Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications

Linkage analysis and map construction using molecular markers is far more complicated in full-sib families of outbreeding plant species than in progenies derived from homozygous parents. Markers may vary in the number of segregating alleles. One or both parents may be heterozygous, markers may be dominant or codominant and usually the linkage phases of marker pairs are unknown. Because of these differences, marker pairs provide different amounts of information for the estimation of recombination frequencies and the Linkage phases of the markers in the two parents, and usually these have to be estimated simultaneously. In this paper we present a complete overview of all possible configurations of marker pairs segregating in full-sib families. Maximum likelihood estimators for the recombination frequency and LOD score formulas are presented for all cases. Statistical properties of the estimators are studied analytically and by simulation. Specific problems of dominant markers, in particular with respect to the probability of detecting linkage, the probability of obtaining zero estimates, and the ability to distinguish linkage phase combinations, and consequences for mapping studies in outbred progenies are discussed.