Genetics

R.  Hodgman in the journal of Animal Science stated that most breeders are ignorant of elementary genetics and that as a result, the percentage of unsound stock and defects are on the rise.

Phil Bull from Timeform said " if we don't understand the rudiments of mendelian heredity then we have no right to be talking about pedigrees at all."

Pedigree analysis and genetic inheritance are intrinsically linked and extensively used by geneticists in all fields to trace the inheritance of factors.

Genes are units of heredity made up of DNA which determine how traits and abilities are passed on and should be of interest to all breeders. The horse genome project is in its infancy, but it will have some exciting developments in the future on sport ability, as well as the genes responsible for disease and defects.

Each horse has 32 sets of chromosomes  with 31 known as autosomes,  plus the sex chromosomes – XX in females, XY in males.

Each cell in the body has 2 complete sets of chromosomes making 64 gene pairs. A horses genetic makeup is a mixture of dominant, co-dominant and recessive genes which are inherited via the pairs of autosomal  chromosomes from each parent, and the sex chromosomes.

Genes are sections of DNA that contribute to certain traits and functions by a process of coding proteins, that influence the physiology of the horse. Each gene has a fixed position (locus) on a chromosome.  There is a pair of genes for each trait - one from each parent.

ALLELES 

Have you ever wondered why the same  mating combination between a mare and a stallion does not result in foals with the same traits - why full siblings can be so different?

A gene is made up of 2 different alleles - one allele is inherited from each parent to form a pair for each trait. All the horses traits are coded in the alleles. The sperm and egg cells are the only ones that contain just one allele for each trait. Each trait is inherited by a gene that is passed onto the foal unchanged.

A trait may not be seen in a horse but can still be passed onto the next generation. An allele can be dominant or recessive and this controls which traits are expressed. If both alleles are identical then a horse will be homozygous for that trait and it will be passed on to the foal.

If the alleles are dissimilar  – one dominant and one recessive allele -  then the horse is said to be heterozygous for that trait - but will still display the dominant gene in the phenotype.  The recessive allele will not be expressed visually.

Two copies of a recessive allele are needed for a recessive gene to be displayed. Recessive alleles only reveal themselves when there is no dominant allele to mask it.

You cannot tell by looking at a horse if the second allele is dominant or recessive -  dominant alleles are never hidden by their related recessive alleles, but they will mask the recessive one which may crop up in the next generation. A trait may not be seen in a horse but can still be passed on.

When a trait is displayed then for sure there is one dominant allele in the genotype.

Just because a horse shows a trait such as a certain shoulder angle - does not mean it will pass it on - we do not know how the horse inherited that particular trait - this is why breeding to strengthen or correct faults in the phenotype can be so unreliable.

A horse needs double dominant genes to display the trait and have 100% chance of passing it on to the next generation -  and there would need to be several foals to view in order to work out if the horse is homozygous for a particular trait.

The alleles are the primary determinants of the horse's phenotype (conformation) -from  genes at specific loci - all working together through dominant, recessive, co-dominant and polygenic patterns of inheritance. 

 It is the genotype - what cannot be seen - that is responsible for creating the phenotype - that which can be seen. 

The parent's genes determine what the horse will look like - what the parents actually look like has no reliability  of being passed on at all  - and this is what makes breeding ' type to type' so difficult.
 

MENDELS LAWS OF INHERITANCE
 

Gregor Mendels work on pea plants in the 18th century was the foundation for the modern study of genetics. Mendels first law of Inheritance is the Law of Dominance.
 

 If a horse has a dominant and a recessive allele the dominant allele will always be expressed in the phenotype. The dominant allele hides the recessive allele
 

Recessive genes are much more of a problem and there are hundreds of these genes floating around in horses. These hidden recessive genes are stealthily prowling in the background  of the genotype, lying in wait in a dormant state. Some of these recessive genes can be valuable but most are not.

Undesirable recessive genes wont do any harm in a heterozygous state - but if they are homozygous they have no choice but to be expressed - and poor traits can be just as easily cemented as good ones

Most horses inherit and exhibit recessive genes in their phenotype - they can bring about undesirable changes in conformation and phenotypical characteristics

These are inherited from parents who are not affected by the particular trait themselves. The similar recessive allele (two copies)  must be present in both parents  to produce it– they are carriers. Where receissive genes are displayed in the offspring, the foal may look nothing like the parents nor have their sport talent or temperament that can normally be expected from those bloodlines.  Recessive genes can be inherited from ancestors that are far back in the pedigree that have been lying in wait to meet the right partner

Similarly for recessive genetic disorders such as WFFS - 

If two carriers are bred the foal has a 25% chance of being affected, a 50% chance of being a carrier and a 25% chance of being clear of the defective gene.
 

The goal is not to stop breeding horses that are carriers, but avoid breeding carrier to carrier

Many carriers have super performance genes with desirable traits that are valuable for breeding sport horses.
 

Recessive genes cannot be weakened or diluted, they are either present or not.

Mother nature likes variety diversity and deviations - these are the drivers of evolution - and they allow  for  adaptations for the survival of a species - so  the horse can  evolve to be better suited for survival in different environments and have ongoing reproductive fitness

Mother nature uses a hidden reservoir of recessive genes as the primary tool to encourage modifications  and maintain diversity

This contrasts with human goals  to    mould the   phenotype to better allow the horse to excel in sport performance and to select for uniformity in phenotype and genotype
 

This is why inbreeding has taken place in all livestock breeding including show dogs, cattle, sheep, racing pigeons, horses of all breeds  - and in agricultural crops and seeds - to ensure that traits become homozygous and more reliably passed on. It has produced cows that make more milk, sheep that grow better wool or no wool, and chickens that lay more eggs, as well as uniformity in crops and seeds. A lot of recessive genes have been bred out in these cases.

The horse is actually one of the least inbred animals of all - especially in hybrids like warmbloods -  where one horse can consist of 6 different breeds

Some horses are dominant in passing on their characteristics - these are prepotent animals - but these are rare and most horses are not
 

Mendels second law – the Law of Segregation

 Sex cells (  XX  / XY ) are produced at the time the egg is fertilised by the sperm -  each parent's alleles   randomly  separate from each other so each sperm and egg cell carry only 1 allele for each gene pair – they are halved. Each parent donates only one of its 2 copies.
 

This process is called meiosis – is where a single diploid parent cell with 64 chromosomes undergoes 2 consecutive divisions to produce 4 haploid daughter cells - gametes - each containing 32 chromosomes

Mendels third law of Independant Assortment

Recombination - before the chromosomes are separated they  are shuffled - they cross over, pair up and swap genetic material to create unique  combinations  from the stallion and mare - so no two sperm or egg cells are identical and the foal cannot be an exact copy of the parents - and new combinations not present in the parents are possible

This leads to foals having  new combinations of traits to the parents - which are then subject to the environment as well

This is why full siblings can look and be very different - even though the foal receives 50% of genes from each parent,  - one sibling can inherit a totally different part of the parents genes pool -and the actual genetic makeup of each foal is brand new

This is why breeders cannot get a  repeat replica of their champion horse by mating the same parents

When the egg and sperm combine again at conception and unite to form a single cell -  the full number of chromosomes is restored in the offspring

Mendels Law of Segregation

When mating two heterozygous parents there are 4 possible gene combinations for a foal to inherit - because each parent has only 2 alleles for a specific trait and can only pass one to the foal

These rations apply to single gene traits but are still relevant to breeding horses with sport talent because fertilisation still results in 4 possible genotypes being inherited by the foal which will then be influenced by the environment as well

At fertilisation the  4 combinations are

1. Homozygous dominant -   AA

2. Heterozygous  -   Aa

3.  Heterozygous -  aA

4. Homozygous recessive  -   aa
 

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Ken Beer has stated that his understanding of  Mendels law is that this process  results in 4 possible outcomes  for each sex - for the chromosomes to come together in the foal. So basically, there is a 1 in 4 chance  of getting the best genetic outcome for each sex from each mating. 

This is why it is a good idea to repeat a mating which is ideal in all elements. Although it may not be practical without advanced reproductive techniques to achieve 4 male and 4 female foals - it is a good idea to repeat a mating  until you get two of the same sex to hopefully get the dominant genotype.

Beer said for  the second law of mendels  -   with 4 matings of the same sex there will always be a dominant foal which will be the best performer with the most talent.  There will also be a recessive one with the least talent.  The other 2 variable foals can be nearly as good as the dominant one or nearly as bad as the recessive one - or have abilities somewhere in between

If the mating is genetically compatible and all other factors are favorable - the  chances of getting 2 out of 4 top foals is far greater than if the matings were chosen randomly

Sometimes the first foal from an ideal mating  may not actually be the best one -   I have found that often the second foal is the better one.
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These processes can explain how a mating from two champion parents can produce an elite sport horse, or a very average horse, or even a very disappointing horse which is completely different from what was expected based on the quality of the parents and the bloodlines.  This is one of the reasons why full siblings can be so different.
 

As Ken Mclean noted –" that most horse people are reluctant to understand that a sibling to a champion performer (especially of the opposite sex ) will be unlikely to have the same level of sport talent and characteristics – and that genetically it cannot possibly be the same horse."

Perhaps another reason why siblings can be so different is the X chromosome.  The mare has two X chromosomes and we do not know which one is passed on to her progeny, or if it is a random process each time

One of the X chromosomes is much bigger than the other and could possibly carry alot more genetic information as well as sex-linked genes.  Perhaps the champion sibling inherited the bigger X chromosome, and the very average sibling received the smaller X
 

Mitochondrial DNA  is another form of genetic inheritance. Mitochondria are located within the cell but outside the nucleus. There are also organelles within the cell which provide the mitochondria with the energy required for the cells to work the entire machinery of the horse.
MDNA is only passed by mares on the X chromosome, and it is not subject to the mendelian laws of inheritance. See more about mDNA here.

Complex Genetic Traits
 

Many of the important traits for breeders - athletic performance, sport ability, and conformation, are created by many multiples of gene interactions all working together.  We need a much deeper understanding of these traits affecting performance and conformation.
 

As a breeder it doesn't take long to realise that  the foal's conformation is not balanced out into a blended mixture of the parents most desired traits

Complex polygenic traits cause ongoing variation in the phenotype -  which is intrinsically linked to performance.
 

Performance is strongly affected by environmental factors – a horse must receive the correct upbringing, nutrition and handling and must meet the right rider who has the ability to educate and compete the horse
 

A scientific study on showjumpers found several possible genes associated with performance, many connected with the N-RAP gene – the nebulin related anchoring protein gene, associated with muscle structure.

 As at least 60% of the horse is muscle, a lot of its performance relies on muscle and muscle contraction.

Another study showed that the greater the quantity of mitochondria present per unit of muscle weight, the greater the oxidative capacity of the muscle.
So, performance aptitude in racing, showjumping and dressage and other horse sports may be linked with muscular function.
 

All these studies are in their infancy. As mentioned before much research is being done in elite human athletes, and of course racehorses, which could be informative for horse breeders in the future.

Epigenetics
 

This growing field of research looks at how a horse or foals DNA can be modified by the environment -  which can then alter the expression of genes.
A foal is born with its own DNA which of course plays a major role in that foal's future sport potential, but the environment also has a defining role as to  how external influences can change  the  way genes are expressed.

Epigenetic changes can be permanent or reversible, and do not change the foals own individual unique DNA - only how it may be expressed.
 

The stallion's lifestyle can alter the sperm epigenome and affect embryo development after fertilisation.
 

Maternal nutrition, stress, exposure to heat or drugs and chemicals at the time of conception or during pregnancy can affect the foal's health.
The prenatal and early postnatal periods are also critical as the development of the foal makes it very sensitive to the environment.

Diet plays a very important role in a foal's development in establishing the gut microbiome which is taking on increased importance for bodily function and gut / brain interactions - as it is in humans

Overfed pregnant mares can lead to OCD developing in the foal.

Even problems in a horse's feet can be traced to deficiencies in diet, movement and definitely in hoof management.
 

A cleft palate can be caused by inadequate folate which changes the epigenetic regulation of the developing embryo.

Epigenetic changes can also be triggered by gender imprinting.

Gender Imprinting

Certain important genes can be turned on or off depending on the sex of the parent they were inherited from.
 

At least 80% of the DNA in a horse or any mammal, is made up of what is called junk DNA, and was thought to have no function until recently.
 

Studies have shown that this junk DNA has been preserved in the genome for thousands of years - as mother nature does not do things without a reason,  it was fair to assume that it did have some function in determining particular traits.
 

It has been found that sequences in this junk DNA can act as switches which determine when and where certain genes are expressed. It marks the DNA with “chemical tags”, and nutrition and the environment can change these chemical tags as cells constantly adjust to their environment. 

This junk DNA provides these on off switches which regulate the behaviour and interaction of many other genes.
 

Imprinted Genes
 

Dr Doug Antczek did a study called the Maternal Grandsire Effect which found that some key genes will only be expressed depending on the sex of the parent it was inherited from - it will be switched off when transmitted by one sex or the other.
 

So, if contributed by one sex it is switched off, while the other sex passes on an active form of the gene.
 

If a gene is paternally imprinted, it is turned off if passed on by the stallion.
If a gene is maternally imprinted, it is switched off if passed on by the dam.
 

So a gene can be turned off in the offspring of a stallions sons and turned on in the offspring of his daughters.
 

Dr Antczek says these silent imprinted genes can be expressed in the next generation if they are passed on by a parent of the opposite gender.

So when a mare passes on an imprinted gene only her sons offspring can show its effect.
A stallion can pass on information on an imprinted gene but only his daughters offspring can show its effect.
 

Champion racehorse Secretariat was used as an example of gender imprinting.  He was an incredible racehorse himself and still holds track records today. Yet his performance at stud was lack lustre and despite being a very popular and expensive sire both his sons and daughters failed to live up to expectations on the track. 

His stallion sons had almost no success at stud, but his daughters produced progeny that were superb runners and broodmares that made him highly influential as a broodmare sire.
 

This maternal grandsire effect could explain why some stallions fail to establish a dynasty of stallion sons – but instead are able to leave a legacy of superb broodmares and become highly valuable broodmare sires.

Similarly, stallions like Weltmeyer and Rubinstein failed to leave a string of top stallion sons who had great success at stud - but both stallions produced superb broodmares who have appeared as dam sires in top stallions and sport horses.

Perhaps this is an example of an imprinted gene which was turned off when inherited from the stallion - but turned on when inherited from a mare

On the other hand, stallions such as Donnerhall and Sandro Hit have left behind top stallion sons, and this is certainly a fascinating subject worthy of study - breeders have long wondered why some stallions fail to carry on lines of successful stallion sons.
 

Research has shown that there is a significant difference between the very best sire lines and the very best broodmare sire lines.

Jay Leimbach in his excellent articles in racing and breeding, said the same can be said of Phalaris who became the major foundation sire of the century. He said that today 90% of leading sire lines trace to Phalaris in the male line, yet he never appeared as broodmare sire of a single important sire.
 

Northern Dancer is another stallion who established an absolute dynasty of stallion sons and grandsons at stud, yet he is rarely seen as broodmare sire of major stallions.
 

This is not the same as sex linked inheritance via the X chromosome where a stallion can have daughters who have much better performance than his sons – These are passed on only by the X chromosome.
 

But these two factors, sex linked inheritance via the X chromosome and gender imprinting where genes are switched off when transmitted by a parent of one sex or other, could perhaps explain the considerable difference between sires of sires and top broodmare sires.
 

Continue on to the other Genetics pages by the drop down on the main menu.