Comparative Transcriptome Analysis of Triticum aestivum in Response to Nitrogen Stress

Abstract—Nitrogen (N) is an essential macronutrient for plant growth and development. Insufficient supply of N leads to extensive physiological and biochemical changes in plant. However, the molecular mechanisms of response to N are still unknown. In this study, global transcriptome profiles of wheat (Triticum aestivum L.) leaf and root under limited and sufficient N conditions were generated using Illumina RNA-sequencing. Then SeqPrep and Sickle were used to filter the raw reads and genes were assembled and predicted using Trinity. The Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) for wheat transcripts were obtained from GO and KEGG databases, respectively. Clusters of orthologous group terms were obtained using Blastx 2.2.24+ in STRING 9.0. Differentially expressed genes (DEGs) were then screened using edgeR software with false discovery rate <0.05 and |log₂FC| ≥ 1, followed by the protein–protein interaction (PPI) network construction for DEGs using Cytoscape. As a result, 126 956 transcripts were obtained. Among them, 47 590 transcripts were categorized into 56 GO terms, such as metabolic process; 25 607 transcripts were assigned to 42 KEGG pathways, such as metabolic pathways; and 27 194 unique sequences were classified into 25 COG categories, such as transcription. Moreover, 1267 (179 up-regulated and 1088 down-regulated) and 1996 DEGs (868 up-regulated and 1128 down-regulated) were obtained in leaf and root, respectively. In the PPI networks, BRADI1G77050.1, BRADI2G40600.1 and rpl2 were found to be the hub nodes. Thus, these screened DEGs might be associated with N metabolism and stress response in wheat, especially BR-ADI1G77050.1, BRADI2G40600.1 and rpl2.