Expression data of Arabidopsis grown under low or sufficient nitrogen availability

Nitrogen availability in the soil is a major determinant of crop yield. While the application of fertilizer can substantially increase the yield on poor soils, it also causes nitrate pollution of water resources and high costs for farmers. Increasing the nitrogen use efficiency in crop plants is a necessary step to implement low input agricultural systems. We exploited the genetic diversity present in the world-wide Arabidopsis thaliana population to study adaptive growth patterns and changes in gene expression associated with chronic low nitrate stress, with the aim to identify biomarkers associated with good plant performance under low nitrate availability. Transcription and epigenetic factors were identified as important players in the adaptatiion to limited nitrogen in a global gene expression analysis using the Affymetrix ATH1 chip. Six lines with contrasting growth characteristics on low N were used for gene expression analysis, the accessions El-0 and Fei-0, and the mixed RILs KB006, NG064, NG087, SG063. For each line, root and shoot samples were taken from plants grown on 0.4 mM or 9 mM nitrate. Three biological replicates were used per organ and treatment, in total 72 samples. One replicate consisted of a pool of 30 plants harvested from three plates.

土壤有效氮含量是作物产量的主要决定因素。施用化肥虽可在贫瘠土壤中大幅提升作物产量，但同时会引发水资源硝酸盐污染，且增加农户的生产成本。提高作物的氮素利用效率，是推行低投入农业体系的必要举措。

本研究利用全球拟南芥（Arabidopsis thaliana）种群的遗传多样性，探究长期低硝酸盐胁迫下的适应性生长模式与基因表达变化，旨在筛选出低氮条件下植株优良生长相关的生物标志物。通过Affymetrix ATH1基因芯片开展全基因组基因表达分析，我们鉴定出转录因子与表观遗传因子是植物适应限氮环境的关键调控因子。

本研究选取6个在低氮（N）条件下生长特征差异显著的株系进行基因表达分析，包括种质系El-0与Fei-0，以及混合重组自交系（Recombinant Inbred Line, RIL）群体KB006、NG064、NG087、SG063。针对每个株系，分别采集在0.4 mM或9 mM硝酸盐培养基上培养的植株的根与地上组织样本。每个器官与处理设置3次生物学重复，总计72个样本；每个重复由3个培养平板上收获的30株植物混合制备而成。