Experimental design example. Strains are crossed and hybrid progeny are collected. The progeny are grouped by phenotype and the pooled DNA of each group is subjected to high-throughput DNA sequencing. Loci that affect the phenotype show an enrichment for one strain in each pool, while other unlinked loci segregate evenly. The bottom two plots show simulated (unobserved) allele frequencies in the pool with blue lines and (observed) allele frequencies computed from simulated 50X sequencing coverage in red.
Edwards and Gifford BMC Bioinformatics 2012 13(Suppl 6):S8 doi:10.1186/1471-2105-13-S6-S8