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Although this is an extremely flexible technique, the resolution of the
detected loci is limited by the number of recombinations present in the test
cross ( Darvasi, 1998; Lynch and Walsh, 1998 ). Typically this means that the
resolution of each QTL is rather low, and relatively few QTL have been
refined to the causative gene (often referred to as Quantitative Trait Genes or
Quantitative Trait Nucleotides if the exact mutation is identified) though this
is beginning to change.
Association mapping is a similar technique, but frequently uses a single
outbred population and a high-density SNP analysis, to identify QTL. The
difference with this technique is that as outbred or single large populations
are used, many more recombinations are present and therefore the resolution
is far greater. In contrast, however, many more markers are required per
individual and population substructure can be an issue. Additionally, in such
large populations, the genetic architecture tends to be very complicated
(as far more polymorphisms and alleles are being considered than in a
standard QTL cross which utilizes inbred populations/individuals and most
commonly only two different populations). Results with association mapping
in large populations in humans tend to show that very few QTL with large
effects are present, and very little of the variance present can be explained
by the loci which are discovered ( Carlson et al., 2004 ). However, in the
case of domestic animals, they possess many features that make them more
amenable to this analysis ( Goddard and Hayes, 2009 ). Firstly, the strong
directional effects of domestication selection can mean that fewer markers
are required as haplotype blocks are larger (for instance in the case of the
dog ( Karlsson et al., 2007 )) and the genetic architecture is less complex than
more outbred populations, in terms of the numbers of alleles present which
affect the trait at any given QTL. This does have the drawback that only
large regions are identified, however, when combined with multiple breeds
very narrow regions can be identified. Jones et al. used this to tentatively
map QTL for distinct breed characteristics,
including pointing, herding,
boldness and trainability ( Jones et al., 2008 ).
Selective Sweep Mapping
Linkage disequilibrium and the identification of selective sweeps is potentially
an extremely powerful tool for the dissection of genetic architecture, and
shows great potential in domestic populations ( Andersson and Georges, 2004 ).
The basis of selective sweeps is that when a new mutation arises in a popula-
tion and is then subjected to strong directional selection, not only it but the
haplotype it arose in will go to fixation. The surrounding SNP markers will
therefore “hitch-hike” alongside the mutation ( Smith and Haigh, 1974 ).
Once fixation is reached, depending on the strength of selection and the
time that has elapsed since fixation, this signature of selection will be slowly
eroded. In the case of domestic populations, the strength of selection is often
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