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Genetics  by John Eberth
To begin I will start with what is known that is 100% true and scientifically accurate and correct.

There are many different phenotypes of dwarfism, which means there are many different types of dwarfs that have different problems and physical abnormalities.
That being said, there are obviously many different mutations in different genes causing these different dwarf types.

With that you need to consider which type(s) is/are the most prevalent and each sample of each type being identical in its abnormalities to be consistent in it phenotype.

OK, now the most prevalent type I have seen and documented is a type that is very similar to cattle dwarfism, which shows symptoms and phenotypes consistent with a human type of dwarfism called achondroplasia. This type of dwarfism in humans by chance (or maybe not) is also the most prevalent type of dwarfism in humans as well.

Now in order to be an achondroplasic dwarf in humans you must have one parent that is an achondroplasic dwarf or be an achondroplasic person born by two normal parents from a spontaneous mutation in a bone growth gene, I will spare you the specifics, but this type of dwarfism is called a dominant genotype, which means that if you have even only one copy of the gene you show the disease, so a human with Dd heterozygous genotype is a dwarf, dd is a normal person, and DD is a homozygous genotype dwarf, which is worse than Dd.
Now for miniature horses it is different, a dwarf of achondroplasic characteristics, is born to two parents that look like normal horses. This is what is called a recessive genotype, which means you can have the mutated gene and not show the disease. This means that a horse that looks normal can carry a mutated gene recessively and not show the disease characteristics, or phenotype. So, in order for a dwarf to be born, both horses, sire AND dam MUST carry the gene to produce a dwarf. THIS IS A FACT for a recessive disease gene to show its phenotype, both the sire and dam are carriers of the diseased gene, and BOTH passed their copy of that diseased gene to the foal that shows the phenotype of the disease. So it takes both the sire and dam to make a dwarf.

Now the statistical calculations are not complicated but in order for simplicity I will tell you that if two horses, that are carriers of the recessive diseased gene are mated, you have a 25% chance of the foal being a dwarf. Now those calculations are based on the total number of potential offspring that both of the horses could produce in a lifetime from the billions of sperm and millions of eggs that could be used to reproduce within the approx. 25 years of reproductive viability of the mare and stallion. So you need to put things in statistical context if you can.

I know of stallions that have never produced a dwarf, I know mares that have never produced a dwarf, I know stallions that didn't produce a dwarf for 10 years then bam, I know mares that didn't produce a dwarf for 10 or more years then bam, so it needs to be put into statistical context. I hope you can understand what I am trying to say.
I know stallions that have a dwarf every year, I know mares that have had 2 or 3 dwarfs, so try to see the mathematical picture if you can. You are playing Russian Roulette.
I do believe a large portion of miniatures are carriers of a type of dwarf gene, remember there are many types. But I know for statistical fact that there are mares and stallions that do not carry any type of dwarf gene, now I know more stallions than mares and that is because of numbers and those numbers used to calculate statistical significance for gene carriers. Now if we are talking about achondroplasia then I can give you better numbers. It would be ludicrous for me to speculate total breed percentages because of the bad label any horse gets from producing a dwarf, so many people lie about if a horse has produced one or not, so it could be a very large number or it could be smaller than any of us think. But what I know that exists in all the bloodlines somewhere, I would think the percentage will be greater than 25%- 50% for achondroplasia, that does not count the other types of dwarfism I KNOW exist and are more rare, so the total percentage of horses that are carriers of some type of dwarfism is going to be high.

There has been some research done, pretty much all done by UC Davis Genetics Lab and University of Kentucky Equine Genetics Lab. Both have preliminary information but there is nothing that I know of as of now that is anything other than speculative and no formal articles or definitive results. This is because of lack of public funding from AMHA or any other donator. There are no science articles per say that are from any peer review journals that have been written on this disease in our breed so you won't find any scientific info either. The sample "dwarfs" used by UC Davis were very limited and I do not know how many different types of dwarfism there were of the samples they have, I do know there were many different types I saw them. The same is the case for UK, however, in my research I have collected more samples than both schools combined and of the same phenotype. I know these things because of my internship on dwarfism at UC Davis under the late Dr. Ann Bowlingin 1994, and my own graduate studies at UK. Understand that there are many different types of dwarfism and/or skeletal bone growth abnormalities. So you cannot put all "dwarfs" in the same category. The different phenotypes seen means there are different mutations in different genes, so it is quite complicated. I have done some work in this area at UK for my graduate studies, and at the time, I took over what UK had done to try and get somewhere.

My research is privately funded by me, so it is taking much more time than normal. I am not doing this as an ego trip, but on the contrary, my business and my life has been in this breed, so that said, I am looking to better the breed not for me, but for it as a whole. This has nothing to do with bloodlines or farm names, but of breeding a better horse, and making it easier for everyone to do so. Because believe me, there are lots of horses of all bloodlines that are carriers, but there are some statistically that are definitely not carriers, so it is just a matter of time and money to find the mutated gene and develop a marker for a test for it.
I do strongly feel that a horse that is a recessive carrier still be able to be registered and used for breeding. My reasons are simple, one is that I know many extremely good quality specimens of miniatures that for all purposes is of great genotype and phenotype quality desired in this breed but that are also recessive carriers, second that there are other horse breeds that have diseases that are tested for and those horses that test as carriers still can be registered and bred, one example is HYPP in quarter horses. I do feel that if and when a test is designed that all miniatures must be tested and designated on there papers if they are a carrier and obviously if a horse is tested and comes back as a dwarf and not just a carrier then there will be absolutely no reason for dwarfs to be able to still get registered in our breed registry, like what is going on right now. The third reason I have, is that when two carriers are bred you only have a 25% chance of producing a dwarf, interestingly you also have a 25% chance of producing a foal that is homozygous normal or the ability to produce foals 100% of the time that are normal even if that foal is later bred to carriers, so there is a lot there to be used for the betterment of the breed if people would just learn some basic things about genetic inheritance, and they are very basic.
To also answer another question about inheritance. For the achondroplasia type of dwarfism I commonly see in miniatures, it is right now thought of as a disease that is inherited as an autosomal recessive trait, which means to show the disease the foal ABSOLUTELY HAS TO HAVE EACH COPY OF THE GENE COME FORM BOTH PARENTS. Now the only way you can get a dwarf foal and that foal to have only one copy of the gene and show the characteristics is if the disease is inherited as an autosomal dominant, which means one of the parents would be a dwarf. If you have a mutated gene that causes a disease and that mutated gene is DOMINANT over the normal gene, then you only need one copy of the mutated gene to show the disease. Now, the ALL the dwarfisms in the miniatures that I have seen are the results of dwarfs from normal parents, meaning this is a recessive mutated gene, and it takes two to show the disease, this is NOT a dominant disease where it only takes one copy to show, if it did all carriers would be dwarfs, do you follow.

Now if someone bred a miniature dwarf to a normal horse the foal would be normal UNLESS the normal parent was actually a carrier then the foal has a 50% chance of being a dwarf.
What you are asking about when a horse that looks normal but has some slight characteristics that look like a dwarf, i.e., extremely dished head, is that does that horse carry the recessive dwarf gene. Well, I am going to give you an answer that has not been scientifically proven in the case of the miniature horse but other similar instances like this that have been scientifically proven to occur. What I am about to tell you involves very complicated dominant and recessive gene interactions and there is really no way I will be able to fully explain this unless I had diagrams to show you what happens. There are some terms for what you see in miniatures, they are called penetrance and expressivity of recessive genes that become co-expressed or over-expressed with its counterpart dominant gene. These terms generalize what is actually a very complicated biochemical interaction between regulator genes of those genes that now are co-expressed. Just so you know there are actually anywhere from a handful to dozens of regulator genes that regulate the expression or productivity of a single gene or genes that produce either a structural characteristic or a protein that is involved in the life support of the body. In simple terms, your eye color is the light bulb that is on, there are a multitude of genes that make that eye color appear in your eye just like there are a multitude of switches and fuses that allow that light bulb to turn on.

So what is going on in the miniature is that those horses that have characteristics that might be slightly like a dwarf means that that horse most likely is carrying the dwarf gene recessively, however because there is penetrance or expressivity occurring you are seeing that recessive gene being co-expressed with the dominant normal gene. No, this has not been proven scientifically as fact in the miniatures, but the same type of thing occurs in every organism known to man at some point and time with any number of dominant and recessive genes. I will give you a basic example. In certain flowers that have the red color gene as a dominant color gene, and the white color gene as a recessive gene, there occurs in some strains that are carrying both genes that the color of the flower to be pink. Now do not get fictional here, the red and white do not combine and fade the color out. On the cellular level, the color cells on the flower's petals, actually are red cells and white cells of approx. equal numbers, causing the pink color. Now, technically this is called co-dominance of the color genes, however, the white is a generally is a recessive color gene in flowers, but because of penetrance and expressivity of the recessive gene being co-expressed with the dominant gene you get to see both causing a different color.
So what I am saying is that in my professional opinion, the horses that are showing slight dwarf characteristics but overall are normal looking, they most likely are carriers of the recessive dwarf gene with penetrance expressivity. So in my opinion those miniatures showing some penetrance of certain characteristics of the dwarf gene are just as good as one that is just a carrier, HOWEVER, AND IT IS A BIG HOWEVER , I would NOT AT ALL breed a horse with a monkey mouth, or a short neck, and I SURE would not breed a horse that had a bad mouth, short neck AND an extremely dished head, all in one horse, that could very well be an actual dwarf, just a really good one that is functionally better than most. Just like there are "tall" dwarfs in humans!!!!! REMEMBER a monkey mouth is an undesirable inferior characteristic, it actually can be in and of itself a separate genetic defect from the dwarf characteristics, because it is seen in large horse breeds that obviously are not carriers of the dwarf gene. The short neck is an inferior trait as well, the dished head is really one person's opinion since you see Arabians and their heads and you know we all are breeding for an Arabian type head, so there will be varying opinions on if that is an inferior trait due to dwarf gene or is it an actual sound gene that is producing a dished head.?? We don't know!!! AN extreme head I would question, and it will probably obvious if I saw it if I thought it was actually from the penetrance of the dwarf gene. I do not feel that these extreme headed horses are any worse than a carrier that "shows no dwarf characteristics," AND genetically there are not. BUT, if you want to get technical here, the miniature is a dwarf pony, but has conformation that is physiologically and biomechanically sound, and has conformation that falls within correct basic horse conformation standards,ie correct bite, straight legs. Remember there is no test and some things are personal opinions.

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