Degree Type


Date of Award


Degree Name

Doctor of Philosophy




Plant Breeding

First Advisor

Thomas Lubberstedt


Nitrogen (N) is an important macroelement for promoting crop growth and development, and is essential for increased grain yield. However, less than half of the N fertilizer applied goes into the grain, and excess N goes back into the environment. Developing maize hybrids with improved nitrogen use efficiency (NUE) can help minimize N losses, and in turn reduce adverse ecological, economical, and health consequences. The root system plays a major role in the acquisition of N, as well as water and nutrients; thus, selecting for root architecture traits ideal for N uptake might help improve NUE in maize. This project made use of doubled haploid (DH) lines that were developed from a single backcross (BC1) generation between landraces from the Germplasm Enhancement of Maize (GEM) project and two inbred lines (PHB47, PHZ51) with expired plant variety protection. The overall goal of this project was to identify single nucleotide polymorphisms for genes affecting seedling root traits and adult agronomic traits in maize, and evaluate if these polymorphisms are associated with grain yield in maize under high- and low-N conditions.

Molecular profiles of the GEM-BC1DH lines were obtained using 62,077 genotyping-by-sequencing (GBS) and 7,319 single nucleotide polymorphism (SNP) chip markers, respectively. The mean percentages of recurrent parent genotype (%RP) were higher than the expected 75%. Monomorphic marker correction was done using Bayes’ theorem, with an underlying assumption that the short recurrent parent segments are monomorphic markers instead of arising from double recombination events. After correction, the mean %RP decreased to 77.78% for GBS and 76.9% for SNP chip markers. Pearson correlation for %RP showed close correlation (r= 0.92) between the two marker systems. Population structure revealed that the GEM-DH lines were grouped into two main groups, which were consistent with the established heterotic groups, stiff-stalk and non-stiff-stalk. Distribution of GBS and SNP chip markers differed, where GBS markers were more evenly distributed compared to SNP chip markers.

Genome-wide association studies (GWAS) were conducted in the GEM-DH panel using 62,077 GBS markers. Using three GWAS models, namely general linear model (GLM), mixed linear model (MLM), and Fixed and random model Circulating Probability Unification (FarmCPU) model, multiple SNPs associated with seedling root traits were detected, some of which were within, or in linkage disequilibrium with gene models that showed expression in seedling roots. Trait associations involving the SNP S5_152926936 in Chromosome 5 were detected in all three models, particularly the trait network area, where this association was significant among all three GWAS models. The SNP is within the gene model GRMZM2G021110, which is expressed in roots at seedling stage. Similarly, GWAS for plant height, anthesis to silking interval, and grain yield under high and low nitrogen conditions from per se and testcross yield trials were conducted. Multiple SNPs associated with agronomic traits under high and low nitrogen were detected, some of which were within or linked to known genes/QTL. There were consistencies in some SNPs associated with traits under high and low N. Testcrosses that were performed better than the check hybrid PHB47/PHZ51 were also identified. Weak positive correlations were observed between most per se seedling root traits and per se grain yield under high and low N conditions. The GEM-DH panel may be a source of allelic diversity for genes controlling seedling root development, as well as agronomic traits under contrasting N conditions.

Copyright Owner

Darlene Lonjas Sanchez



File Format


File Size

171 pages