Advanced intercross lines and genetic markers

The chicken combs used in this study were obtained from an F8 population generated by crossing a line of selected White Leghorn maintained from the 1960s and a population of Red Junglefowl obtained from Thailand. A genetic map, consisting of 651 informative SNP markers, was used in conjunction with 326 F8 individuals (201 males and 125 females) for the interval mapping. These markers resulted in a map of length ∼9,200 cM, with an average marker spacing of ∼16 cM. Of these markers, 551 were fully informative (differentially fixed between the parental populations), with the markers selected so as to be evenly spread over the genome (as reflected in the average marker spacing) (Wright et al. 2010, 2012). This marker density is greater than the recommended 20–30 cM marker intensity for QTL analyses (Darvasi and Soller 1994). A more detailed description of the intercross can be found in Johnsson et al. (2012).