Degree Type


Date of Award


Degree Name

Doctor of Philosophy




Plant Breeding

First Advisor

Thomas Lübberstedt


Molecular characterization of a given set of maize germplasm could be useful for understanding the use of the assembled germplasm for further improvement in a breeding program, such as analyzing genetic diversity, selecting a parental line, assigning heterotic groups, creating a core set of germplasm and performing association analysis for traits of interest. In this study, we used single nucleotide polymorphism (SNP) markers to assess the genetic diversity in a set of doubled haploid (DH) lines derived from “C0” (BSSS(R)C0), “C17” (BSSS(R)C17) and the cross “C0/C17” (BSSS(R)C0/BSSS(R)C17) of the Iowa Stiff Stalk Synthetic (BSSS) maize population. With the aim to explore if we have potentially lost diversity from C0 to C17 derived DH lines and to observe whether useful genetic variation in C0 was left behind during the selection process since C0 could be a reservoir of genetic diversity that could be untapped using DH technology. Assessing the genetic relationship and genetic divergence within and among the evaluated cycles of selection will allow us to explore the BSSS DH lines' breeding potential for broadening the genetic base of the Stiff Stalk (SS) heterotic pool. Additionally, we quantify the BSSS progenitors' contribution in each set of DH lines using a high-resolution detection of identity by descend (IBD) segments. The DH lines developed plus the 16 progenitors were evaluated in a per se evaluation trial and phenotypic data were collected on an individual plot basis for male flowering, female flowering, anthesis-silking interval, plant height, ear height, flag leaf angle, tassel length, and the number of primary tassel branches to compare C0, C17, and C0/C17 derived DH lines for plant architecture traits and identify DH lines with both significant C0 background and in addition modern plant architecture traits conferring adaptation to high plant density, that could be used as genetic resources. Using the genotypic and phenotypic information of the BSSS DH lines, we performed Genome-Wide Association Studies (GWAS) to identify regions in the genome associated with these plant architecture changes. The molecular characterization analysis confirmed the apparent separation and the loss of genetic variability from C0 to C17 through the recurrent selection process. The progenitors had a higher genetic contribution in C0 compared with C0/C17 and C17 derived DH lines. Although genetic drift can explain most of the genetic structure genome-wide, phenotypic data provide evidence that selection has altered favorable alleles frequencies in the BSSS maize population. Descriptive statistical analysis confirmed trait variability in the different groups of DH lines. Considerable variation between populations was observed for all traits except for plant height. As expected, phenotypic differences (P ≤ 0.001) were found between different groups of DH lines, indicating a wide range of variability present. DH lines within the C0_DHL group had the highest mean values for flowering time, ear height, flag leaf angle, and the number of primary tassel branches and were statistically different (P ≤ 0.001) between the groups of DH lines. Using GWAS analysis, significant SNP markers-trait associations were found in flowering and plant architecture traits using different GWAS analysis models. 38 SNP markers were found associated with different evaluated traits across more than one method tested and among the groups of DH lines. The genome regions with the highest significance were found on chromosomes 2 and 7 for the traits number of primary tassel branches and flag leaf angles. By searching for candidate genes up and downstream of the 38 in common significant SNP markers, 55 candidate genes were associated with flowering time and different plant architecture traits. Molecular characterization information provided by this research will help maize breeders better understand how to utilize the current set of DH lines developed from the BSSS maize population. Additionally, identifying candidate genes for plant architecture traits in this study may help to elucidate the genetic basis of these plant architecture traits.


Copyright Owner

Alejandro Ledesma M



File Format


File Size

125 pages