  Modern maize breeding relies upon selection in inbreeding populations to
improve the performance of cross-population hybrids. The United States
Department of Agriculture - Agricultural Research Service reciprocal recurrent
selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa
Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest
standing models of selection for hybrid performance. To investigate the genomic
impact of this selection program, we used the Illumina MaizeSNP50 high-density
SNP array to determine genotypes of progenitor lines and over 600 individuals
across multiple cycles of selection. Consistent with previous research (Messmer
et al., 1991; Labate et al., 1997; Hagdorn et al., 2003; Hinze et al., 2005),
we found that genetic diversity within each population steadily decreases, with
a corresponding increase in population structure. High marker density also
enabled the first view of haplotype ancestry, fixation and recombination within
this historic maize experiment. Extensive regions of haplotype fixation within
each population are visible in the pericentromeric regions, where large blocks
trace back to single founder inbreds. Simulation attributes most of the
observed reduction in genetic diversity to genetic drift. Signatures of
selection were difficult to observe in the background of this strong genetic
drift, but heterozygosity in each population has fallen more than expected.
Regions of haplotype fixation represent the most likely targets of selection,
but as observed in other germplasm selected for hybrid performance (Feng et
al., 2006), there is no overlap between the most likely targets of selection in
the two populations. We discuss how this pattern is likely to occur during
selection for hybrid performance, and how it poses challenges for dissecting
the impacts of modern breeding and selection on the maize genome.
