拟南芥氮营养途径相关基因模块的分子机制研究

Excessive use of fertilizers in agriculture and their losses to the environment have caused severe pollution. This problem can be addressed in part by improving crops’ nutrient use efficiency. The proposed project will use gene modules to systematically dissect the molecular mechanisms of nitrogen uptake and utilization in Arabidopsis, with a goal of finding new clues for crop improvement. The process of nitrogen uptake and utilization in plants includes four key steps: 1. Development of plants root system architecture (RSA), including increasing RSA to enlarge nutrients absorbing surface; 2. Plant’s response to, and uptake and assimilation of nitrate or ammonia; 3. Transport of nitrogen between different tissues; 4, Remobilization of nitrogen from older tissues. Previously, via analyzing larger-scale transcriptome data, we have constructed an Arabidopsis gene network based on the graphical Gaussian model (GGM). The network connects genes with similar functions or genes participating in the same pathways. It enabled the identification of 662 gene modules that function in a variety of plant processes, such as development, nutrients uptake and utilization, metabolism, and stresses response. Among them are 9 gene modules participating in the different steps of nitrogen uptake and utilization. This project will focus on a module involved in nitrate signaling and a module functioning in root hair development, identify key regulatory genes within these two modules, and dissect their roles in nitrogen uptake and utilization. Understanding these genes’ functions will enhance our understanding of nitrogen nutrient pathways from a systematic perspective and provide new clues for crop improvement regarding nitrogen use efficiency.

近年来，随着农业生产中化肥施用量的不断攀升，大量化肥流失到环境中，造成严重的污染问题。提高农作物养分吸收利用效率，减少化肥用量迫在眉睫。本项目将关注模式植物拟南芥氮素吸收利用的各个环节，利用生物大数据构建基因网络，从中挖掘作用于这些不同环节的基因模块，找出模块中的关键基因并解析其功能。这些环节包括：1.植物根系系统的发育；2.植物对氮的响应、吸收和同化；3.氮在植物体内的运输；4.氮的再转运。在前期工作中，通过对拟南芥基因表达大数据的分析，我们构建了一个基于图形化高斯模型的基因网络，从中发现了众多参与植物发育、营养、代谢、胁迫应答等不同生命途径的基因模块，其中有9个作用于氮吸收利用各个环节。本项目将选取两个分别参与硝酸盐响应和根毛发育的基因模块，挖掘模块中的关键基因并解析其功能，探明它们在氮营养途径中的作用，以期在系统水平上增进对氮营养途径分子机制的了解，为农作物分子改良提供理论基础。

本项目聚焦两类转录因子在硝酸盐响应途径及根毛发育过程中的功能。研究发现两个HHO类转录因子在拟南芥根部和叶子中均有表达，且它们的表达会受到硝酸盐诱导。对双突变体的研究表明，这两个转录因子可能抑制硝酸盐响应途径基因的表达。另外，我们发现两个在根部特异表达的WRKY类转录因子参与调控根毛发育。在它们的双突变体中，根毛数量大大减少，而根毛长度也大大缩短。进一步的转录组分析表明，这两个WRKY转录因子可能调控EXTENSIN类基因的表达。另一方面，为了寻找更多的可能参与硝酸盐响应及根毛发育途径的上游转录因子，我们分析了大规模的拟南芥RNA-Seq转录组数据，构建了一个拟南芥普适性基因表达调控网络EXPLICIT。对于任意一个拟南芥RNA-Seq样品，该网络模型能根据1678个转录因子的表达量精确预测出其余29182个靶基因的表达量。该网络还能用于推导任意拟南芥基因或生物学途径的上游转录因子。利用该网络，我们得以推导出更多可能参与硝酸盐响应及根毛发育途径的上游转录因子。