Using Natural Allelic Diversity to Evaluate Gene Function

Genomics has developed a wide range of tools to identify genes that play roles in specific pathways. However, relating individual genes and alleles to agronomic traits is still quite challenging. We describe how association analysis can be used to relate natural variation at candidate genes with agronomic phenotypes. Association approaches in plants can provide very high resolution and can evaluate a wide range of alleles rapidly. We discuss issues related to experimental design, germplasm sample, molecular assay, population structure, and statistical analysis necessary for association analysis in plants.