Quantitative Trait Locus mapping
Used to locate which loci are associated with a certain trait throughout the genome.
- We can figure out which % of the variation in the trait is controlled by each locus
- Can also tell us about interactions betweenloci
- Works best with lab populations since it works best if we sequence many individuals,
- Works even better if you have family/pedigree data.
Genetic linkage / Linkage maps
- By calculating recombination frequencies for pairs of genes we can see how the genes are ordered and their distances from each other on each chromosome
- We express distance in centimorgans (cM)
- 1% recombination frequency = 1cM = 1% change that the two markers will become separated in meiosis.
- See chart below showing crossing over and separating of B B genes on chart:
!GenomicAnalysis_1, p.12
Example: Tiger Moths
- WW and Wy genotypes are white, and yy genotypes are yellow:
- white individuals have a frequency dependent mating advantage, and fly more
- yellow individuals have lower levels of predation and stronger chemical defenses
- We are looking for the genetic basis of this trait
Part 1: Linkage Mapping to find candidate genes
- They did some crosses in the lab and generated RADseq data
- For our assignment, we have been providedwith processed data
- genotypes for each marker and phenotypes for each individual
- We will run linkage mapping analysis to find candidate genes for wing colour
- What genotypes will we expect in the offspring of this cross:
!GenomicAnalysis_1, p.19