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Analysis of Genotyping-by-Sequencing data in a maize (Zea mays L.) breeding program

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Title: Analysis of Genotyping-by-Sequencing data in a maize (Zea mays L.) breeding program
Author: Cooke, Alison R.
Department: Collaborative International Development Studies
Program: Bioinformatics
Advisor: Robinson, J. Andrew B.Lee, Elizabeth A.
Abstract: As genotyping-by-sequencing data becomes more abundant, new applications of this technology in breeding programs are possible. This research utilized publically available data in conjunction with data from the University of Guelph maize breeding program. Using a genetic similarity matrix, a network diagram and dendrogram were generated, reflecting the maize heterotic patterns. Hierarchical clustering was used to identify putative parents of University of Guelph lines from a publically available dataset. For lines derived from inter-heterotic breeding crosses, parental linkage blocks were identified and visualized across the chromosomes. The marker data was also used in conjunction with grain yield data for association mapping using a mixed model approach. This method identified 123 quantitative trait loci for additive effects for grain yield in Stiff Stalk lines, accounting for approximately 9.38% of the phenotypic variance. Breeders can increase the utility of their marker data in their breeding program by applying the methods described here.
Date: 2016-12
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