title: Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties.
abstract: Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world's major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudo-outbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs.
authors.affiliation: Genetics Programme and Biomathematics and Statistics Scotland, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland.
authors.forename: Nils
authors.initials: N
authors.lastname: Rostoks
authors.forename: Luke
authors.initials: L
authors.lastname: Ramsay
authors.forename: Katrin
authors.initials: K
authors.lastname: MacKenzie
authors.forename: Linda
authors.initials: L
authors.lastname: Cardle
authors.forename: Prasanna R
authors.initials: PR
authors.lastname: Bhat
authors.forename: Mikeal L
authors.initials: ML
authors.lastname: Roose
authors.forename: Jan T
authors.initials: JT
authors.lastname: Svensson
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.forename: David F
authors.initials: DF
authors.lastname: Marshall
authors.forename: Andreas
authors.initials: A
authors.lastname: Graner
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Close
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
mesh_terms: D003433:Crosses, Genetic; D018745:Genome, Plant; D006239:Haplotypes; D001467:Hordeum / Q000235:genetics*; D007178:Inbreeding; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide