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Key message Global transcriptome analysis in maize revealed differential nitrogen response

Key message Global transcriptome analysis in maize revealed differential nitrogen response between genotypes and implicate a crucial role of transcription factors in driving genotype by nitrogen interactions at gene expression level. of genes were involved in G??N interactions, but a significant enrichment for transcription factors was detected, particularly the AP2/EREBP and WRKY family, suggesting that transcription factors might play important roles in driving G??N interaction at gene expression level for nitrogen response in maize. Taken together, these results not only provide novel insights into the mechanism of nitrogen response in maize and set important basis for further characterization but also have important implications for other genotype by stress conversation. Electronic supplementary material The online version of this article (doi:10.1007/s00299-015-1822-9) contains supplementary material, which is available to authorized users. are responsible for nitrate uptake from the environment (Ho et al. 2009; Miller et al. 2007). Glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle is predominantly responsible for assimilating ammonium into amino acids (Lam et al. 1996; Xu et al. 2012). Notably, overexpression of in maize can lead to an increase of 30?% in kernel number (Martin et al. 2006). A large number of quantitative trait loci (QTLs) for physiological and agronomic traits have Arry-380 been identified in maize using quantitative genetic approaches to associate metabolic functions and agronomic traits to DNA markers (Agrama et al. 1999; Hirel et al. 2007; Kant et al. 2011). Previous studies have found QTL for grain yield and yield components overlapping the location of genes for N metabolism (Gallais and Hirel 2004; Hirel et al. 2001). Next generation sequencing technology provides an unprecedented opportunity to characterize transcriptome-wide responses to environmental changes. An increasing number of transcriptome sequencing studies on maize development under different N conditions have been performed to identify N-responsive genes and regulatory control of the expression patterns (Amiour et al. 2012; Humbert et al. 2013; Simons et al. 2014). Results from these studies have shown that this transcriptional response to nitrogen availability is usually highly complex, contingent on a variety of developmental, metabolic, and regulatory factors (Amiour et al. 2012; Humbert et al. 2013; Simons et al. 2014). The recent transcriptome-wide studies further showed that different maize genotypes responded differently to nitrogen availability (Bi et al. 2014; Zamboni et al. 2014). These results suggested that there is wide variation of genotype by nitrogen (G??N) conversation at gene expression Arry-380 level. However, a further understanding of how maize genotypes interact with different N levels at transcriptional level is usually lacking. Studies that are specifically designed to identify genes with significant G??N conversation and characterize their regulatory features are needed in maize. Dissecting genotype by environment interactions at the transcriptional level has started to become an important approach for dissecting complex traits and understanding traits evolution (Cubillos et CTNND1 Arry-380 al. 2014; Degenkolbe et al. 2009; Des Marais et al. 2012, 2013, 2015; Geng et al. 2013; Grishkevich and Yanai 2013; Idaghdour and Awadalla 2012; Lasky et al. 2014; Laudencia-Chingcuanco et al. 2011; Lowry et al. 2013; Richards et al. 2012; Snoek et al. 2013). In this study, using transcriptome sequencing, we performed a comprehensive genotype by nitrogen (G??N) analysis for two maize inbreds Zheng58 and Chang7-2, the parents of Zhengdan958, a maize hybrid with the largest planting area in China. The previous investigation of nitrogen use efficiency for 27 representative Chinese inbreds has shown that both Zheng58 and Chang7-2 are nitrogen-efficient inbreds at both normal and low nitrogen levels compared to other inbreds (Cui et al. 2013). However, in the response sensitivity, Chang7-2 showed a relatively greater differential response between nitrogen conditions than Zheng58 (Cui et al. 2013). The objectives of this study were to examine the transcriptomic responses to nitrogen changes in Zheng58 and Chang7-2, and further identify genes with significant G??N effects and characterize their expression patterns and functional features. We showed that Zheng58 and Arry-380 Chang7-2 showed a contrasting agronomic and transcriptomic responses to the nitrogen treatments. Transcription factors were significantly enriched among genes with significant G??N interactions, which implicates that transcription factors might play a crucial role in modulating the G??N interactions at transcriptional level. Materials and methods Herb materials Zheng58 and Chang7-2 were produced in 2011 at the Shangzhuang experimental station of China Agricultural University in Beijing under normal nitrogen (NN) and low nitrogen (LN) conditions. The NN treatment indicates the application of the general agronomic fertility treatment (450?kg/ha urea). While for the LN treatment, no nitrogen fertilizer was applied. The LN experiments were conducted in locations where nitrogen fertilizer was not applied during the preceding 2?years. A total of four genotype-condition combinations, namely NN_Zheng58, NN_Chang7-2, LN_Zheng58 and LN_Chang7-2, were tested. In NN.