Utilisation and conservation of farm animal genetic resources 93
Chapter 4. Genomics reveals domestication history and facilitates breed development
to use a synthetic breed from the cross of two divergent breeds and randomly interbred for several generations cf. admixture mapping discussed later.
3.2.3. Selection mapping of QTL
In analysing large comparative genomic data sets, e.g. large SNP data sets it is possible to determine how and where both positive and negative selection has afected variation
Box 4.4. Detecting QTL’s in a F2 design. Let us imagine that we have genotyped animals from two diferent breeds. Morphologically
one breed has a large body size and a white colour and the other a small body size and a black colour. Let us consider a marker with a diferent allele being ixed in the lines. In the F2 animals
all possible combinations of morphological and marker alleles will appear. We can classify the animals to the genotypes MM, Mm and mm. he MM animals have a large body size, whilst
the mm animals are smaller with the Mm being intermediate. his would suggest that the Mm marker is close to a QTL related to growth. his is not the case for the colour trait because
now all the colour phenotypes appear with the same frequencies in the diferent weight classes. Obviously, sophisticated statistical techniques regression, maximum likelihood and Bayesian
methods will be implemented in practice in estimating both the position and the efect of the putative QTL
X
F
1
x F
1
MM
F
2
mm
Parental lines
Mm MM
mm The marker is associated
to the pig growth but not to the pig colour
94 Utilisation and conservation of farm animal genetic resources
Miguel Toro and Asko Mäki-Tanila
in farm animal populations. When a candidate gene for a trait, included in the breeding programme, is associated with a selective sweep in the genome, this could be used as
evidence for its inluence on the genetic variation. Myostatin was described before as the mutations causing extreme muscle mass double muscling of Belgian Blue Charlier
et al., 1995. Double muscling has been actively selected in several cattle breeds - despite
its adverse efects on calving. When three double-muscled and six non-double-muscled cattle breeds were analysed for the gene and 18 markers on the same chromosome,
there was a correlation between heterozygosity and the distance from the gene and linkage disequilibrium was greater in double-muscled breeds Wiener
et al., 2003. he results were not as consistent as would be expected and the authors considered the
age and history of selection to be distorting the patterns. Analogously, before genetic diversity patterns are implemented in locating QTL mediating variation in production
traits, it will be important to have information on such possible deviating factors in the breeds. Selection mapping has been successfully applied in comparing rat populations
for resistance to anticoagulants Kohn
et al., 2000.
3.2.4. QTL mapping in bottlenecked and admixture populations
Linkage disequilibrium is crucial for associating markers with loci mediating a variation in quantitative trait. Information on the distribution of LD is therefore important in
assessing the results from genome wide QTL studies. Such information is also critical in designing cost-eicient investigations. Many breeds are stemming from a small number
of founders and have experienced bottlenecks alternating with periods of population growth. he number of founders and bottlenecks afect the sampling of haplotypes and
thereby cause LD which can be used in localising genes in the QTL regions. Linkage disequilibrium extends over longer distances in young populations and enables the use
of fewer markers in an association study, but with the drawback that the position of the causal mutation will be poorly deined. Within modern dairy breeds LD extends
over several tens of centi-Morgans Farnir
et al., 2000. he older haplotypes shared by diferent breeds can then be used for a higher resolution mapping.
here has been varying degrees of gene exchange between farm animal populations since domestication, and where possible, even introgression of genes from wild populations.
he formation of a breed has in some cases aimed at the utilisation of more developed breeds in upgrading local landrace populations to reach a generally accepted breed
status. A good example of this is the wide use of Shorthorn in the development of several European cattle breeds.
Modern genetic improvement programmes in pigs and chicken are based on lines specialised on a small number of traits, whilst the production animals are their hybrids.
Kategori