Maize growth and development depends highly in the capacity of the plants to absorb Nitrogen (N) from the soil. Producing a high-yielding maize crop that requires less N input is currently one important goal of maize breeding programs. In order to understand the dynamics of N use in maize, the study of phenotypic and genetic response to N deficiency must be performed. Using lines from the high resolution IBM2Syn10-DH population, the goals of this study were: 1) to identify the phenotypic response of the root system architecture (RSA) of 14-day old maize seedlings grown under contrasting levels of N; 2) to discover Quantitative Trait Loci (QTL) that are associated with the RSA response to N variation; 3) to analyze the agronomic response of DH lines grown in 4 environments under contrasting N treatments; and 4) detect QTL associated with the variation of this agronomic response.

A subset of IBM2Syn10-DH lines grown in a cigar roll culture under controlled growth chamber conditions was used to gather phenotypic data to perform a QTL analysis of the RSA traits. A Low N (LN) treatment increased primary root length (PRL), lateral root length (LRL), and lateral root number (LRN) by 8.5%, 31% and 20%, respectively. Alternatively, crown root number (CRN) increased 6.4% and shoot length (SL) grew 12.9% longer under HN treatment. A total of 57 QTL among 8 traits were identified using composite interval mapping (CIM) and a high density genetic map. The results suggest that genomic regions are triggered by N deficiency stress, and control the root system growth for better nutrient acquisition and remobilization.

Several agronomic traits and grain quality traits were measured at independent environments in two locations in Iowa and two consecutive years. Overall, the data showed that effective LN treatments reduced the DH-lines performance significantly. Grain yield decreased up to 63% at one environment. Grain protein (GPRT) was significantly reduced by 10% under LN conditions. A total of 302 QTL were identified across all trait/environment/N-level combinations. Important QTL clusters located in chromosomes 1, 4, 5, 8 and 10 harbored QTL detected under LN or HN treatments. These clusters are located near loci gln4 and gln5, which regulate the activity of glutamine synthetase; an enzyme involved in N-assimilation and N-remobilization for the production protein in the grain of maize.