Association mapping, a method to detect quantitative trait loci: statistical bases

Traditionally, QTL mapping has been used as methodology to understand the genetic control of polygenic traits and has been useful for identifying QTL in different species, however QTL mapping presents limitations, such as the difficulty to build segregating populations in some species, the presence of only one meiotic generation and the reduced genetically diversity derived of just two parental. Recently, association genetics studies are becoming an important methodology to identify quantitative trait loci and to find diagnostic molecular markers associated with complex traits. This methodology overcomes some barriers of QTL mapping and it is an alternative to apply in plant breeding in direct way. However, it is necessary to considerer important aspects in this methodology to avoid false associations between trait-markers. Association genetics employs as parameter linkage disequilibrium to find these associations. Here we present methods to analyze and establish population structure, factors that affect linkage disequilibrium and how to measure it and methods to perform association mapping.