lSummary of Part 2:
1. Covered the basics of QTL analysis and mapping.
2. Reviewed difference between genetic and physical maps.
3. Discussed interpreting features of QTL maps including the LRS function, the additive effect function, the bootstrap bars, and the permutation thresholds.
4. Illustrated technics to generate a list of positional candidates.
5. Discussed some factors used to evaluate candidate genes.
What does a QTL signify? A good QTL is a claim that a particular chromosomal region contains a causal source of variation in the phenotype. The importance of this hypothesis depends on the quality and relevance of the phenotype and the statistical strength of the QTL. As usual, test and be skeptical.