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The genomic impacts of drift and selection for hybrid performance in maize

Justin P. Gerke, Jode W. Edwards, Katherine E. Guill, Jeffrey Ross-Ibarra, Michael McMullen
Genetics 2015 v.201 no.3 pp. 1201-1211
Agricultural Research Service, agronomic traits, ancestry, corn, genetic drift, genetic variation, genome, haplotypes, heterozygosity, hybrids, inbreeding, marker-assisted selection, models, population growth, population structure, recurrent selection, single nucleotide polymorphism
Modern maize breeding relies upon selection in inbreeding populations to improve performance in cross-population hybrids. The United States Department of Agriculture - Agricultural Research Service (USDA-ARS) reciprocal recurrent selection experiment between the BSSS and BSCB1 populations represents one of the longest standing models of selection for this type of 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, 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 historical 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. As observed previously, the regions most likely targeted by selection do not overlap between 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.