Quantitative Trait Loci and Single Nucleotide Polymorphism

tional physical map data (especially on the Z chromosome), has paved the way for defining gene function and genetic background for phenotypic variation in the chicken (Miller, 2006). Inbred lines and crosses derived from them provide a powerful tool for detection of gene’s function and interactions involved in controlling various traits such as immunity, disease resistance, growth, and production. Furthermore, preserved selected lines are still essential to define the genetics of many traits, and are important for a variety of problems in basic and applied avian biology (Miller, 2006). The most important step in the selection of a candidate population for linkage analysis is the generation of appropriate resource populations. Abstract. Three single cross populations were generated in order to analyze factors affecting the ability to detect true linkage with minimum false positive or false negative associations, and to detect associations between markers and quantitative traits. The three populations are: (1) a broiler ! broiler cross of a single sire and 34 dams, resulting in 266 progeny; (2) a broiler ! broiler cross of a single sire and 41 dams resulting in 360 progeny; and (3) a broiler ! layer cross of a single sire with 56 dams resulting in 1180 progeny. Based on these three resource populations we show that: a) gradient selective genotyping was more effective than the random selective genotyping; b) selective genotyping was significant at a selected proportion less than 62% of the cumulative truncation point; c) as few as 10% of selected individuals (5% of each of the two tails) were sufficient to show significant association between markers and phenotypes; d) a gradient slices approach was more powerful than using replicates of the extreme groups; and e) in resource popula-