Analytical Approaches and Population Types for Finding and Utilizing QTL in Complex Plant Populations

In the past decade plant geneticists began using complex plant populations to identify QTL by association analysis, and the practice is becoming commonplace. Plant populations present unique challenges for association analyses. Plant populations vary in complexity and structure and analyses generally derived from human genetics have been applied to them,in a broad fashion. We review analytical techniques and their application in different plant populations. Analyses were classified as either family-based (FBAA) or population-based (PBAA). Over time, the different analyses have been generalized to accommodate a variety of populations, and are complementary. The PBAA are suited for populations with individuals that share little ancestry. Use of PBAA in these types of populations has dominated plant association analyses with success, though PBAA is unlikely to detect some important QTL in highly structured populations. Both PBAA and FBAA are suited for populations of related individuals. The use of FBAA in a breeding population warrants special attention due to features such as large population size, availability of phenotypic data, immediate relevance to marker-assisted selection, ease of QTL validation, and the computational simplicity of tests that require linkage for significance. Specific recommendations for PBAA and FBAA are made as well as some suggestions for future directions of research.