Final Report Summary - 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.The goal of this project was to explore the limits of the GWAS approach using the model plant Arabidopsis thaliana, moving beyond marker-trait linkage disequilibrium to full sequence information. This goal was accomplished as evidenced by two landmark papers (Cell, 2016) describing full genome data for over 1135 lines, and a companion paper that added in data about gene expression and epigenetic regulation in the same set. Other contributions of the project include description of novel statistical methods, and a studies exploring particular features of the data, like variation for genome size.
