Testing for Linkage Between a Marker Locus and a Major Gene Locus in Half-Sib Families

Abstract

Large half-sib families are commonly generated in animal breeding by mating one male to many females. One such situation is where sires must be progeny tested to determine their genotype at a major gene locus. The families of those sires found to be heterozygous for the major gene provide a good pedigree structure for a linkage analysis between the gene and genetic markers. This is the case even when the dams have not been individually identified for the progeny test, and so the only genotype information known about them is that they are noncarriers of the major gene (marker genotype is unknown). This article examines the methods and general application of linkage analysis between a marker locus and a major gene locus for large half-sib families. The methods presented, which use information from all the progeny, are compared with those using only the progeny that can be assigned as being recombinant or nonrecombinant (given the sire's phase). The use of all the progeny has the most advantage for diallelic systems with unequal gene frequencies of the marker alleles in the dam population. It is also shown that in many cases the lack of dam marker information does not result in a great loss of information.