A transcriptional-level gene regulation strategy in Chinese fir seedlings under nitrogen deficiency

To screen the genes related to nitrogen use efficiency, a Chinese fir clone named X6 was subjected to low nitrogen (LN) stress and was used along with control (CK) plants for de novo RNA sequencing of root transcriptomes. The differences in the expression of genes under both conditions were determined. A total of 4,300 significant differentially expressed genes (SDEGs) were obtained by comparing the transcriptomes of the plants in the LN and CK groups. Among these genes, 2,970 were upregulated, and 1,330 were downregulated. All the SDEGs obtained from the LN and CK samples were subjected to KEGG annotation and classification. Using classification and statistical analysis with WEGO software, KEGG pathway annotations were obtained for 980 SDEGs, which were related to 222 metabolic pathways, and the pathway for nitrogen metabolism was determined. Twenty-four unigenes related to nitrogen metabolism in the Chinese fir were screened. They were found to encode seven enzymes: nitrate reductase (NADH, NR1), ferredoxin-nitrite reductase (NIR1), glutamine synthetase (GS), glutamate synthase (ferredoxin; Fd-GOGAT), glutamate synthase (NADPH/NADH, NADH-GOGAT), glutamate dehydrogenase (NADP+, GDH1), and glutamate dehydrogenase (NAD(P)+,GDH2), as well as two transporters, namely, ammonium transporter (AMT) and nitrate transporter (NRT). Under nitrogen-deficient conditions, AMT, NRT, NR1, and GS were significantly upregulated, whereas NIR1, NADH-GOGAT, and GDH2 were significantly downregulated; the other genes showed no significant changes. This is the first report on the global transcriptome response of the Chinese fir to nitrogen deficiency. Our results might help illustrate the preference of the Chinese fir for NH4+ rather than for NO3−. Our data provide insights into the coordinated system of nitrogen metabolism in this valuable tree species. Low nitrogen (LN, the nitrogen present in distilled water, which was determined to be less than 0.01mM) and nitrogen sufficient (CK, nitrogen concentration of 5.03 mM) treated Chinese fir root were generated by deep sequencing.