This semester I have been doing a module called "Animal Breeding and Genetics". I find genetics interesting so have quite enjoyed this module. I have my exam in it this afternoon. We have had 2 different sections to the module, the first part was about Mendelian genetics. This is the usual dominant and recessive gene stuff. Then we have had a molecular genetics section, this is the new type of genetics with all the genomes being developed and using technology to look at what genes the animal is carrying. We have a seen question on this topic on the exam and the question can be seen below...
"With specific reference to genes involved in coat colour determination, demonstrate how molecular genetics has either corroborated or enhanced our knowledge gained from classical genetics."
Below is my answer I have written to it! I am going to put this on a schedule for when I have done the exam so nobody can copy my answer! I have decided to put a twist on it by discussing coat colour but also the diseases that are linked to it.
Molecular genetics has allowed a number of improvements t be made when selecting horses to breed from. There are 11 genes involved with coat colour and they are under polygenic control. When looking at dominant and recessive genes, Mendelian genetics can be used. However, in many cases it is difficult to determine the genotype of the animal and predict their offspring outcome so molecular genetics are useful in these cases. There are also many diseases that are linked to coat colour that may need to be taken into account when selecting animals to breed.
Basic Coat Colours
There are three basic coat colours that are coded for in the genome, these are then altered by other genes. These are black, brown and chestnut. The extension locus is involved with the expression of red and black pigment while the agouti locus controls the distribution of it.
There are a number of genes controlling the white patterns on horses. These include the appaloosa gene, dominant white, tobiano and overo genes. There is a progressive grey gene that will result in an animal turning grey by the age of 6-8 years independent on what their previous coat colour was.
The equine genome was made available in 2006 and this has allowed a wealth of new information to be developed. Coat colours and diseases linked to these can now be selected for or against using a DNA test. These are particularly useful when the horse has no breeding or pedigree records to distinguish the animal's genotype.
Polymerase Chain Reaction (PCR) can be used as a DNA test. A sample of DNA is taken from the horse and this method rapidly processes a number of copies of a section of the DNA. This can then be analysed to see if certain genes are present.
Image of PCR tubes (From Wikipedia)
Selecting For Health And Coat Colour
There are a large number of diseases in the horse that have been linked to their coat colour. Molecular genetics has allowed these links to be looked at and the causes behind them.
When looking at the progressive grey gene it has been found that around 70% of these grey horses develop melanomas by the age of 15 years. Animals that are homozygous (have to copies of the same gene) for this trait are more likely to develop the condition.
There is a gene called the lethal white gene, this is also called overo. Carriers of the gene are hard to distinguish without a DNA test. It can result in a black normal foal being born. On the other-hand it can result in a white foal being born with intestinal tract abnormalities that will die soon after birth. This has been found to be due to a single base pair change (missense mutation) (Finn et al, 2009).
The dominant white gene is another gene that has diseases linked to it. It has been found that the "KIT" gene is faulty in animals with problems here. This gene is involved with the development of blood, the gonads and skin pigmentation. Therefore mutations in this area can cause disease. This has been identified using molecular genetic tests. At least 14 different mutations have been found on this gene.
A Quarter Horse had a mutation of the KIT gene in the year 2000 and went on to become a prominant stallion. This mutation was called W10. There is now a diagnostic test available to detect for this mutation.
Hasse et al (2009) identified some of these KIT mutations using PCR. In four of the seven looked at, individual horses were responsible. The mutations were due to two frameshift mutations, two missense mutations and three splice site mutations.
Another problem seen in horses that is related to coat colour is congenital stationary night blindness, this is seen in appaloosa horses. In these horses, they will be cautious of light and may be difficult to train. Recently, molecular genetics has found a different expression of the TRMP-1 gene in the skin and the retina that is resposible for both night blindness and the leopard complex phenotype (Webb and Cullen, 2010).
With the molecular tests that are now available, there is no reason why horses carrying these mutations should be bred from. This would reduce the prevalence of these diseases. However, caution would have to be taken with this approach not to reduce the genetic diversity of the animals as this could also have a detrimental effect.
Another potential use for molecular genetics when looking at coat colour is to asses the remains of horses that have been found from ancient history. Svensson et al (2011) looked at the coat colour from 26 horses from the Iron Age in Sweden. They used coat colour SNPs in the horses and PCR was used. They wanted to investigate regional differences or preferences for specific coat colour that may be related to traditions they had. They found black, bay and chestnut were all common, two horses were found with tobiano spotting. There were no clear geographical differences in coat colour between the horses looked at.
In conclusion, the use of molecular genetics has been an important development into the knowledge and understanding of equine coat colour. In the future, more research should be carried out into this area. It will help to improve the breeding of horses by not just selecting for coat colour but with the prevention of diseases. This knowledge from horses may also be used to look at other species such as donkeys and zebras.
I am sorry but I don't have all the references for this information, I have taken it from various sources!
I have chosen to take a full module on molecular genetics next semester as it is an important developing area in animal science at the moment.