Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

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 eff...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2006-12, Vol.103 (49), p.18656-18661
Main Authors: Rostoks, N, Ramsay, L, MacKenzie, K, Cardle, L, Bhat, P.R, Roose, M.L, Svensson, J.T, Stein, N, Varshney, R.K, Marshall, D.F
Format: Article
Language:English
Subjects:
Alleles
Barley
Biological Sciences
Chromosomes
Crops
Crosses, Genetic
elite inbred varieties
Genetic linkage
Genetic loci
genome
Genome, Plant
Genomes
Genomics
Genotypes
Haplotypes
Hordeum - genetics
Hordeum vulgare
inbred lines
Inbreeding
Linkage Disequilibrium
outcrossing
Phenotypic traits
plant breeding
Plant populations
Plant propagation
Polymorphism, Single Nucleotide
Population parameters
Population structure
single nucleotide polymorphism
varieties
whole-genome association mapping
Winter
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Summary: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 pseudooutbreeding 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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0606133103