Early molecular events associated with nitrogen deficiency in rice seedling roots

Ping-Han Hsieh, Chia-Cheng Kan, Hsin-Yu Wu, Hsiu-Chun Yang, Ming-Hsiun Hsieh
2018 Scientific Reports  
Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (−N, 1 h), focusing on amino acid analysis and identification of −N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of −N treatment, indicating that part of the N-deficient signals could be
more » ... mediated by glutamine. Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by −N. Some of the −N-regulated genes encode transcription factors, protein kinases and protein phosphatases, which may be involved in the regulation of early −N responses in rice roots. Previously, we used similar approaches to identify glutamine-, glutamate-, and ammonium nitrate-responsive genes. Comparisons of the genes induced by different forms of N with the −N-regulated genes identified here have provided a catalog of potential N regulatory genes for further dissection of the N signaling pathwys in rice. Rice is a staple food for almost half of the world's population 1 . The production of rice, especially in Asian countries, is important in food security. The Green Revolution rice cultivars developed in 1960's, which constitute most of the rice varieties grown today, require large amounts of nitrogen (N) fertilizers to produce high yields 2 . However, the production of N fertilizer requires a lot of energy. Furthermore, only 20-30% of the applied N fertilizer is taken up by the rice plant 3,4 . Most of the N fertilizers applied to rice are lost to the air or water, which causes substantial environmental problems. Thus, the use of N fertilizer is costly to farmers and the environment. The current agricultural practices are not enconomically and environmentally sustainable. Therefore, considerable efforts have been directed toward improvement of N management and development of new rice varieties with better N use efficiency in the past decades to ensure sustainable agriculture 5-9 . Despite decades of study, the improvement of N use efficiency in crop plants is still one of the scientific "Grand Challenges" in the 21 st century. To face this challenge, we need to have a better understanding of the genetics behind N uptake, transport, metabolism, and remobilization in crop plants, especially when N is limited in the environment. Since N is a major constituent of amino acids, nucleic acids, chlorophyll, ATP, coenzymes, plant hormones, and secondary metabolites, N deficiency affects all aspects of plant function, from metabolism to resource allocation, growth and development 8-10 . To cope with N deficiency, plants have evolved complex morphological, physiological, and biochemical adaptaions to the adverse environments. For instance, plants will increase its capacity to acquire N by stimulating root growth relative to shoot growth in response to N deficiency 10 . The expression of high affinifity nitrate and ammonium transporter genes was induced by N starvation (−N) [11] [12] [13] . Furthermore, the remobilization of stored N and the release of ammonium via the biosynthesis of phenylpropanoids were stimulated by N deprivation 14, 15 . It is evident that plants have evolved regulatory systems to adjust metabolism, conserve resources and activate the acclimatory pathways enabling them to adapt to N-deficient conditions. Nevertheless, the molecular mechanisms underlying the N-deficient responses are still largely unknown in plants. Global gene expression profiling using microarrays or RNA sequencing (RNA-Seq) has been a successful approach to study the molecular aspects of nutrient and stress responses. For instance, microarrays were used in several studies to identify nitrate-responsive genes in Arabidopsis and rice [16] [17] [18] [19] [20] [21] [22] . Ammonium is believed to be the
doi:10.1038/s41598-018-30632-1 pmid:30111825 pmcid:PMC6093901 fatcat:23x3mxtkxjbrhfbt3n2gpcjuxm