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

• 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
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0606133103

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.