Trait Mapping Approaches Through Association Analysis in Plants

Previously, association mapping (AM) methodology was used to unravel genetic complications in animal science by measuring the complex traits for candidate and non-candidate genes. Nowadays, this statistical approach is widely used to clarify the complexity in plant breeding program-based genome-wide breeding strategies, marker development, and diversity analysis. This chapter is particularly focused on methodologies with limitations and provides an overview of AM models and software used up to now. Association or linkage disequilibrium mapping has become a very popular method for discovering candidate and non-candidate genes and confirmation of quantitative trait loci (QTL) on various parts of the genome and in marker-assisted selection for breeding. Previously, various QTL investigations were carried out for different plants exclusively by linkage mapping. To help to understand the basics of modern molecular genetic techniques, in this chapter we summarize previous studies done on different crops. AM offers high-resolution power when there is large genotypic diversity and low linkage disequilibrium (LD) for the germplasm being investigated. The benefits of AM, compared with traditional QTL mapping, include a relatively detailed mapping resolution and a far less time-consuming approach since no mapping populations need to be generated. The advancements in genotyping and computational techniques have encouraged the use of AM. AM provides a fascinating approach for genetic investigation of QTLs, due to its resolution and the possibility to study the various genomic areas at the same time without construction of mapping populations. In this chapter we also discuss the advantages and disadvantages of AM, especially in the dicotyledonous crops Fabaceae and Solanaceae, with various genome-size reproductive strategies (clonal vs. sexual), and statistical models. The main objective of this chapter is to highlight the uses of association genetics in major and minor crop species that have trouble being analyzed for dissection of complex traits by identification of the factor responsible for controlling the effect of trait. Graphical Abstract.