An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability.

Wei Xin,Ming Du,Lina Zhang,Xiaoxi Zhen,Liqiang Chen,Jiping Gao,Wenzhong Zhang,Jun Yi,Yanze Zhao

doi:10.3390/ijms20235893

Abstract

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.

Highlights

Rice is one of the most widely grown food crops globally, and approximately 50% of the global population eat rice as a staple food [1]
The purpose of our study was to identify strategies rice roots use to respond to nitrogen availability, which could be used for research to improve nitrogen use efficiency (NUE) and yield in rice
Inorganic nitrogen is absorbed and transported by specific transport proteins, such as ammonium transporters (AMTs) and nitrate transduction was significantly affected in rice roots [20]

Summary

Introduction

Rice is one of the most widely grown food crops globally, and approximately 50% of the global population eat rice as a staple food [1]. Rice yields have continued to increase due to the application of a large number of chemical fertilizers, nitrogen [2,3]. With this significant increase in rice yield, considerable and unreasonable nitrogen fertilizer application has caused many problems such as the reduction of the nitrogen fertilizer utilization rate, a rise in production costs, and environmental pollution, which have seriously influenced the sustainable development of rice production [4,5]. Root architectural and physiological characteristics are closely related to the growth of the shoot, yield formation, and nitrogen uptake and utilization. Fan et al [7] found that rice root architecture characteristics and physiological activity have significant effects on nitrogen use efficiency at various stages of rice growth. Understanding the molecular mechanisms that control root development is critical to improving nutrient uptake efficiency and yield in crops

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