Sleper, Joshua2017-10-092017-10-092017-06https://hdl.handle.net/11299/190495University of Minnesota Ph.D. dissertation.June 2017. Major: Applied Plant Sciences. Advisor: Rex Bernardo. 1 computer file (PDF); vii, 67 pages.Linkage among quantitative trait loci prevents the release of hidden genetic variation, but also preserves desirable gene combinations. This dissertation, which includes three studies, shows the continuing enigma of linkage in maize (Zea mays L.) breeding. The first study aimed to determine if the additional recombinations in doubled haploids induced from F2 instead of F1 plants leads to a larger genetic variance and a superior mean of the best lines. In two maize populations, inducing doubled haploids from F2 plants did not improve the mean, and it increased the genetic variance for moisture, but not for yield and plant height. The second study aimed to determine if multi-allelic markers or haplotypes improve the prediction accuracy of genomewide selection in three-way breeding populations, which could have three alleles per locus. In both simulated and empirical maize populations, accounting for multiple alleles did not improve the prediction accuracy over a biallelic model. The third study aimed to determine if genomewide markers can be used to partition trait effects into independent and correlated portions, and if selection on the independent portion was more effective than selection on the entire trait. Results from four cycles of selection showed that selection only for the independent portion did not lead to higher responses for yield, moisture, and plant height. Overall, genetic linkage both assists and confounds molecular breeding efforts in maize.endouble haploidgeneticsgenomewide selectionmaizemolecular markersplant breedingThesis or Dissertation