Quantitative trait locus
In genetics, a section of a chromosome is referred to as a quantitative trait locus (abbreviated QTL , plural quantitative trait loci , German: region of a quantitative trait ) for which an influence on the expression of a quantitative phenotypic trait of the organism in question has been proven in corresponding studies . While discrete features, such as the flower color of plants , exist in several different, separate states, quantitative (continuous) features such as body size and weight can be measured on a continuous scale without gradation. The identification of chromosome segments with an influence on the expression of such characteristics is of particular interest in human genetics to find disease-relevant genes , in agricultural breeding research and in evolutionary biology . Studies to identify QTL have been conducted since around 1990.
Determination of Quantitative Trait Loci
To analyze QTL, studies with a large number of individual living beings are used to examine the expression of a certain characteristic in relation to variations in genetic markers. These markers are sections of the DNA sequence that appear in different individuals in different forms, called alleles . For QTL analyzes, gene markers with a high degree of polymorphism , i.e. a high number of different alleles, are of particular interest. Here are RFLP , - SNP - and STR particularly frequently used as a marker polymorphisms. All of these polymorphisms are so-called anonymous markers, as they are not assigned any functional meaning and, as a rule, they do not correspond to a specific gene.
For so-called genome-wide QTL studies, a larger number of markers is selected that are evenly distributed over the entire genome of the living organisms to be examined. The number of markers in relation to the total genome size is referred to as the marker density; a higher marker density allows the QTL to be better confined to a smaller chromosomal area. Based on such a marker selection, two different investigation approaches are possible.
Association Studies
In so-called genome - wide association studies, the corresponding alleles are determined for each marker in all individuals in a study group. Assuming that a certain marker has no relation to the investigated quantitative trait, a comparable distribution of the alleles is assumed in all areas of the trait expression. In this case, the frequency of the individual alleles of a marker does not differ between groups of individuals with differences in the characteristic expression.
An increasing or decreasing frequency of certain alleles of a marker with increasing or decreasing expression of the examined characteristic, or an otherwise markedly different allele distribution of a marker in different areas of the characteristic expression, for example the large and the small individuals of the examined group, is a Indication of an association between this marker and the examined characteristic. This is due to the fact that the smaller the distance between a marker and a gene that influences the expression of the trait, the greater the likelihood that this marker will be inherited coupled with this gene. As a result, the allele distribution of this marker is no longer random, but is associated with the characteristic expression. The likelihood of this is determined by a so-called LOD score . A LOD score greater than three for a marker is generally viewed in QTL studies as an indicator of a QTL at the position of that marker.
More often, analogous to the approach described, two study groups are examined that differ markedly in terms of the characteristics, for example one cultivated form of a plant species with normal growth height and another with dwarfism, or a group of patients with a certain disease and another group of healthy people . In this case, the allele frequency in both groups is determined for each marker. Markers with markedly different allele distribution between the two groups then show an association with the examined characteristic. The two study groups examined should, however, be as similar as possible in phenotype and genotype, with the exception of the characteristic to be examined . For association studies, depending on the relevance of the markers to be examined for the characteristic expression, a number of individuals up to three or four digits is required. They are therefore carried out particularly in the field of breeding research on plants and small animals.
Coupling studies
In coupling studies, the inheritance of the selected markers is examined in first-degree relatives, i.e. either between parents and their children or between siblings who are similar in terms of the trait to be examined. If a marker has no relation to the examined characteristic, assuming random inheritance, a parent and child are identical (concordant) with regard to their respective allele of this marker in 50 percent of all examined cases. However, the closer a marker is to a gene that influences the trait under investigation, the more the frequency of concordant parent-child combinations deviates from the 50 percent probability resulting from random inheritance. This is known as transmission disequilibrium (inheritance imbalance ) or linkage imbalance .
Similarly, with two siblings, the distribution to be expected based on random inheritance is that 25 percent of all sibling pairs do not have a common allele for a certain marker, have a common allele in 50 percent of all cases and agree in both alleles in 25 percent of all cases. Here, too, a deviation from this distribution for a certain marker in a corresponding number of sibling pairs examined indicates a proximity of this marker to a gene that has an influence on the examined characteristic. This respective gene and the marker are linked .
Coupling studies are particularly relevant if a sufficiently large number of individuals is not available for association studies, if the influence of the individual QTL on the characteristic expression is only slight or if the markers to be examined only have a few different alleles. They are therefore particularly relevant in human genetics.
Another concept based on the analysis of sibling pairs is called Affected Family Based Control (AFBAC). A group of sibling pairs is examined that are discordant with regard to the relevant characteristic, i.e. differ in this characteristic in two different states. For example, these can be siblings with a normal weight and an overweight person. If the allele distribution of a marker in the persons with one variant of the characteristic value deviates from the persons with the other variant, this is an indication of a connection between this marker and the characteristic value. Even if AFBAC studies are based on the examination of first-degree relatives, they are classed as association studies, since inheritance is not examined. However, if there is a sufficiently large number of fully examined families, a combination of AFBAC and coupling examinations within the same study group is also possible.
Relevance of Quantitative Trait Loci
For discrete traits, identifying the genes that are responsible for their inheritance is in many cases comparatively easy. As a rule, only one or a few genes are involved in the expression of such characteristics, so inheritance often corresponds to a classic inheritance pattern or can be described with sufficient accuracy by such. In contrast to this, the expression of quantitative traits is almost always determined by the interactions of a larger number of genes and by additional interactions of genetic predisposition with environmental factors . Such inheritance, referred to as “polygenetic”, does not follow a classic inheritance, since the proportion of each individual gene in the characteristic expression is comparatively small and also depends on the interactions mentioned. The identification of the genes involved in the expression of a quantitative characteristic is therefore methodologically very complex.
Identifying Quantitative Trait Loci is the first step in identifying genes for quantitative traits. By determining QTL, chromosomal sections are determined in which possible candidate genes are located. The size of the QTL and thus the number of candidate genes results from the marker density. A targeted investigation of a found quantitative trait locus with a higher marker density enables further narrowing down to individual genes. The number of candidate genes can also be further restricted by determining the known genes that are in the QTL found in appropriate databases and evaluating them with regard to a possible functional relationship to the trait being examined.
Quantitative trait loci primarily play a role in human genetics when identifying disease-relevant genes and gene variations. They are also of interest in breeding research without identifying the responsible genes . Identified QTL are used in the breeding of useful plants and animals for crossbreeding to specifically select crossing partners or offspring with the desired characteristic expression.
literature
- JI Weller: Quantitative Trait Loci Analysis in Animals. CABI Publishing, Wallingford 2001, ISBN 0-85199-402-4
- NJ Camp, A. Cox: Quantitative Trait Loci: Methods and Protocols. Series: Methods in Molecular Biology. Volume 195. Humana Press, Totowa 2002, ISBN 0-89603-927-7
- AH Paterson: Molecular Dissection of Quantitative Traits: Progress and Prospects. In: Genome Research. 5/1995. Cold Spring Harbor Laboratory Press, pp. 321-333, ISSN 1088-9051
- TF Mackay: The Genetic Architecture of Quantitative Traits. In: Annual Review of Genetics . 35/2001. Annual Reviews, pp. 303-339, ISSN 0066-4197