This detailed collection explores genome-wide association studies (GWAS), which have revolutionized the investigation of complex traits over the past decade and have unveiled numerous useful genotype–phenotype associations in plants. The book describes the key concepts and methods underlying GWAS, including the genetic architecture underlying variation for phenotypic traits, the structure of genetic variation in plants, technologies for capturing genetic information, study designs, and the statistical models and bioinformatics tools used for data analysis. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of invaluable implementation advice that leads to the most fruitful research results.