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 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.barley ͉ linkage disequilibrium ͉ oligo pool assay L inkage disequilibrium (LD), the nonrandom association of alleles at distinct loci in a sample population, is now routinely exploited to map disease genes in humans (1-4). In crop plants, the potential of exploiting LD in population-based association mapping, with the objective of estimating the position of a gene conferring a specific trait or phenotype by using LD between alleles of genetically mapped markers, has become a focus of considerable interest. A major attraction of association mapping is the potential to locate genes responsible for a wide range of traits in sample populations by using preexisting phenotypic data collected during crop improvement and cultivar registration programs. In addition, as association mapping exploits all historical recombination events that have occurred during establishment of the sample population (2, 5, 6) mapping resolution may greatly exceed that possible in small biparental experimental crosses.As spurious associations between phenotypes and marker loci can be caused by population structure, the extent and structure of LD within a sample population must be known before selecting an appropriate association mapping strategy (1). This is particularly true when looking at an inbreeding crop species such as barley where such complicating factors are expected to be more prevalent. In maize, a naturally outcrossing species, LD decays rapidly over 1-2 kb (7) and in diverse populations of Arabidopsis, an inbreeding species, LD extends to Ϸ1 cM (250 kb), although isolated populations exhibit LD Ͼ50 cM (8). Barley in addition to being an inbreeder has, as well as other crop plants, undergone a severe population bottleneck during domestication (9). In addition, the progenitors of contemporary European spring and winter barley varieties were selected from a relatively small number of successful European landraces d...

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

“…The SNP markers used were originally ascertained on smaller discovery panels of barley cultivars (Rostoks et al, 2005(Rostoks et al, , 2006Close et al, 2009), and hence ascertainment bias may influence the results. Moragues et al (2010) tested a set of 1536 SNP markers on a large set of 500 cultivars and 169 landraces, evaluating ascertainment bias and its effect on diversity and proposed two reduced sets of 384 SNPs optimized for European cultivars and Syrian and Jordanian landraces, respectively.…”

A high-density transcript linkage map of barley derived from a single population

“…We expected that our strategy of using 3 0 ESTs would provide a higher level of polymorphism than the one based on exon SNPs only (for example, Rostoks et al, 2006). This expectation was based on the report of higher SNP rates in non-coding regions (for example, UTRs, introns and intergenic regions) than in exons in humans (Venter et al, 2001) and soybean (Van et al, 2005).…”

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

“…Unlike linkage studies of bi-parental mapping populations, in wild populations LD patterns depend on a long history of recombination and therefore enable to obtain improved mapping resolution. On the other hand, LD is affected by population structure and selection, and hence linkage between markers may not necessarily reflect physical proximity (Flint-Garcia et al 2003;Rostoks et al 2006). The extent of LD in barley, a selfing plant and a relative of wheat, was found to be much lower in wild populations (Hordeum spontaneum) than in a cultivated collection (H.…”