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Modern Genetic Analysis Chapter 18. Quantitative Genetics
Locating the Genes

It is not possible with purely genetic techniques to identify all the genes that influence the development of a given trait. This is true even for simple qualitative traitsfor example, the genes that determine the total antigenic configuration of the membrane of the human red blood cell. About 40 loci determining human blood groups are known at present; each has been discovered by finding at least one person with an immunological specificity that differs from the specificities of other people. Many other loci that determine red-cell membrane structure may remain undiscovered because all the individuals studied are genetically identical. Genetic analysis detects genes only when there is some allelic variation. In contrast, molecular analysis, by dealing directly with DNA and its translated information, can identify genes even when they do not varyprovided the gene products can be identified.

Even though a trait may show continuous phenotypic variation, the genetic basis for the differences may be allelic variation at a single locus. Most of the classical mutations in Drosophila are phenotypically variable in their expression, and in many cases the mutant class differs little from wild type, so many individuals that carry the mutation are indistinguishable from normal. Even the genes of the bithorax gene complex, which have dramatic homeotic mutations that turn halteres into wings (see pages 520521), also have weak alleles that increase the size of the haltere only slightly on the average, so individuals of the mutant genotype may appear to be wild type.

It is sometimes possible to use prior knowledge of the biochemistry and development of an organism to guess that variation at a known locus is responsible for at least some of the variation in phenotype. This locus then is a candidate gene for investigation of continuous phenotypic variation. An example is the variation in activity of the enzyme acid phosphatase in human red blood cells. Because we are dealing with variation in enzyme activity, a good hypothesis would be that there is allelic variation at the locus that codes for this enzyme. When H. Harris and D. Hopkinson sampled an English population, they found that there were, indeed, three allelic forms, A, B, and C, with different activities. Table 18-1 shows the mean activity, the variance in activity, and the population frequency of the six genotypes. Figure 18-9 shows the distribution of activity in the entire population and how it is composed of the distributions of the different genotypes. Table 18-1 shows that, of the variance in activity in the total distribution (607.8), about half is explained by the average variance within genotypes (310.7), so half (607.8 310.7 = 297.1) is accounted for by the variance between the means of the six genotypes. Although much of the variation in activity is explained by the mean differences between the genotypes, there remains variation within each genotype that may be the result of environmental influences or of the segregation of other, as yet unidentified, genes. This partial explanation of variation by alleles at a single identified locus is typical of what is found by the candidate gene method, and the proportion of variance associated with the single locus is usually less than what was found for acid phosphatase. For example, the three common alleles for the gene apoE that encodes the protein apolipoprotein E account for only about 16 percent of the variance in blood levels of low-density lipoproteins that carry cholesterol and are implicated in excess cholesterol levels.

Marker Gene Segregation

The genes segregating for a quantitative trait, so-called quantitative trait loci, or QTLs, cannot be individually identified in most cases. It is possible, however, to localize those regions of the genome in which the relevant loci lie and to estimate how much of the total variation is accounted for by QTL variation in each region. This analysis is done in experimental organisms by crossing two lines that differ markedly in the quantitative trait and differ in alleles at well-known loci, marker genes, where the different genotypes can be distinguished by criteria such as some visible phenotypic effect that is not confused with the quantitative trait (say, eye color in Drosophila) or by the electrophoretic mobility of the proteins that they encode or by the DNA sequence of the genes themselves. The F1 between the two lines is then crossed with itself to make a segregating F2 or it may be backcrossed to one of the parental lines. If there are QTLs closely linked to a marker gene, then the different marker genotypes in the segregating generation will also carry the QTL alleles that were linked to them in the original parental lines. Thus different marker genotypes in the F2 or backcross will have different average phenotypes for the quantitative character.

Linkage Analysis

The localization of QTLs to small regions within chromosomes requires that there be closely spaced marker loci along the chromosome. Moreover, it must be possible to have parental lines that differ from each other in the alleles carried at these loci. For most of the history of genetics these requirements could not be met, even in a genetically well known species such as Drosophila, because most marker loci were known from severe morphological mutants that had deleterious effects on the viability and fecundity of their carriers. As a result, it was not possible to create a line that carried large numbers of mutant alleles that would distinguish it from an alternative line carrying the wild-type alleles. With the advent of molecular techniques that can detect genetic polymorphism at the DNA level (see pages 541542), a very high density of variant loci has been discovered along the chromosomes of all species. Especially useful are restriction-site polymorphisms and tandem repeats in DNA (see pages 343345, 386389, and 505). Such polymorphisms are so common that any two lines selected for a difference in quantitative traits are also sure to differ from each other at known molecular marker loci spaced a few crossover units from each other along each chromosome.

An experimental protocol for localizing the genes uses groups of individuals that differ markedly in the quantitative trait and differ at marker loci. These groups may be created by a number of generations of divergent selection to create extreme lines, or advantage may be taken of already existing varieties or family groups that differ markedly in the trait. These lines must then be surveyed for marker loci that differ between them. A cross is made between the two lines, and the F1 is crossed with itself to produce a segregating F2 or is crossed back to one of the parental lines to produce a segregating backcross. A large number of offspring from the segregating generation are then measured for the quantitative trait and characterized for their genotype at the marker loci. A marker locus that is unlinked or very loosely linked to any QTLs will have the same average value of the quantitative trait for all its genotypes, whereas one that is closely linked to some QTLs will differ in its mean phenotype from one of its genotypes to another. How much difference there is in the mean phenotype between the marker locus genotypes depends both on the strength of the effect of the QTLs and on the tightness of linkage between the QTLs and the marker locus. Suppose, for example, that there are two selected lines that differ by a total of 100 units in some quantitative character and that the high line is homozygous + / + at a QTL, whereas the low line is homozygous / , and that each + allele at this QTL accounts for 5 units of the total difference between the lines. Further suppose that the high line is M / M and the low line is m / m at a marker locus 10 crossover units away from the QTL. Then, as shown in Figure 18-10, there are 4 units of difference between the average gamete carrying an M allele and an average gamete carrying an m allele in the segregating F2, or 8 units of the difference between the two original homozygous lines. Thus we have accounted for 8 percent of the average difference between the lines, although the QTL actually accounts for 10 percent of the difference. The discrepancy comes from the recombination between the marker gene and the QTL.

This technique has been used to locate chromosomal segments associated with such traits as fruit weight in tomatoes and bristle number in Drosophila. Typically, any marker region will account for a few percent of the effect, but taken altogether it is possible to account for as much as half of the total difference between lines. Unfortunately, in human genetics, although marker-gene segregation can be used to attempt to localize single-gene disorders, the small size of human pedigree groups makes the marker-segregation technique inapplicable for quantitative trait loci.

© 1999 by W. H. Freeman and Company. All rights reserved.