ABSTRACT
Neutral molecular markers, such as isozymes, restriction fragment length polymorphism or simple sequence repeat, have brought about important advances in the understanding of the structure of genetic diversity in numerous species. This chapter focuses on the analysis of the diversity of genes of interest and the study of this molecular diversity for the purpose of functional validation or fine mapping. Numerous studies have described the molecular diversity of genes, mostly in maize and A. thaliana. Maize has a overall high molecular diversity that varies considerably among genes. Vertical sequencing studies of candidate genes have resulted in the identification of intraspecific polymorphisms and are increasing in number. Even with the fast evolution of sequencing techniques and costs, it may be valuable to conduct the process of genotyping in two stages: the sequencing of a subsample of the collection and then the genotyping of the entire collection with appropriate marker techniques.
