Selection and Genetic Drift in North American Maize

Characterizing the impact of selection and genetic drift in the formation of heterotic groups and patterns in maize can reveal important insights into the mechanism underlying adaptation, and the relative importance of each force in defining population structure. The objectives were to characterize the role selection for hybrid performance had in defining population structure in both a reciprocal full-sib selection (RFS) program and a large collection of historically important inbred lines. The Illumina GoldenGate Assay was used to genotype the University of Nebraska-Lincoln Replicated Recurrent Selection (UNL-RpRS) program. Eight cycles of S1-progeny and RFS selection were conducted for an index approximating grain yield. The distance between S1-progeny programs was compared to the distance between RFS selection programs. No evidence was found to suggest a significant genome-wide impact of selection for hybrid performance. This result suggests that, genome-wide, selection was not a strong force in diverging populations. To further investigate the roles of selection and genetic drift a second dataset was generated with genotype-by-sequencing data accompanied by increased sample size for each population in the UNL-RpRS program. A dense physical map was generated, which allowed genomic localization of selection signatures associated with directional selection and also selection for hybrid performance. The RFS and S1-progeny selection programs left similar signatures of selection across the genome. A scan for directional selection identified similar regions under selection across replicate populations, which suggests that adaptation is occurring from standing genetic variation. A large collection of inbred lines was collected and grouped into four eras, which represented the double-cross, three-way cross to single-cross transition, single-cross, and advanced single-cross eras of maize breeding, respectively. A small number of inbred lines were found to contribute to the parentage of the next era. The inbred lines identified here were also major contributors in other studies as well. Scanning the genome for localized selection signatures revealed genes putatively associated with cold tolerance and resistance to fungal and bacterial pathogens, which is consistent with the notion that selection for increased yield has selected hybrids with increased tolerance to biotic and abiotic stresses. Advisor: Aaron J. Loren