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Document Type

Dissertation - University Access Only

Award Date


Degree Name

Doctor of Philosophy (PhD)


Plant Science

First Advisor

Jose L. Gonzalez-Hernandez


QTL linkage analysis for plants has relied on large single-cross mapping populations derived from phenotypically divergent parent lines. This approach creates a disjunction between QTL mapping and marker-assisted breeding efforts aimed at pyramiding QTL, since no direct bridge exists between the populations within which these activities are conducted. Through this body of research, we demonstrate the application of linkage analysis directly in wheat breeding populations to enable markerassisted pyramiding for FHB resistance QTL. In the first study, we apply multipoint linkage analysis of general pedigrees to early generation wheat breeding populations for development of dense framework linkage maps. Using this approach, a linkage map consisting of 3,807 loci was developed. The linkage maps showed high concordance with the SNP consensus map for wheat. This suggests that linkage mapping in early generation plant breeding populations represents a reliable and efficient approach to support molecular breeding efforts. In the second study, we apply identical-by-descent (IBD)-based linkage analysis to map and pyramid FHB resistance QTL segregating in four-way cross spring wheat breeding populations. Resistance QTL were mapped to chromosomes 2A, 2B, 3B and 7D. QTL on chromosomes 2B, 3B and 7D are corroborated by previous mapping studies, whereas the QTL on chromosome 2A represents a novel source of indigenous FHB resistance. Marker haplotypes for parent lines founding these populations can be used for marker assisted pyramiding of resistance alleles. In the final study, we combined genome-wide SNP genotyping with IBD-based linkage analysis of four-way cross winter wheat breeding populations to map and pyramid FHB resistance QTL from native sources of resistance. QTL were detected on chromosomes 1AS, 1BS, 2AS, 3AS, 3BS, 4AC, 4AL, 4BL, 4D, 6AC, 6AS, 6D and 7D. QTL conferring native resistance from the cultivars Lyman and Overland were mapped for the first time. We conclude that linkage analysis methods for pedigreed populations can be adopted to detect multiple QTL segregating for complex traits in plant breeding populations. Therefore, these methods have promise for facilitating marker-assisted breeding. However, there are a number of limitations with current implementations of these approaches that need to be addressed before they can be routinely exploited in plant breeding programs.

Library of Congress Subject Headings

Wheat -- Varieties -- Disease and pest resistance -- Genetic aspects
Fusarium diseases of plants
Wheat -- Genome mapping
Wheat -- Breeding


Includes bibliographical references



Number of Pages



South Dakota State University


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