Genome-Wide Association Studies (GWAS) are processes that are performed to scan the entire genome of sampled individuals and associate hundreds of thousands or even millions of genetic variants in these individuals with target phenotypic traits or characters. This book is written to introduce and demonstrate with examples the theoretical and practical knowledge and skills that may be needed in GWAS studies, from theoretical knowledge to data structures and the use of well-known software. The book is designed to be used both as a learning resource and as a reference source. In addition to GWAS, the book also provides basic information for population structure, genetic diversity and genomic selection studies.