MAXMAP · Developing maximum-resolution genotype-phenotype maps using whole-genome polymorphism data

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association studies (GWAS) have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation. They are particularly useful when inbred lines are available because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost-effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we propose to continue our groundbreaking GWAS work in the model plant Arabidopsis thaliana. We will explore the limits of the approach, moving beyond marker-trait linkage disequilibrium to full sequence information. We will carry out GWAS of important life-history traits using over 1000 inbred A. thaliana lines for which nearly complete sequence information is available. The GWAS will be complemented by linkage mapping in F2 crosses to eliminate confounding linkage disequilibrium, associations will be verified experimentally, and confirmed causal polymorphisms will be added to the model in an iterative manner in order to create an increasingly refined genotype-phenotype map.