RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes
RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes
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DOI：
10.1111/tpj.13744
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发表时间：
2017-12-01
期刊：
影响因子：
7.2
通讯作者：
Wilson, Zoe A.
中科院分区：
文献类型：
--
作者：
Lin, Hong;Yu, Jing;Wilson, Zoe A.
在植物中，正常的花药和花粉发育涉及许多重要的生物学事件和复杂的分子调控协调。了解雄性生殖发育过程中的基因调控关系对基础生物学和作物育种至关重要。在这项工作中，我们开发了一个水稻花药发育基因共表达网络（RiceAntherNet），可以预测花粉发育过程中的基因调控关系。RiceAntherNet是从57个水稻花药组织芯片中产生的。利用msp 1 -4、ostdl 1a、gamyb-2、tip 2、udt 1 -1、tdr、eat 1 - 1、ptc 1和mads 3 -4等9个水稻雄性不育突变体的基因芯片数据对网络进行了探索和测试。在这些变化的基因中，构建了三个表现出差异表达模式的进化枝，以鉴定与花粉形成相关的基因。其中许多基因在花粉发育中具有已知的作用，例如Clade 1中的7个基因（OsABCG 15、OsLAP 5、OsLAP 6、DPW、CYP 703 A3、OsNP 1和OsCP 1）参与水稻花粉壁的形成。此外，进化枝1包含12个基因，其在拟南芥中的预测直系同源物已被报道为花粉发育过程中的关键，并可能在水稻中发挥类似的作用。进化枝2中的基因表达早于进化枝1（花药阶段2-9），而进化枝3中的基因表达晚于进化枝1（花药阶段10-12）。RiceAntherNet是在植物花药和花粉发育过程中鉴定新基因的有价值的工具。提供了一个网站（https：www.cpib.ac.uk/anther/riceindex. html）以呈现用于基因表征的表达谱。这将有助于确定基因之间的关键关系，从而能够表征与花药和花粉调控网络相关的关键基因。
In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages. The microarray datasets from nine rice male sterile mutants, including msp1-4, ostdl1a, gamyb-2, tip2, udt1-1, tdr, eat1-1, ptc1 and mads3-4, were used to explore and test the network. Among the changed genes, three clades showing differential expression patterns were constructed to identify genes associated with pollen formation. Many of these have known roles in pollen development, for example, seven genes in Clade 1 (OsABCG15, OsLAP5, OsLAP6, DPW, CYP703A3, OsNP1 and OsCP1) are involved in rice pollen wall formation. Furthermore, Clade 1 contained 12 genes whose predicted orthologs in Arabidopsis have been reported as key during pollen development and may play similar roles in rice. Genes in Clade 2 are expressed earlier than Clade 1 (anther stages 2-9), while genes in Clade 3 are expressed later (stages 10-12). RiceAntherNet serves as a valuable tool for identifying novel genes during plant anther and pollen development. A website is provided (https://www.cpib.ac.uk/anther/riceindex. html) to present the expression profiles for gene characterization. This will assist in determining the key relationships between genes, thus enabling characterization of critical genes associated with anther and pollen regulatory networks.