Basic Topics
Basic Genetics for Horse Breeding
R. Hodgman in the journal of Animal Science noted 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 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.
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 two complete sets of chromosomes making 64 gene pairs. A horse’s genetic makeup is called its genotype.
Genes are sections of DNA that contribute to certain traits and functions by a process of coding proteins which influence the physiology of the horse.
ALLELES
Have you ever wondered why the same mating combination between a mare and a stallion does not result in identical foals each time?
A gene is made up of two different alleles, and one allele is inherited from each parent to form a pair for each gene. Alleles can be dominant or recessive for certain traits.
The alleles are the primary determinants of the horses phenotype, all working together through dominant, recessive, co – dominant and polygenic patterns of inheritance.
It is the genotype – which cannot be seen – that is responsible for creating the phenotype – that which can be seen. It is the parents genes that will determine what the foal / horse will look like – what the parents actually look like themselves has no bearing on this.
This is why type to type breeding can be so unreliable.
Mendels Laws of Inheritance
Gregor Mendels work on pea plants in the 18th century was the foundation for the study of modern genetics.
Mendels First Law of Inheritance is the Law of Dominance
If a horse has both a dominant and a recessive allele to make up a gene pair – the dominant allele will always be expressed in the phenotype. The dominant allele will hide the recessive allele.
If both alleles are identical then a horse will be homozygous for that trait and it will be passed on to and displayed in 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 express the dominant gene in the phenotype.
You cannot tell just by looking at a horse if the second allele is dominant or recessive.
Just because a horse shows a trait such as a certain shoulder angle – does not mean it will pass it on. It depends on whether it is homozygous or heterozygous for that trait , and this is why breeding to strengthen and correct faults in the phenotype can be so unreliable.
Many foals and close bloodline relatives would need to be observed to determine if a horse is homozygous for a particular trait.
Recessive alleles and genes
Recessive alleles are much more of a problem, and there are hundreds of these floating around in horses, lurking in the background of the genotype in a dormant state.
Most horses inherit and express recessive genes in their phenotype and although some are valuable, most are not. They can bring about undesirable changes in conformation and other phenotypical characteristics.
They will not 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.
Recessive alleles are inherited from parents who are not affected by the particular trait themselves. The similar recessive allele must be present in both parents to produce it, and they are known as carriers.
In this way, a trait may not be seen in a horse but can still be passed onto the next generation.
When recessive genes are displayed in the offspring they may look nothing like the parents, nor have the sport talent or temperament that can be expected from those bloodlines.
Recessive genes can be inherited from ancestors who are far back in the pedigree, that have been lying in wait for generations to meet the right partner.
Similarly for recessive genetic disorders such as Warmblood Fragile Foal Syndrome (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.
It is important for breeders to understand that the goal is not to stop breeding horses that are carriers, but avoid breeding carrier to carrier.
Some breeders believe that simply being a carrier of a recessive disorder means there is something intrinsically wrong with the horse and it should be avoided at all costs. This is simply not true. The answer lies is testing breeding stock and remaining aware, as many carriers have superior performance genes with desirable traits that are valuable for breeding sport horses.
Mother Nature
Mother nature likes variety, diversity and deviations – these are the drivers of evolution. They allow for adaptations so the horse can evolve to be better suited for survival in different environments and have ongoing reproductive success.
Mother nature uses a hidden repository 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, 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 six different breeds.
The Law of Segregation
Sex cells ( XX / XY ) are produced at the time the egg is fertilised by the sperm. The parent’s alleles randomly separate from each other, so each sperm and egg cell carry only one allele for each gene pair – they are halved. Each parent donates only one of its two copies.
This process is called meiosis – where a single diploid parent cell with 64 chromosomes undergoes two consecutive divisions to produce four haploid daughter cells called gametes, each containing 32 chromosomes.
This is why breeders cannot usually replicate a champion by repeating the mating with the same parents.
When mating two heterozygous parents there are four possible gene combinations for a foal to inherit – each parent has only two alleles for a specific trait and can only pass one to the foal randomly during meiosis and recombination.
These ratios apply to single gene traits but are still relevant to breeding sport horses because fertilisation results in four possible genotypes being inherited by the foal (which are then influenced by the environment).
At fertilisation the 4 combinations are:
1. Homozygous dominant – AA.
2. Heterozygous – Aa.
3. Heterozygous – aA.
4. Homozygous recessive – aa.
Pedigree expert 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. There will always be a dominant gene combination and a recessive gene combination when the same parents are mated, and there is no way of knowing which mating will bring through the dominant one. So basically, there is a 1 in 4 chance of getting the best genetic outcome for each sex from each mating.
Beer said for the second law of Mendels, with four 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 two 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.
This is why it is a good idea to repeat a genetically compatible mating which is ideal in all elements. Although it may not be practical without advanced reproductive techniques to achieve four male and four female foals from the same mare and stallion, it is a good idea to repeat a mating until you get two of the same sex to hopefully get the foal with the dominant genotype.
If the mating is genetically compatible and all other factors are favorable, the chances of getting two out of four top foals is far greater than if the matings were chosen randomly , or for fashion or commercialism.
Sometimes the first foal from an ideal mating may not actually be the best one. If you feel the first mating has produced the outstanding result, which will not be known for some years in terms of performance, but may have resulted in an outstanding foal with great athleticism and type, then you could keep a filly for performance and breeding and go onto another stallion.
If you get a disappointing result at first attempt, and all elements in the mating are favorable, roll the dice again in an attempt to get the dominant foal. This will give you much better odds of breeding a champion performer than any random mating will.
Mendel’s Third Law: Law of Independent Assortment
Recombination
Before the chromosomes are separated, they are shuffled – they are said to cross over – pair up and swap genetic material to create unique combinations from the stallion and mare. It’s an expansion of the first law in the sense that it applies the idea of random separation to multiple genes instead of just one, even if they are on the same chromosome. The alleles get sorted into the sex cells independently of one another. No two sperm or egg cells are identical, which leads to foals having new combinations of traits from the parents, which are then subject to the environment as well.
When the egg and sperm combine again at conception and unite to form a single cell, the full number of 64 chromosomes is restored in the offspring.
This is why full siblings can look and be very different. The foal receives 50% of genes from each parent, but one sibling can inherit a totally different part of the parents gene pool, and the actual genetic make up of each foal is brand new.
These processes can explain how a mating from two champion parents can produce an elite sport horse, 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. It also explains how 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 larger than the other and could possibly carry a lot 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.
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