Comparative analyses identify adaptive genetic variation in crops and crop wild relatives

Abstract

Comparative population genetic analyses provide a means of identifying adaptive genetic variation. In this dissertation, I apply population genetic approaches to identify putatively adaptive variants in the genomes of crops and crop wild relatives. These approaches have the potential to identify genetic variants that are under selection and thus potentially contributing to local adaptation. As a background to the dissertation, I present in Chapter 1 the state of research in this field at the time I started my PhD and give a brief introduction to the projects described in this dissertation. In Chapter 2, I report a ~50-Mb chromosomal inversion in the wild ancestor of maize - teosinte (Zea mays ssp. parviglumis) and characterized its distribution and abundance in natural populations using population genetic approaches. This is also the first study in plants to apply population genetic approaches to identify chromosomal structural variation. In Chapter 3, I used a population genetic approach to identify genomic regions that contain adaptive mutations resistant to Fusarium head blight in a barley experimental breeding population. The successful application of comparative population genetic approaches in this study suggests this approach can also be used to identify genomic regions that are under selection in other breeding populations. In Chapter 4, I studied the geographic differentiation in wild barley (Hordeum vulgare ssp. spontaneum). I found two genomic regions contribute disproportionately to the population structure in wild barley. These same regions, with reduced evidence of recombination, are strongly associated with environmental variables. Population genetic evidence and previous cytological and genetic studies suggest these two genomic regions may be chromosomal structural rearrangements.