An important assumption in studies with markers using ”non-functional” DNA (not responsible for the production of a protein) is that these markers are neutral i.e. are not associated with alleles for traits under selection. The issue over the neutrality of the markers is important since it is assumed that these markers change in frequency only by genetic drift, rather than by drift and selection. The neutrality of a locus may differ between breeds since: (i) one breed may have important alleles that are not present in another; and (ii) different livestock breeds will be subject to different selection criteria, with these largely dominated by the selection objectives of the breeders concerned.
The genome is organised into chromosomes and this introduces the phenomenon of linkage of alleles on different loci (when no recombination between these loci occur during meiosis, these alleles are transferred as a fixed combination of alleles from one generation to the next). One consequence of linkage is that alleles that are on the same chromosome and close to a new favourable mutation will be tend to increase in frequency alongside the mutation in a process termed ‘hitch-hiking’.
It is very likely that the alleles very closely linked to the mutation will also become fixed in the population. Therefore this region of the chromosome, very close to the locus under selection, will display very low diversity in the neighbouring loci within a breed. An examination of allelic diversity throughout the genome may therefore show patterns of regions of high diversity and by regions of relatively low diversity. This pattern of diversity within the genome is called a signature of selection or selection footprint and may indicate loci important for domestication, or for the characteristics of particular breeds, or simply highly-conserved regions for the species as a whole, whether wild or domesticated. Effective searching for selection footprints is only just beginning in livestock species with the availability of genome-wide markers such as SNPs.
More generally, the expansion in DNA information will allow the diversity of allelic combinations at loci distributed throughout the genome to be studied. This type of diversity within breeds will depend not only on the allele frequencies but also on the extent of linkage of alleles disequilibrium (LD) that is observed. This LD, the transfer of a fixed combination of alleles from one generation to the next, may arise from the breed history of population size and population management over time. E.g. in the past such that combination of alleles was present in the limited number of animals used for breeding in one generation (the intensive use of a popular sire or a genetic bottleneck) or were introduced in the breed by introgression.