YANG DA (1), Paul M. VanRaden (1), Ning Li (2), and Changxin Wu(2)

1. Animal Improvement Programs Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705-2350, USA
2. China Agricultural University, Beijing 100091, People's Republic of China

The reference family panel is the foundation of a gene mapping program because it affects the cost and quality of the genetic linkage maps. An optimum design should be one that minimizes the gene mapping cost for the same quality of linkage maps. A map cost function was defined as the number of genotypes required per unit of map coverage and was used to determine the optimum detection level and to measure the efficiency of each design. For different designs, the optimum detection levels of recombination frequency that minimizes the map cost were found to be in the neighborhood of 0.11-0.15. As the family size increases, the optimum detection level increases and the map cost decreases. Substantial reduction in map cost can be achieved by using highly polymorphic markers. Grandparents are important for small families in the reduction of map cost and become less important as the family size increases or as the detection level decreases. Assuming equal recombination frequency in adjacent marker intervals, the optimum level of recombination frequency for ordering loci was found to be around 0.12, which overlaps the optimum detection level. However, ordering loci would require more genotypes than detecting linkage. To order closely linked loci, much larger sample size would be required. Nine designs applicable to domestic animals were described with seven three-generation and two two-generation families or six full-sib and three half-sib families. Sample size and map cost requirements were derived for three full-sib and three half-sib designs.