QTL analysis detects genetic loci that correlate with phenotypic variation by studying recombinant inbred lines created from crosses between two parental strains, breaking up combinations of alleles at different loci and allowing each locus's contribution to be measured independently. Structured populations are necessary because traits are usually influenced by multiple loci, so inbred strains have intermediate phenotypes due to mixtures of alleles, but recombinant inbred lines separate the alleles to identify the effects of individual loci.

1. Understanding the genotype-to-phenotype map: QTL Reminder: we have to have variation in both genotype and phenotype to find correlations.. QTL is a confusing name—really we mean alleles of loci that are in different areas of the genome that correlate with differences in the phenotypes.

2. How are QTL detected? Structured populations: this shows how recombinant inbred lines are made (using one chromosome as an example). B73 Mo17 So if the very bottom of the chromosome has an orange allele that confers increased growth , then lines 1 and 2 would be larger…provided no other loci were involved.

3. Why structured populations? Multiple loci for a phenotype are almost always found. + - Inbreds (like the orange and green ones indicated in the graphic) almost always have mixtures of ‘+’ and ‘-’ alleles at the different loci, so the inbreds have a ‘medium’ phenotype. We break up the mixtures of loci by doing the crosses, then we homozygose to ‘separate’ the various + and – alleles. + - + - + - - - + + + Note—this process is often called transgressive segregation. What growth phenotype would each RIL have?