title: Whole-genome association mapping in elite inbred crop varieties.
abstract: We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.
authors.affiliation: Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK. Robbie.Waugh@scri.ac.uk
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
authors.forename: David
authors.initials: D
authors.lastname: Marshall
authors.forename: Bill
authors.initials: B
authors.lastname: Thomas
authors.forename: Jordi
authors.initials: J
authors.lastname: Comadran
authors.forename: Joanne
authors.initials: J
authors.lastname: Russell
authors.forename: Tim
authors.initials: T
authors.lastname: Close
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
authors.forename: Pat
authors.initials: P
authors.lastname: Hayes
authors.forename: Gary
authors.initials: G
authors.lastname: Muehlbauer
authors.forename: James
authors.initials: J
authors.lastname: Cockram
authors.forename: Donal
authors.initials: D
authors.lastname: O'Sullivan
authors.forename: Ian
authors.initials: I
authors.lastname: Mackay
authors.forename: Andrew
authors.initials: A
authors.lastname: Flavell
authors.forename: Luke
authors.initials: L
authors.lastname: Ramsay
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D001467:Hordeum / Q000235:genetics*; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D026801:Synteny