ABSTRACT
Association mapping is an attractive approach used to detect complex quantitative trait loci (QTLs) and to identify candidate genes, based on linkage disequilibrium (LD) between genetic markers and genes controlling the phenotype of interest by exploiting the recombination events accumulating over many generations. Many factors affect linkage disequilibrium such as genetic drift, selection within populations, population admixture, recombination, genetic bottlenecks, founder effects and mating systems. Association mapping can be grouped into genome-wide association mapping and candidate-gene association mapping and the appropriate approaches can be selected based on the study of interest in different plant species. The success of association analysis depends on the choice of germplasm, quality of genotypic and phenotypic data, use of the appropriate statistical analysis for the detection of marker- phenotype associations and the validation of marker-phenotype associations. In recent years, it has continued to gain favorability in plant genetic research because of advances in high throughput genomic technologies, interests in identifying novel and superior alleles and improvements in statistical methods. In this chapter, we describe the opportunities and challenges of association mapping in plants for complex trait dissection.
