Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.
Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.
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DOI：
10.1186/1471-2164-11-150
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发表时间：
2010-03-04
期刊：
影响因子：
4.4
通讯作者：
Strauss SH
中科院分区：
文献类型：
--
作者：
Dharmawardhana P;Brunner AM;Strauss SH
毛果杨凭借其基因组序列和其他实验属性，已成为木材发育基因组研究的模式物种。木材来源于树干的次生生长，在幼嫩的发育中的茎中开始形成一环维管形成层。发育中的枝条末端区域提供了从初级生长到次级生长的陡峭发育梯度，这有助于识别在这些生长阶段的每个阶段发挥特殊功能的基因。使用代表大多数转录组的基因组微阵列，我们描绘了横跨初级到次级生长的茎段中的基因表达。我们发现了3,016个在茎发育过程中差异表达的基因(Q-Value≤0.05；>；2倍表达差异)，其中15%的基因编码蛋白质，与已知基因没有显著的相似性。我们确定了碳水化合物活性酶、微管蛋白、肌动蛋白、肌动蛋白解聚因子、Fasciclin样AGPs和血管发育相关转录因子等所有与二次生长相关的基因家族成员。近70%的转录因子在向二次生长过渡过程中表达上调。茎的初生芽伸长区含有特定的碳水化合物、活性酶和膨胀素家族成员，它们可能在初生细胞壁的合成和修饰中发挥作用。参与植物防御和保护功能的基因在初级生长区也是占优势的。我们的结果描述了从初级茎生长到次级茎生长过渡过程中发生的基因表达的全球模式。我们能够确定三种主要的基因表达模式，并在茎发育过程中过度代表基因本体论类别。我们发现的新的调控因子和细胞壁生物发生基因为进一步的功能鉴定提供了候选基因，也为分子育种和生物技术提供了新的工具，旨在提高树木的生长速度、树冠形状和木材品质。
With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth. Using a genomic microarray representing the majority of the transcriptome, we profiled gene expression in stem segments that spanned primary to secondary growth. We found 3,016 genes that were differentially expressed during stem development (Q-value ≤ 0.05; >2-fold expression variation), and 15% of these genes encode proteins with no significant identities to known genes. We identified all gene family members putatively involved in secondary growth for carbohydrate active enzymes, tubulins, actins, actin depolymerizing factors, fasciclin-like AGPs, and vascular development-associated transcription factors. Almost 70% of expressed transcription factors were upregulated during the transition to secondary growth. The primary shoot elongation region of the stem contained specific carbohydrate active enzyme and expansin family members that are likely to function in primary cell wall synthesis and modification. Genes involved in plant defense and protective functions were also dominant in the primary growth region. Our results describe the global patterns of gene expression that occur during the transition from primary to secondary stem growth. We were able to identify three major patterns of gene expression and over-represented gene ontology categories during stem development. The new regulatory factors and cell wall biogenesis genes that we identified provide candidate genes for further functional characterization, as well as new tools for molecular breeding and biotechnology aimed at improvement of tree growth rate, crown form, and wood quality.
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