Association Mapping in Plant Genomes

Abstract

One of the many goals of plant geneticists and breeders pertains to the explanation of phenotypic variation as it relates to changes in DNA sequence (Myles et al., 2009). The development of molecular markers for the detection and exploitation of DNA polymorphisms in plant systems is one of the most significant developments in the field of molecular biology and biotechnology. Linkage mapping has been a key tool for identifying the genetic basis of quantitative traits in plants. However, for linkage studies, suitable crosses, sometimes limited by low polymorphism or small population size, are required. In addition, only two alleles per locus and few recombination events are considered to estimate the genetic distances between marker loci and to identify the causative genomic regions for quantitative trait loci (QTL), thereby limiting the mapping resolution. To circumvent these limitations, linkage disequilibrium (LD) mapping or association mapping (AM) has been used extensively to dissect human diseases (Slatkin, 2008). This approach has received increased attention during the last few years. AM has the potential to identify a single polymorphism within a gene that is responsible for phenotypic differences. AM involves searching for genotype-phenotype correlations among unrelated individuals. Its high resolution is accounted for by the historical recombination accumulated in natural populations and collections of landraces, breeding materials and varieties. By exploiting broader genetic diversity, AM offers three main advantages over linkage mapping: mapping resolution, allele number and time saving in establishing a marker-trait association and its application in a breeding program (Flint-Garcia et al., 2003). Although AM presents clear advantages over linkage mapping, they are often applied in conjunction, especially to validate the associations identified by AM, thus reducing spurious associations.