Abstract
Nitrogen (N) fertilizer has a major influence on the yield and quality. Understanding and optimising the response of crop plants to nitrogen fertilizer usage is of central importance in enhancing food security and agricultural sustainability. In this study, the analysis of gene regulatory networks reveals multiple genes and biological processes in response to N. Two microarray studies have been used to infer components of the nitrogen-response network. Since they used different array technologies, a map linking the two probe sets to the maize B73 reference genome has been generated to allow comparison. Putative Arabidopsis homologues of maize genes were used to query the Biological General Repository for Interaction Datasets (BioGRID) network, which yielded the potential involvement of three transcription factors (TFs) (GLK5, MADS64 and bZIP108) and a Calcium-dependent protein kinase. An Artificial Neural Network was used to identify influential genes and retrieved bZIP108 and WRKY36 as significant TFs in both microarray studies, along with genes for Asparagine Synthetase, a dual-specific protein kinase and a protein phosphatase. The output from one study also suggested roles for microRNA (miRNA) 399b and Nin-like Protein 15 (NLP15). Co-expression-network analysis of TFs with closely related profiles to known Nitrate-responsive genes identified GLK5, GLK8 and NLP15 as candidate regulators of genes repressed under low Nitrogen conditions, while bZIP108 might play a role in gene activation.
Highlights
Maize (Zea mays L.) is one of the most important cereal crops in the world and requires high nitrogen (N) fertilizer input
This paper presents some of the first research on the combination of several network inference
This paper presents some ofnovel the first research on the combination several network inference and analysis methods to identify genes associated with
Summary
Maize (Zea mays L.) is one of the most important cereal crops in the world and requires high nitrogen (N) fertilizer input. The majority of maize yield increase has been achieved by the use of large quantities of inorganic fertilizer. This has caused many problems for both intensive arable farming and the environment [1]. To avoid nitrogen pollution and to maintain a sufficient profit margin, farmers and breeders have to reduce the use of nitrogen fertilizer and employ plant varieties that have better nitrogen use efficiency (NUE). It is crucial to improve NUE by increasing the ability of crops to uptake, assimilate nitrogen
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