Nitrogen utilization is of special significance to maximizing yields, reducing nitrogen fertilization use, and improving the energy balance for agricultural production. We have conducted high resolution quantitative trait loci (QTL) mapping in order to decipher the architecture of nitrogen utilization efficiency (NUtE). QTL mapping in hybrids derived from the intermated B73 × Mo17 recombinant inbred lines (IBMRIL) by Illinois high protein (IHP1) grown under N-limiting and N-sufficient conditions in the field, identified a set of robust QTLs across the genome controlling important agronomic traits and physiological indicators of N utilization.

To narrow down the QTL intervals, a series of strategies were exploited, including construction of fine mapping population as well as saturation of genetic markers powered by the genotyping-by-sequencing (GBS) technique. As a result, several QTL were successfully fine mapped to single genes affecting NUtE, including an asparaginase on chromosome 2 involved in mediating asparagine cycling pathway, along with a HVA22 on chromosome 9 acting as a negative regulator of autophagy. Functional characterization was carried out on these promising candidates by means of mutants, near-isogenic lines and transgenic analyses.

Results from our study provide insights into the underlying genetic basis of maize NUtE, while functional validation of the promising candidates facilitates direct application of marker assisted selection and genetic engineering of better NUtE maize.