title: The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize.
abstract: Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture's 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 running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and >600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. 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.
authors.affiliation: Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 rossibarra@ucdavis.edu justin.gerke@gmail.com.
authors.forename: Justin P
authors.initials: JP
authors.lastname: Gerke
authors.affiliation: Corn Insects and Crop Genetics Research Unit, U.S. Department of Agriculture (USDA)-Agricultural Research Service, Ames, Iowa 50011.
authors.forename: Jode W
authors.initials: JW
authors.lastname: Edwards
authors.affiliation: Plant Genetics Research Unit, USDA-Agricultural Research Service, Columbia Missouri 65211.
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Guill
authors.affiliation: Department of Plant Sciences, Center for Population Biology, and Genome Center, University of California, Davis, California 95616 rossibarra@ucdavis.edu justin.gerke@gmail.com.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Ross-Ibarra
authors.affiliation: Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 Plant Genetics Research Unit, USDA-Agricultural Research Service, Columbia Missouri 65211.
authors.forename: Michael D
authors.initials: MD
authors.lastname: McMullen
mesh_terms: D003198:Computer Simulation; D040961:Genetic Drift; D014644:Genetic Variation; D018745:Genome, Plant; D006824:Hybridization, Genetic; D008957:Models, Genetic; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics*
keywords: artificial selection; genetic drift; heterosis; maize; recurrent selection