Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat

SIMPLE SUMMARY: High nitrogen use efficiency (NUE) in wheat (Triticum aestivum L.) is the key to ensure high yield and reduce pollution. Understanding the physiological and molecular changes that regulate NUE is important for the breeding of high-NUE wheat varieties. Carbon and nitrogen metabolism are the basic metabolic pathways in plants. It becomes important to reveal the underlying molecular mechanisms related to carbon and nitrogen metabolism, which may be helpful to improve NUE. In this paper, two wheat near-isogenic lines (NILs) with contrasting NUE were performed RNA-Sequencing (RNA-Seq) to identify candidate genes associated with carbon/nitrogen metabolism under normal nitrogen conditions. Our research may provide new insights into the comprehensive understanding of the molecular mechanism underlying NUE. ABSTRACT: Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha(−1), corresponding to 1.6 g N pot(−1)). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members, such as ERF, WRKY, NAC, and MYB, were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE.