis, prolamin-box, napus, germination, embryo, maize, plant",
author = "R.K. Basnet and {Moreno Pach{\'o}n}, N.M. and K. Lin and J. Bucher and R.G.F. Visser and C.A. Maliepaard and A.B. Bonnema",
year = "2013",
doi = "10.1186/1471-2164-14-840",
language = "English",
volume = "14",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "Springer Verlag",

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TY - JOUR

T1 - Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes

AU - Basnet, R.K.

AU - Moreno Pachón, N.M.

AU - Lin, K.

AU - Bucher, J.

AU - Visser, R.G.F.

AU - Maliepaard, C.A.

AU - Bonnema, A.B.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

KW - gene-expression profiles

KW - false discovery rate

KW - arabidopsis-thaliana

KW - network analysis

KW - prolamin-box

KW - napus

KW - germination

KW - embryo

KW - maize

KW - plant

U2 - 10.1186/1471-2164-14-840

DO - 10.1186/1471-2164-14-840

M3 - Article

VL - 14

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 840

ER -