Abstract
Comparison of mating structure of F1 in reference family on the efficiency of linkage analysis was investigated using Monte Carlo computer simulation. The genetic linkage map was constructed using a two generation reference population comprising of 24 full sib families and 192 progenies derived from a intercross between 12 F1 sires and 24 F1 dams. F1 animals were produced by crossing three grandsires from a different family line with six grandams from another family line. The mating of F1 was considered to be (1) avoiding sib mating, (2) random mating and (3) full sib mating. A chromosomal map length of 1.2 Morgans was assumed. The average interval between markers was 0.05, 0.10, 0.15 or 0.20 Morgans and all DNA markers or genes had two allelles. The considered markers were placed at regular or random intervals on a chromosome. The marker alleles of each initial population were fixed or random with a 0.5 expected frequency. Chromosomal map length and recombination rate between markers with the lod scores (Z) were estimated using genotypic data from the reference population. Full sib mating of F1 yielded the largest mean square error and avoiding sib mating yielded the smallest mean square error of chromosomal map length and recombination rate. Rate of 3<Z became higher in the order, (1), (2), (3). The difference between (1) and (3) increased with increase in average interval between markers on a chromosome.
