Table 4.

Work flow

Study	Aim	Material	Method	details
Genome scan	Search for QTL	Sub data of F2 population (randomly selected 7 half-sib families)	Linkage analyses of 162 microsatellites on 27 chromosomes	668 F2 hens
Fine-mapping	Focusing on the QTL area	Whole F2 mapping population (17 half-sib families)	6 new microsatellite markers + 5 SNPs	1599 F2 hens
Sequencing	SNP detection	Lohmann Brown, Hy-Line		106 indivuals in LB 20 invidivuals in Hy
Histo-pathology	Tissue analysis	Eggs from a broiler breeding hatchery	Light microscopy study	480 eggs
Confirmation	Association studies in independent commercial lines	1) Lohmann Brown (767 hens)	Mixed models with DMU	whole pure line hen population (767 hens): MCW241 -sub data I: ZO-2 (516 hens) -sub data II: phenotypically extreme 416 hens: panel of 15 SNPs
		2) Hy-Line (290 males)	Linear model with least squares, SAS	-all genotyped with MCW241 -all genotyped with a panel of 5 informative SNPs

Different phases and aims of the study are shown in the 1^st and 2^nd columns. Populations and subsets are presented in the 3^rd column followed with the methods and details in the 4^th and 5^th columns.