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Genomics of sunflower improvement : from wild relatives to a global oil seed Baute, Gregory Joseph


Genetic diversity is a critical component of global food security. We depend on crop wild relatives as a genetic resource for the continued improvement and diversification of many crops. In this dissertation, I use population genomic approaches to investigate aspects of crop evolution in sunflower, which is a widely grown hybrid oilseed. In Chapter 1, the relevant aspects of crop improvement are reviewed, the sunflower system is introduced, and the research chapters are briefly described. In Chapter 2, I used transcriptome sequencing data to scan the genomes of a panel of cultivated and wild sunflowers and identified genes involved in domestication and improvement. Using data from additional wild sunflower species, I also identified widespread introgression of wild alleles into the modern crop gene pool. Chapter 3 describes a genomic survey of a diverse set of about 300 wild sunflower samples using genotyping by sequencing (GBS). The GBS data allowed me to determine evolutionary relationships and detect gene flow among taxa in the sunflower genus. I selected a subset of these wild samples to develop pre-bred lines, which I describe in Chapter 4. Pre-bred lines act as a bridge through which wild alleles may be introduced into breeding programs. Each of the circa 400 pre-bred lines I generated contain different components of their wild parent’s genome which were identified using GBS. Evaluation of these lines in Uganda revealed they could be excellent sources of alleles for disease resistance and drought tolerance. In Chapter 5, I examined relationships among cultivated lines, specifically the two heterotic groups that have been developed for hybrid crop production. Using whole genome sequencing data, I found many genomic regions were targets of selection during the development of these populations, and that patterns of diversity do not support an overdominance model of heterosis. Surprisingly, only two regions, which correspond to introduced wild alleles, are highly differentiated between these two populations. As I conclude in Chapter 6, the history of the use of wild relatives in sunflower breeding is found in the genomes of these plants, and permeates and defines modern lines.

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