When you're dealing with multigenetic traits, figuring out what genes are responsible for a particular trait is harder but not impossible. The strategy for identifying the relevant genes in the genome of a particular organism involves quantitative trait loci mapping (QTL mapping, for short). With QTL mapping, you cross lots of individuals and keep track of how particular genetic markers in the offspring correlate with the character you're interested in. These markers aren't themselves the genes responsible for the quantitative trait, but because they're correlated with the phenotype, they can be used to identify the location on the chromosomes where the genes reside.
A marker gene is any gene that's easy to recognize because its location on the genome is known. Imagine, for example, that people with green eyes are on average taller. We know that tallness is a function of many genes, but now we know that one of these genes is near the gene that controls green eye color. The two genes are in close proximity. They are closely linked — they tend to be inherited together. (Go to Chapter 5 or more details on linkage.)
Here's how QTL mapping works: Scientists know where the marker gene is, and now they know that some gene near it is responsible in part for a multi-genetic trait. The mathematics of how this works is beyond the scope of this book, but what's important is that it does work. (And it works even better for species for which we have a lot of gene sequences where we can go in and see exactly which genes are near the marker loci!)
By using the markers as signposts, scientists can
1. Figure out approximately how many genes underlie a given multigenetic trait
2. Tease apart the details of gene interactions
3. Understand the relative importance of different genes to see which genes have stronger effects than others
4. Voila! Actually have a good idea where to look in the genome for the relevant genes.
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