Identifying Traces of Selection on Quantitative Traits in Plant and Animal Genomes.

摘要

The process of selection produces distinct patterns of genetic variability in the genomes of organisms. These patterns may be leveraged for the purpose of identifying genetic variants that contribute to the variation of the selected trait or traits. Analysis of polymorphisms as potential selection-sites can provide interesting insight into evolutionary processes and the principles that govern heredity. Herein, methods to generate and analyze this type of information are investigated, developed, and applied. First, genotyping-by-sequencing, a technique for identifying and genotyping single nucleotide polymorphisms among individuals, is implemented and explored. Results show that this approach can be cost effective and efficient, but that unless sequencing is conducted to a high coverage, information for most markers will only be available for a subset of individuals. Next, a maize population that was selected for an increased ear number is analyzed. Twenty eight regions that were highly divergent between the base and selected population and putatively under selection are identified. Further analysis suggests that the majority of selection operated on standing genetic variation, and that fixation of favorable alleles was a rare occurrence. Thirdly, a window-based method for analysis of genetic differences among populations is developed. This method is based on the derivatives of cubic smoothing spline functions. It is demonstrated to increase the power of studies that seek to identify selection based on population divergence information by defining appropriate windows for analysis. Fourth, a method for identification of loci that have been jointly affected by selection is implemented in a diverse panel of chickens representing 72 distinct breeds. An assortment of selective sweeps impacting segments of DNA are identified, as well as up to three instances of cis-acting epistatic selection. Finally, these methods are placed into the broader context of scans for selection. Methods for identifying selected regions of genomes are described, and the prospects and limitations generally relating to these studies are discussed.