Marker-assisted selection
The second application of a genetic marker is the tracing of alleles with a favourable effect in marker-assisted selection. Many genetic markers were found in production animals that were closely linked to a QTL with a favourable effect on many traits. Only a few QTL have been found; therefore the use of markers in selection was limited until genomic selection was introduced.
The third application of a genetic marker is the tracing of alleles with an unfavourable effect. First rate examples are monogenic recessive genetic defects that are present in all species. The next table gives an overview of the total number of recorded genetic defects per species, the disorders that are monogenic recessive traits (Mendelian trait), the disorders from which the mutation in DNA is known and for which a genetic marker available and the number of genetic defects that can be used to study human diseases:
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Genetic markers for monogenic recessive traits are very valuable, because they can be used to detect the heterozygote carriers of the allele, heterozygous animals that do not show any symptoms of the genetic defect but do transmit it to 50 per cent of their offspring. The mating of two heterozygous animals gives with a chance of 25 per cent offspring that is showing the symptoms of the genetic defect.
Genomic selection
The fourth application of genetic markers is genomic selection. Genomic selection is a form of marker-assisted selection in which a very large number of genetic markers covering the whole genome are used. In this case all quantitative trait loci (QTL) are closely linked at the chromosomes with at least one marker. The large number of markers is obtained by chips using Single Nucleotide Polymorphims (SNP’s), a point mutation of a single nucleotide. The genomic selection is based on the analysis of 10.000 up to 800.000 SNP’s. This high number of genetic markers is used as input in a genomic prediction formula that predicts the breeding value of an animal.
In animal breeding, the genetic markers have the highest value for the improvement of traits with a low heritability and for traits that can be established in one sex, late in life or after slaughter.
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DefinitionsGenomic selection is selection for a trait of interest with a very large number of genetic markers covering most QTL-loci related to the trait An SNP is a single nucleotide polymorphism caused by a mutation of a single nucleotide |
A complicating factor is recombination between SNP’s and QTL’s. This means that the value of animals in the reference population slows down when the number of generations between them and the test population increases (more chance for recombination events). And it implies that it is highly recommended to continue the recording of phenotypic data of future generations.
Whole genome sequencing
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A SNP is a location on the genome where a single base is replaced by another one. In other words, a SNP is the result of a point mutation. This is illustrated in the figure below where pieces of DNA sequence are given for four individuals. All four individuals are identical except for a single position, where the bases A and G both occur. The only genetic variation between these four individuals, considering this piece of DNA, can be described by considering the variation in this SNP. As it only involves a single nucleotide, the number of alleles is only 2 at maximum. In theory it could happen that the same nucleotide has mutated twice, resulting in three varieties, so three alleles, but in practice this is never the case. In an increasing number of species very many SNP (>>>100,000) have been detected. Commercial companies have designed so-called SNP chips that are used for genotyping animals for a selection of SNP (varying in size from 10,000 to >700,000 SNP), that are spread nicely across the genome.
And when you want to read the complete DNA sequence of an animal, when you want to identify all nucleotides at all chromosomes you can choose for Whole Genome Sequencing. Costs are still decreasing, so this methods is applied moreover when e.g. the genetic variation in a population has to be established very accurately.
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