Gene Expression Biomarkers Provide Sensitive Indicators of in Planta Nitrogen Status in Maize  

Abstract

Over the last several decades, increased agricultural production has been driven by improved agronomic practices and a dramatic increase in the use of nitrogen-containing fertilizers to maximize the yield potential of crops. To reduce input costs and to minimize the potential environmental impacts of nitrogen fertilizer that has been used to optimize yield, an increased understanding of the molecular responses to nitrogen under field conditions is critical for our ability to further improve agricultural sustainability. Using maize (Zea mays) as a model, we have characterized the transcriptional response of plants grown under limiting and sufficient nitrogen conditions and during the recovery of nitrogen-starved plants. We show that a large percentage (approximately 7%) of the maize transcriptome is nitrogen responsive, similar to previous observations in other plant species. Furthermore, we have used statistical approaches to identify a small set of genes whose expression profiles can quantitatively assess the response of plants to varying nitrogen conditions. Using a composite gene expression scoring system, this single set of biomarker genes can accurately assess nitrogen responses independently of genotype, developmental stage, tissue type, or environment, including in plants grown under controlled environments or in the field. Importantly, the biomarker composite expression response is much more rapid and quantitative than phenotypic observations. Consequently, we have successfully used these biomarkers to monitor nitrogen status in real-time assays of field-grown maize plants under typical production conditions. Our results suggest that biomarkers have the potential to be used as agronomic tools to monitor and optimize nitrogen fertilizer usage to help achieve maximal crop yields.

Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis

“…The high phosphate concentration in the maize leaves could be caused by comparably high Pi supply in the nutrient solution and the length of the experiment. However, comparison of our results with the transcriptional response of maize leaves to low-N conditions in the experiments by Yang et al (2011) shows that our results are in agreement with other studies. Nitrate and Pi deficiencies are both very common in nature.…”

“…The concentration of photosynthesis genes in ME3 indicated that the process was regulated in coordination. This is in agreement with similar studies in Arabidopsis (Scheible et al, 2004;Bi et al, 2007;Krapp et al, 2011), rice (Lian et al, 2006), and maize (Yang et al, 2011). In the maize source leaves analyzed in our experiment, transcripts for the antenna proteins of PSI and PSII were down-regulated under low-N conditions (Fig.…”

“…Transcription patterns of nitrate reductase followed the ME18 and showed also genotypedependent differences, with raw array signals from B73 being generally higher than from A188 (Table IV). Comparison of transcriptome responses in different maize lines recently also showed that marker genes for N deprivation are not simply characterized by their absolute transcript values at any given time but by their linear response to the analyzed stress situation (Yang et al, 2011). Furthermore, genotype-specific transcript levels would not necessarily translate into different levels of activity because in addition to the transcriptional control, nitrite reductase activity is also regulated on the posttranslational level by phosphorylation and interaction with Mg 2+ (Huber et al, 1994).…”

“…However, the central role of the N status requires rearrangements in many further parts of plant metabolism. Large-scale microarray analysis of N statusdependent changes is now available from Arabidopsis (Arabidopsis thaliana; Wang et al, 2000Wang et al, , 2003Price et al, 2004;Scheible et al, 2004;Bi et al, 2007;Gutiérrez et al, 2007;Krapp et al, 2011), rice (Oryza sativa; Lian et al, 2006), and maize (Yang et al, 2011). These identified numerous N status-responsive transcripts involved in the nitrate transport and assimilation, the OPP pathway, amino acid metabolism, organic acid metabolism, tetrapyrrole biosynthesis, major carbohydrate, and protein, lipid, and secondary metabolism to changes in the N status of the plant (Wang et al, 2000(Wang et al, , 2003Scheible et al, 2004;Bi et al, 2007;Krapp et al, 2011) but also many genes with unknown roles in adaption to low-N stress.…”

Arabidopsis cryptochrome 1 functions in nitrogen regulation of flowering

“…Earlier microarray studies have shown that thousands of Arabidopsis genes (∼7% of the Arabidopsis transcriptome) are N-responsive (18). To search for key factors involved in N-regulated flowering, we performed a modified SSH screen with Arabidopsis seedlings grown on media containing different levels of N. We first determined the appropriate N treatment levels and Arabidopsis floral transition times.…”