Nitrate Responsive Transcription in Maize Is Highly Dynamic Across the Lifecycle

Nitrate (NO₃^-) is the predominant form of inorganic nitrogen (N) accessed by crop plants in an agricultural system. To understand how to modify crop plants to maximise N uptake we characterised the transcriptional response of maize to low N. To approximate steady-state N supply and demand, which cereal crops experience in the field, we grew dwarf maize with sufficient (2.5 mM) and limiting (0.5 mM) NO₃^- provision for the entire lifecycle. Maize plants grown with limiting NO₃^- were able to maintain the same biomass and yield as those grown with sufficient NO₃^- by increasing NO₃^- uptake capacity, chiefly through increasing transcription of genes encoding high affinity NO₃^- transporters (NRT2). We undertook a transcriptomic analysis of leaf and root tissue at seven key time points to identify genes responding to both NO₃^- provision and N demand changes due to development across the lifecycle.  We found the majority of NO₃^- responsive transcription occurs at 11 (D11), 18 (D18) and 29 (D29) days after emergence, and primarily in the root at D11 and D29 and in the leaf at D18 (for reference, anthesis occurs on D31).  Overall, there were surprisingly few patterns of differential gene expression over the lifecycle, but the composition of classes of genes differentially regulated at individual time points was unique.  A second major goal of this analysis was to identify genes which have similar NO₃^- responsive transcription to NRT2s, implying their involvement in regulating NO₃^- uptake.  We identified a cluster of 98 probe sets which share an expression pattern with the NRT2 genes across the lifecycle.  The cluster is enriched with genes encoding lipid transport proteins and lipid metabolism enzymes and suggests that lipid-mediated signalling or trafficking may be central to the control of the NO₃^- uptake system and NRT2 regulation.  Manipulation of these genes may produce increased N uptake which is a crucial step in improving nitrogen use efficiency in cereal crops.