小麦DNA去甲基化酶基因全基因组鉴定及其在籽粒发育中的表达分析

Genome-Wide Investigation and Expression Analysis of DNA Demethylase Genes in Wheat(Triticum aestivum)during the Grain Development

DNA去甲基化酶(dMTase)是一种高度保守的表观遗传修饰因子,涉及许多生物学过程,包括生长发育、应激反应和次生代谢。本研究基于小麦基因组数据,对小麦DNA去甲基化酶基因(TadMTase)进行了全面鉴定和生物信息学分析。结果表明,小麦基因组中包含18个TadMTase基因,分布于小麦15条染色体上。系统进化分析将TadMTase分为ROS、DML3、DML4和DML5等4个亚家族,亚家族之间的TadMTase基因序列长度和内含子数量存在差异,但同一个系统进化树分支中的亚族成员具有高度相似的基因结构、保守motifs和结构域,为植物dMTase基因家族的直系同源基因,在进化方面具有保守性。亚细胞定位预测TadMTase均定位于细胞核中;通过与小麦祖先物种的进化及共线性分析,发现在小麦异源六倍体形成过程中存在部分TadMTase基因丢失;TadMTase基因家族启动子区域包含大量光信号、植物激素、胁迫响应和生长发育等相关顺式作用元件;转录组数据分析表明TadMTase基因在不同组织器官和籽粒发育不同时期表达模式不同,有一定的组织特异性。进一步RNA-Seq和荧光定量PCR分析表明TaROS1b-1A.1和TaROS1a-5A/D分别在籽粒的种皮和胚乳发育时期显著上调表达,且在强筋和弱筋小麦品种中表达存在差异。结果为TadMTase基因在调控小麦籽粒生长发育及其品质形成中的调控机制提供参考。

DNA demethylases(dMTase)is a highly conserved epigenetic modifier involved in many biological processes,including growth and development,stress response,and secondary metabolism.Based on the available genome database,bioinformatic analysis was used to comprehensively identify dMTase in wheat.A total of 18 members of dMTase gene family were identified from wheat genome,which were unevenly distributed on 15 wheat chromosomes.Based on phylogenetic analysis,the wheat dMTase(TadMTase)genes were divided into four subfamilies,including ROS,DML3,DML4,and DML5.Among four subfamilies,the length and intron number of TadMTase genes were different,but the members of the subfamily in the same phylogenetic tree branch in the same group had highly similar gene structures,protein motifs and domains.Subcellular localization showed that these proteins were located in the nucleus.Phylogenetic analysis with ancestral species of wheat revealed that the gene loss events of dMTase genes occurred during the evolution of wheat.Furthermore,multiple cis-acting elements were observed in the promoter of TadMTase,including light responsiveness,phytohormone responsiveness,stress responsiveness,and plant growth and development-related elements.The expression profile analyses revealed that TadMTase genes showed differential gene expression patterns in various tissues.Further RNA-seq and qRT-PCR analyses showed that TaROS1b-1A.1 and TaROS1a-5A/D were significantly up-regulated in seed coat and endosperm development stages,with different expression patterns between strong-gluten wheat and weak-gluten wheat.In summary,our study provided a reference for elucidating the regulatory mechanism of TadMTase,especially in wheat grain development and quality formation.