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An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability

1
Rice Research Institute of Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture, Shenyang 110866, China
2
Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(9), 2349; https://doi.org/10.3390/ijms20092349
Received: 17 April 2019 / Revised: 7 May 2019 / Accepted: 8 May 2019 / Published: 11 May 2019
(This article belongs to the Special Issue The Molecular Basis of Carbon and Nitrogen Metabolism in Plants)
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Abstract

Nitrogen (N) is an extremely important macronutrient for plant growth and development. It is the main limiting factor in most agricultural production. However, it is well known that the nitrogen use efficiency (NUE) of rice gradually decreases with the increase of the nitrogen application rate. In order to clarify the underlying metabolic and molecular mechanisms of this phenomenon, we performed an integrated analysis of the rice transcriptome and metabolome. Both differentially expressed genes (DEGs) and metabolite Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that carbon and nitrogen metabolism is significantly affected by nitrogen availability. Further analysis of carbon and nitrogen metabolism changes in rice under different nitrogen availability showed that high N inhibits nitrogen assimilation and aromatic metabolism pathways by regulating carbon metabolism pathways such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP). Under low nitrogen, the TCA cycle is promoted to produce more energy and α-ketoglutarate, thereby enhancing nitrogen transport and assimilation. PPP is also inhibited by low N, which may be consistent with the lower NADPH demand under low nitrogen. Additionally, we performed a co-expression network analysis of genes and metabolites related to carbon and nitrogen metabolism. In total, 15 genes were identified as hub genes. In summary, this study reveals the influence of nitrogen levels on the regulation mechanisms for carbon and nitrogen metabolism in rice and provides new insights into coordinating carbon and nitrogen metabolism and improving nitrogen use efficiency in rice. View Full-Text
Keywords: rice; transcriptome; metabolome; carbon metabolism; nitrogen metabolism; nitrogen use efficiency (NUE) rice; transcriptome; metabolome; carbon metabolism; nitrogen metabolism; nitrogen use efficiency (NUE)
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Xin, W.; Zhang, L.; Zhang, W.; Gao, J.; Yi, J.; Zhen, X.; Li, Z.; Zhao, Y.; Peng, C.; Zhao, C. An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability. Int. J. Mol. Sci. 2019, 20, 2349.

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