Population Genetic Signals Of Selection In Maize Breeding

Since the advent of modern plant breeding in the 1930s, North American maize has undergone a dramatic adaptation to high-input agriculture. Despite the importance of genetic contributions to historical yield increases, little is known about the underlying genomic changes. Here I present the work of two studies using high-density SNP genotyping to characterize genome-wide patterns of genetic diversity, ancestry, and selection in North American maize. First I show the results from a broadscale analysis of four hundred lines spanning the history of modern maize breeding.  These show a steady increase in genetic differentiation and loss of diversity within breeding pools.  However, overall it appears that selection has had limited impact on patterns of diversity and ancestry across all North American maize, and instead that breeding progress has mainly involved selection and recombination of relatively common alleles, contributed by a representative but limited set of ancestral lines. Second I show analysis of a single breeding population selected for multiple cycles.  Although dramatic changes in diversity and haplotype structure in this population are consistent with directional selection, genetic drift by far appears to be the predominant force across most of the genome.  Together, these results illustrate how the forces of selection, genetic drift and variable recombination impact maize diversity and improvement.