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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.
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DefinitionsHitch-hiking is the change in the frequency of an allele due to selection on a closely linked locus with a positive allele Signature of selection or selection footprint is the pattern of reduced diversity neighbouring on a chromosome to a gene that has been strongly selected for or against within a population |
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.
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DefinitionsLinkage is the phenomenon by which alleles at loci that are close together on a chromosome and which have been inherited together from one parent of an individual tend to be passed on together to an individual’s offspring. The closer the loci are on a chromosome the stronger is this phenomenon. When the loci are on different chromosomes then this tendency is completely absent Linkage disequilibrium is a fixed combination of alleles in haplotypes. Over time recombination events between loci will remove this combination, more quickly the further away the loci are from each other Bottleneck is a period when the number of parents used to reproduce the breed was particularly small. In such a period the genetic drift is high due to a marked reduction in the size of the population Introgression is transfer of an allele or set of alleles from one breed to another. This is achieved by the crossing of a number of parents from the donor breed to the recipient breed, followed by systematic backcrossing to the recipient breed, with parents chosen to be carriers of the desired alleles. Markers can be used to detect these carriers |
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