QTL Mapping in Plant Populations

Abstract

Markers being detectable genetic loci, and having identified many of them polymorphic between two homozygous individuals, can be seen independently following Mendelian segregation among the progenies following recombination between these two parents. In combination, they follow linkage and recombination principles, paving way to determine the degree of nearness they might have in each chromosome (linkage group) they exist on. The process of arranging these markers in order based on their relative genetic distances between them is called mapping. Arrangement of a large set of markers distributed throughout the genome thus result in a number of marker groups which are independent of each other and without sharing any genetic distance information between them. These groups, equivalent to the basic number (X) of haploid genome of the individual are otherwise called as linkage groups or they are the chromosomes themselves. Basic principles of gene mapping One approach to gene mapping (linkage analysis) uses families with a known pedigree structure. Individuals are genotyped at random markers spread across the genome. If a disease gene is close to one of the markers then, within the pedigree, the inheritance pattern at the marker will mimic the inheritance pattern of the disease itself. Linkage analysis has been highly successful at finding genes for simple genetic diseases: i.e., those in which a single major gene is responsible for the disease in a given pedigree, and environmental factors are not very important. A second approach to gene mapping (association, or disequilibrium mapping) uses associations at the population level. The idea is that a disease mutation arises on a particular haplotype background, and so individuals who inherit the mutation will also inherit the same alleles at nearby marker loci. This process is complicated by recombination and mutation. In a sense, association mapping is not fundamentally different from linkage analysis, but instead of using a family pedigree, we have an unknown population genealogy. Because the population genealogy is much deeper than a family pedigree, disequilibrium mapping permits much finer-scale mapping than does linkage analysis (Hastbacka et al., 1992). It has also been argued (Risch and Merikangis, 1996) that in conjunction with new technology for rapid genotyping, this method will 38