Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.
Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.
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DOI：
10.1186/1471-2164-14-840
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发表时间：
2013-12-01
期刊：
影响因子：
4.4
通讯作者：
Bonnema G
中科院分区：
文献类型：
--
作者：
Basnet RK;Moreno-Pachon N;Lin K;Bucher J;Visser RG;Maliepaard C;Bonnema G
芸苔属植物种子是植物生长的基本单位和植物油的来源。种子发育受到许多动态代谢过程的调节，这些代谢过程由空间和时间表达基因的复杂网络控制。我们通过测量来自两个不同B的发育种子的转录本丰度进行了全球微阵列基因共表达分析。芜菁形态类型：小白菜（叶型）和黄沙逊（油型）以及它们的两个双单倍体（DH）后代，（1）研究种子发育中代谢过程的时间，（2）探索两种形态型种子发育中的主要转录差异，（3）确定B中遗传基因组学研究的最佳时期。芜菁籽B的小白菜和黄籽甘蓝的种子发育阶段相似。但胚和种皮的颜色在这两种形态型之间存在差异。在本研究中，大多数转录变化发生在25和35 DAP之间，这表明B种子发育过程的时间。芜菁的发育阶段比相关种B晚。油菜。使用加权基因共表达网络分析（WGCNA），我们确定了47个“基因模块”，其中27个与时间和/或基因型变异显着相关。一个额外的层次聚类分析确定了种子发育过程中的基因表达模式的广谱。基因表达的主要变化是根据发育阶段，而不是形态差异。由于脂类是芸苔属植物种子的主要贮藏物质，因此我们对脂类代谢的调控进行了更详细的研究。四个共调节基因簇被确定与17个推定的顺式调控元件预测在其1000 bp的上游区域，无论是特定的或共同的不同的脂质代谢途径。这是第一个在B种子发育过程中对转录本丰度进行全基因组分析的研究。拉帕。关键的生理事件，主要的表达模式，和推定的顺式调控元件的鉴定提供了有用的信息，以构建基因调控网络在B。为种子质量性状的遗传基因组学研究提供了起点。本文的在线版本（doi：10.1186/1471-2164-14-840）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/1471-2164-14-840) contains supplementary material, which is available to authorized users.
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WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
DOI：
10.1073/pnas.1003530107
发表时间：
2010-05-04
影响因子：
11.1
作者：
Le, Brandon H.;Cheng, Chen;Goldberg, Robert B.
通讯作者：
Goldberg, Robert B.
影响因子：
7.4
作者：
Beisson, F;Koo, AJK;Ohlrogge, JB
通讯作者：
Ohlrogge, JB
DOI：
10.1002/9781118223086.ch8
发表时间：
2012-01-01
期刊：
PLANT HORMONE ETHYLENE
影响因子：
--
作者：
Bogatek, Renata;Gniazdowska, Agnieszka
通讯作者：
Gniazdowska, Agnieszka
影响因子：
--
作者：
Hu Y;Wu G;Cao Y;Wu Y;Xiao L;Li X;Lu C
通讯作者：
Lu C