Combining Quantitative and Population Genetics to Map Phenotype to Genotype in Ipomoea

Understanding the genetic basis of adaptive traits is one of the central goals of modern plant biology. Deciphering how phenotype maps to the genotype is a complex problem that requires answering multiple questions: Is the phenotype environmentally induced, or is it genetically controlled? What gene(s) underlie the phenotype? Are the gene(s) associated with other phenotypes which might impact its evolutionary potential? These questions can be answered using a combination of quantitative and population genetic approaches. In this thesis, I apply these approaches to two complex adaptive phenotypes -- leaf shape in Ipomoea batatas (sweetpotato) and herbicide resistance in Ipomoea purpurea (common morning glory) -- to identify putative genes and mechanisms contributing to phenotype. Further, I synthesize a framework for analyzing genetic correlations that underlie most complex traits. I show that leaf shape variation is extensive and largely under genetic control in sweetpotato, and likewise, identify genes putatively associated with leaf shape variation. I also show that although simple leaf shape descriptors are not environmentally controlled when considered together these can be influenced to a great extent by the environment. Next, using genome-wide resequencing, RNA-Seq and functional tests I show that the detoxification mechanism underlies the polygenic herbicide resistance in the common morning glory. Using linkage analysis, I identify a role of intrerchromosomal linkage disequilibrium in maintaining the resistance alleles over generations. Moreover, I identify loci associated with the cost of resistance and show the potential role of genetic-hitchhiking in maintaining the cost. Lastly, I review the current methods available for studying the genetic basis of trait correlations, and highlight the pitfalls associated with such methods. I thus synthesize an analytical framework which can more precisely identify the genes and mechanisms underlying trait correlations. Together, my thesis identifies the genetic basis of adaptive phenotypes in the genus Ipomoea and thus narrows the gap between genotype and adaptive phenotypes.PhDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/172662/1/gsonal_1.pd