Effects of Mating Types of Reference Family and Degree of Polymorphism on Constructing Genetic Linkage Map

Abstract

Effects of mating types of reference family, and number of marker alleles and the frequency were investigated using Monte Carlo computer simulation. The genetic linkage map was constructed using a reference population of intercross (F₂) or backcross comprising of 24 full sib families and 192 progenies derived from a cross between 12 sires and 24 dams. F₁ animals were produced by crossing three grandsires from a different breed with six grandams from another breed. Five types of reference populations were used to investigate the effect of mating types: F₂, four types of backcross between F₁ sires and purebred dams in male or female line, and between F₁ dams and purebred sires in male or female line. Each dam produced eight progenies. A chromosomal map length of 1.2M (Morgans), different number of alleles and their frequencies were assumed. The considered average intervals between markers were 0.05, 0.10, 0.15 or 0.20M with standard deviation of 0.0, 0.01, 0.02 or 0.03M, respectively. The distance between markers and lod scores were estimated using genotypic data from a reference population. F₂ had a higher led score than backcross, hence F₂ was preferred to backcross in the construction of linkage map. Efficiency of linkage analysis in the F₂ increased consistently, but the rate declined steadily as the number of alleles increased. The efficiency of linkage analysis did not depend on marker spacing.