I think that one major difference is the amount of work then analysis of results required between the two techniques. Homozygosity mapping is based on a mutation happening in a founder person on one chromosome. The change will be passed on to the children along with half of the founder genome but still linked to close marker alleles. With each generation the uninteresting part of the genome is halved to the next generation but the change and closely linked markers will always stay together. If we have an inbreeding situation 6 generations down then the change will be inherited from both parents and the child will be affected ( if heritance is recessive.). The close markers will also be inherited so a region of homozygosity by descent is created and the change is in that region.

In this case and assuming the change is rare in the population then the generations of the family have done most of the work and after 6 generations 1/(2exp6) of the genome may contain the gene and 63/64 has been excluded so not too many more markers ned to be run in areas of interest which are obvious by visualisation since they are homozygous for the markers nun. Homozygosity mapping can be carried out on affected individuals only without needing other relatives but exclusion mapping has an absolute need for parenal dna and other family members dna to establish linkage

Exclusion mapping excludes areas where the gene is not so hundreds of markers have to be analysed on a number of families for linkage and some of these may be linked but not informative and the analysis is more complicated . Recent chip technology and NGS has changed this greatly as the amount of information gained on each sample is huge

The mapping of genes involved in rare recessive disorders in large outbred population is often a difficult task because of the lack of families with multiple affected individuals. Homozygosity mapping is an efficient gene mapping method applicable to rare recessive disorders in inbred populations. Indeed, the method takes advantage of the fact that inbred affected individuals are likely to have two recessive copies of the disease allele from a common ancestor; i.e. two identical‐by‐descent (IBD) alleles. Since small chromosomal regions tend to be transmitted whole, affected individuals will also have identical‐by‐descent alleles at markers located nearby the disease locus and thus will be homozygous at these markers. The basic idea of the method to locate genes involved in rare recessive traits is thus to search for regions of homozygosity that are shared by different affected individuals ( Génin and Todorov ,2007).