Transcriptome analysis of tobacco root response to different concentrations of nitrate

Abstract

We aimed to explore genes and transcription factors (TFs) in tobacco (Nicotiana tabacum L.) that were closely related to responses to different concentrations of nitrate (NO 3 − ) in tobacco root. Cultivar K326 was used in this study. The RNA sequence data generated from K326 treated with high or low concentration of NO 3 − supplied at different time points (0, 6, 12, and 24 h) were analyzed to determine the transcriptome response of tobacco root to NO 3 − supply. The expression of numerous genes was altered after high and low NO 3 − treatment. Further analysis revealed 1981 and 3573 differentially expressed genes (DEGs) from low and high NO 3 − treatment groups, respectively. Comparative analysis identified 567 low-NO 3 −specific, 2159 high-NO 3 − -specific, and 1414 commonly expressed genes. Combining short time-series expression miner (STEM) and weighed gene co-expression network analysis (WGCNA) results, 136 and 416 DEGs were identified from low and high NO 3 − groups, respectively, among which, 12 were TFs. In the constructed protein−protein interaction (PPI) network, three DEGs in high NO 3 − group (LOC107807186, LOC107792457, and LOC107786314) exhibited highest degrees. Within low NO 3 − group, LOC107798206, LOC107815159, and LOC107779796 had highest degrees. Among the 12 TFs, LOC107778750, LOC107810552, and LOC107804260 had the highest degrees. Our data provides valuable information about genes, especially the 12 TFs, which were induced by different concentrations of NO 3 − in tobacco root. These findings may be useful for identification of high or low NO 3 − treatment-induced genes and TFs, as well as for understanding potential gene regulation mechanisms in response to NO 3 − supply in tobacco.