Genome-Wide Patterns of Genetic Diversity and Association Mapping in Sunflower

Association mapping has become a valuable approach for the genetic dissection of complex traits, especially given the development of high-throughput genotyping platforms that have enabled the simultaneous interrogation of thousands of molecular polymorphisms. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. Overall, we found variable levels of linkage disequilibrium (LD). In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed elevated levels of differentiation between the two major breeding groups within the sunflower gene pool. We also used these data to perform association analyses on plant architecture (i.e., branching) and flowering time and successfully identified numerous associations underlying these agronomically and evolutionarily-important traits.