title: Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations.
abstract: Knowledge about the forces generating and conserving linkage disequilibrium (LD) is important for drawing conclusions about the prospects and limitations of association mapping. The objectives of our research were to examine the importance of (1) selection, (2) mutation, and (3) genetic drift for generating LD in a typical maize breeding program. We conducted computer simulations based on genotypic data of Central European maize open-pollinated varieties which have played an important role as founders of the European flint heterotic group. The breeding scheme and the dimensioning underlying our simulations reflect essentially the maize breeding program of the University of Hohenheim. Results suggested that in a plant breeding program of the examined dimension and breeding scheme, genetic drift and selection are major forces generating LD. The currently used population-based association mapping tests do not explicitly correct for LD caused by these two forces. Therefore, increased type I error rates are expected if these tests are applied to plant breeding populations. As a consequence, we recommend to use family-based association tests for association mapping approaches in plant breeding populations.
authors.affiliation: Institute for Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Stich
authors.forename: Albrecht E
authors.initials: AE
authors.lastname: Melchinger
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Piepho
authors.forename: Sonia
authors.initials: S
authors.lastname: Hamrit
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schipprack
authors.forename: Hans P
authors.initials: HP
authors.lastname: Maurer
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
mesh_terms: D000483:Alleles; D001947:Breeding; D002874:Chromosome Mapping; D003198:Computer Simulation; D005060:Europe; D040961:Genetic Drift; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D018598:Minisatellite Repeats; D008957:Models, Genetic; D009154:Mutation; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics*