Using the Complementation Test to Assess a Putative QTL

Suppose that two alleles have the same homozygous phenotype—white eyes, say. To test whether these are actually alleles of the same gene, the stocks are crossed to produce individuals that inherit one allele from one parent and one from the other parent. If these individuals look the same as the original homozygotes, then it is likely that both alleles are variants of the same gene. If, on the other hand, the cross produces wild-type individuals, then the alleles are likely to be in different genes, and their different effects are said to complement. The same idea can be used where the phenotype is a quantitative trait and where one of the alleles is a putative QTL. If the effect of a QTL is increased when it is put against a loss-of-function mutation in a candidate gene, then it is likely to be due to a more or less recessive allele at the same locus. Figure WN14.3 shows how this method was used to demonstrate that a QTL responsible for differences between maize and teosinte was identical to the gene tb1. Just as with discrete alleles, the test is not foolproof: It relies on the QTL being recessive, and alleles at different loci may fail to complement if their effects interact epistatically. Nevertheless, it is the simplest approach in cases where a stock is available that carries mutations to the candidate gene (see Mackay 2001b).