title: The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations.
abstract: Barley was introduced to North America ∼400 yr ago but adaptation to modern production environments is more recent. Comparisons of allele frequencies among growth habits and spike (inflorescence) types in North America indicate that significant genetic differentiation has accumulated in a relatively short evolutionary time span. Allele frequency differentiation is greatest among barley with two-row vs. six-row spikes, followed by spring vs. winter growth habit. Large changes in allele frequency among breeding programs suggest a major contribution of genetic drift and linked selection on genetic variation. Despite this, comparisons of 3613 modern North American cultivated barley breeding lines that differ for spike-type and growth habit permit the discovery of 142 single nucleotide polymorphism (SNP) outliers putatively linked to targets of selection. For example, SNPs within the Cbf4, Ppd-H1, and Vrn-H1 loci, which have previously been associated with agronomically adaptive phenotypes, are identified as outliers. Analysis of extended haplotype sharing identifies genomic regions shared within and among breeding populations, suggestive of a number of genomic regions subject to recent selection. Finally, we are able to identify recent bouts of gene flow between breeding populations that could point to the sharing of agronomically adaptive variation. These results are supported by pedigrees and breeders' understanding of germplasm sharing.
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108 agonzale@umn.edu pmorrell@umn.edu.
authors.forename: Ana M
authors.identifier: http://orcid.org/0000-0002-4332-5986
authors.initials: AM
authors.lastname: Poets
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Mohammadi
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Kiran
authors.initials: K
authors.lastname: Seth
authors.affiliation: DuPont Pioneer, Mankato, Minnesota 56001.
authors.forename: Hongyun
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Thomas J Y
authors.initials: TJ
authors.lastname: Kono
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Fang
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Smith
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108 agonzale@umn.edu pmorrell@umn.edu.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Morrell
mesh_terms: D001947:Breeding; D019143:Evolution, Molecular; D051456:Gene Flow; D005787:Gene Frequency; D040961:Genetic Drift; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D001467:Hordeum / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: breeding; evolution of crops; genetics; identity by state; introgression