Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat. Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat

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 nitrogen application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. The use of near-isogenic lines (NILs) in transcriptome analysis can reduce genetic background noise. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling in NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions. The results showed that 7,023 DEGs (4,738 up-regulated and 2,285 down-regulated) were identified in the 1Y vs 1W comparison. The responses of 1Y and 1W to normal nitrogen differed significantly in the transcriptional regulation mechanisms. Several genes belonging to the GS and GOGAT gene families were up-regulated 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 Overall design: A total of twelve samples, including two treatments (N1 and N0). Each treatment was detected at a time point with 3 replicates. Two forms of Nitrogen fertilizers treatments: normal nitrogen (1.6g pot–1), which is referred to as N1, and a control (no nitrogen application), which is referred to as N0.

氮（Nitrogen, N）是作物产量形成的必需营养元素。遗憾的是，作物的氮肥利用效率（Nitrogen Use Efficiency, NUE）会随着施氮量的增加而逐渐降低。目前，学界对不同小麦基因型间氮肥利用效率差异的分子机制仍知之甚少。在转录组分析中采用近等基因系（Near-Isogenic Lines, NILs）可有效降低遗传背景噪音。本研究利用RNA测序（RNA-Sequencing, RNA-Seq）技术，对比了正常施氮条件下高氮肥利用效率近等基因系1Y与低氮肥利用效率近等基因系1W的转录组表达谱。结果显示，在1Y与1W的对比组中，共鉴定出7023个差异表达基因（Differentially Expressed Genes, DEGs），其中4738个基因上调表达，2285个基因下调表达。1Y与1W对正常施氮的响应在转录调控机制上存在显著差异。相较于1W，1Y中谷氨酰胺合成酶（Glutamine Synthetase, GS）和谷氨酸合酶（Glutamine:2-Oxoglutarate Aminotransferase, GOGAT）基因家族的多个基因呈上调表达；增强的碳代谢过程可能为1Y的氮代谢提供更多碳骨架、代谢能量及还原当量。本研究还鉴定到ERF、WRKY、NAC、MYB等多个转录因子（Transcription Factor, TFs）家族成员。综上，本研究鉴定的候选基因为进一步解析小麦基因型间氮肥利用效率差异的分子机制提供了新的研究线索。整体实验设计：本研究共设置12个样本，包含2个施氮处理组（N1与N0）。每个处理组设置3次生物学重复，并于对应时间点进行检测。氮肥处理分为两种形式：正常施氮组（施用量为1.6g·盆⁻¹，记为N1）与空白对照组（不施加氮肥，记为N0）。