Association mapping of partitioning loci in barley

Abstract

Background: Association mapping, initially developed in human disease genetics, is now being applied to plant species. The model speciesArabidopsisprovided some of the first examples of association mapping in plants, identifying previously cloned flowering time genes, despite high population sub-structure. More recently, association genetics has been applied to barley, where breeding activity has resulted in a high degree of population sub-structure. A major genotypic division within barley is that between winter- and spring-sown varieties, which differ in their requirement for vernalization to promote subsequent flowering. To date, all attempts to validate association genetics in barley by identifying major flowering time loci that control vernalization requirement (VRN-H1andVRN-H2) have failed. Here, we validate the use of association genetics in barley by identifyingVRN-H1andVRN-H2, despite their prominent role in determining population sub-structure.Results: By taking barley as a typical inbreeding crop, and seasonal growth habit as a major partitioning phenotype, we develop an association mapping approach which successfully identifiesVRN-H1andVRN-H2, the underlying loci largely responsible for this agronomic division. We find a combination of Structured Association followed by Genomic Control to correct for population structure and inflation of the test statistic, resolved significant associations only withVRN-H1and theVRN-H2candidate genes, as well as two genes closely linked toVRN-H1(HvCSFs1andHvPHYC).Conclusion: We show that, after employing appropriate statistical methods to correct for population sub-structure, the genome-wide partitioning effect of allelic status atVRN-H1andVRN-H2does not result in the high levels of spurious association expected to occur in highly structured samples. Furthermore, we demonstrate that bothVRN-H1and the candidateVRN-H2genes can be identified using association mapping. Discrimination between intragenicVRN-H1markers was achieved, indicating that candidate causative polymorphisms may be discerned and prioritised within a larger set of positive associations. This proof of concept study demonstrates the feasibility of association mapping in barley, even within highly structured populations. A major advantage of this method is that it does not require large numbers of genome-wide markers, and is therefore suitable for fine mapping and candidate gene evaluation, especially in species for which large numbers of genetic markers are either unavailable or too costly.