15.5: Quantitative Trait Locus (QTL) Analysis
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- Ying Liu
- City College of San Francisco
Most of the phenotypic traits commonly used in introductory genetics are qualitative, meaning that the phenotype exists in only two (or possibly a few more) discrete, alternative forms, such as either purple or white flowers, or red or white eyes. These qualitative traits are therefore said to exhibit discrete variation . On the other hand, many interesting and important traits exhibit continuous variation ; these exhibit a continuous range of phenotypes that are usually measured quantitatively, such as intelligence, body mass, blood pressure in animals (including humans), and yield, water use, or vitamin content in crops. Traits with continuous variation are often complex, and do not show the simple Mendelian segregation ratios (e.g. 3:1) observed with some qualitative traits. Many complex traits are also influenced heavily by the environment. Nevertheless, complex traits can often be shown to have a component that is heritable, and which must therefore involve one or more genes.
How can genes, which are inherited (in the case of a diploid) as at most two variants each, explain the wide range of continuous variation observed for many traits? The lack of an immediately obvious explanation to this question was one of the early objections to Mendel's explanation of the mechanisms of heredity. However, upon further consideration, it becomes clear that the more loci that contribute to trait, the more phenotypic classes may be observed for that trait (Figure \(\PageIndex{1}\)).
If the number of phenotypic classes is sufficiently large (as with three or more loci), individual classes may become indistinguishable from each other (particularly when environmental effects are included), and the phenotype appears as a continuous variation (Figure \(\PageIndex{2}\)). Thus, quantitative traits are sometimes called polygenic traits , because it is assumed that their phenotypes are controlled by the combined activity of many genes. Note that this does not imply that each of the individual genes has an equal influence on a polygenic trait – some may have major effect, while others only minor. Furthermore, any single gene may influence more than one trait, whether these traits are quantitative or qualitative traits.
We can use molecular markers to identify at least some of the genes (those with a major influence) that affect a given quantitative trait. This is essentially an extension of the mapping techniques we have already considered for discrete traits. A QTL mapping experiment will ideally start with two pure-breeding lines that differ greatly from each other in respect to one or more quantitative traits (Figure \(\PageIndex{3}\)). The parents and all of their progeny should be raised under as close to the same environmental conditions as possible, to ensure that observed variation is due to genetic rather than external environmental factors. These parental lines must also be polymorphic for a large number of molecular loci, meaning that they must have different alleles from each other at hundreds of loci. The parental lines are crossed, and then this F 1 individual, in which recombination between parental chromosomes has occurred is self-fertilized (or back-crossed). Because of recombination (both crossing over and independent assortment), each of the F 2 individuals will contain a different combination of molecular markers, and also a different combination of alleles for the genes that control the quantitative trait of interest (Table \(\PageIndex{1}\)).