Horse Genetics Decoded
January 20, 2012
Learn what “percent of blood” really means in a pedigree and for a breeding program.
Understanding the numbers behind the pedigree is key to developing a good breeding line. Journal photo.
From The American Quarter Horse Journal
Have you ever seen something like this written down, “5 X 4 X 3” or “22 percent the blood of King,” and wondered exactly what it meant?
“It’s a number that helps you get an idea of how much blood (genes) you have in an individual’s pedigree that come from a particular common ancestor,” explains pedigree analyst and respected author Larry Thornton.
Each individual in a pedigree is assigned a percentage value based on which generation(s) they appear in the pedigree. To find the percent of blood, you simply add the percentage values together for every time that ancestor appears in the pedigree.
“My old genetics professor stressed that percent of blood is not an absolute number, it’s only an estimate,” Larry says. “The reason why is there are what we call ‘recombinations’ and ‘mutations’ in the genetic world, and genes are not always passed on perfectly. Genes sometimes change places or simply change on the chromosome, so the gene from the common ancestor doesn’t necessarily get passed on at a particular location on the chromosome.”
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The common ancestor definitely passes on genetic material, but it’s not always in the form that was expressed in that ancestor.
“Percent of blood is really the maximum potential of genes from that common ancestor that could have been passed to an individual,” Larry says.
The real importance of percent of blood is to understand why it’s used in a breeding program.
Setting Type
“Percent of bloods is just a tool that we can use as breeders,” Larry says, “to monitor the percentage of genes in a family of horses from a common ancestor. So you can perpetuate those genes generation after generation.
“You use it as a measuring tool to help you set traits or ‘type’ with inbreeding and line breeding,” he says. “That’s the reason why the old-time (Quarter Horse breeders) inbred: to set the breed up, to breed homozygous individuals able to pass on common traits each time.”
Homozygous gene pairs carry two identical genes for a trait at a given location on the chromosome, ensuring that a homozygous individual will pass on that trait to the next generation. Inbreeding is intended to give the individual produced more homozygous gene pairs.
It’s important to remember that you’re concentrating the desirable and undesirable traits carried by that individual.
Typically, breeders gradually moved from close inbreeding to line breeding. “We look at inbreeding and line breeding in two different ways,” Larry says. “With inbreeding, we’re trying to make the animal more homozygous for the positive traits in the common ancestor that we’re inbreeding to.
“In line breeding, we’re just trying to keep a high percentage of genes from that individual without actually paying a whole lot of attention to homozygosity. Yes, the line-bred individual tends to be more homozygous, but the more intense we get with inbreeding, then they are even more homozygous.”
All line breeding is a form of inbreeding, but the way breeders distinguish between the two varies.
“In my own writing, if the common ancestor is in the third generation and/or further back, I’ll call that line breeding, but if it appears in the first and second generation, that’s inbreeding,” Larry says.
“But in the Thoroughbred industry, the common ancestor could appear in the fourth and fifth generations, and they’ll term that inbreeding, where I would call that line breeding.”
Percent of blood can help breeders look at a pedigree and estimate an ancestor’s potential influence on an individual.
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The Importance of Numbers
“I learned a lot from studying the King Ranch and their early inbreeding and line breeding program to Old Sorrel,” Larry says.
“As their herd progressed, Old Sorrel wasn’t close up (in the pedigrees). He might have been three or four generations back, but their horses still had a percent of blood of around 50 percent for Old Sorrel, because of the multiple crosses to him.
“But they were very strict about ensuring that only the best individuals were carried on to the next generation,” he says.
“That’s something that people don’t understand today. Someone will call and ask me, ‘I have a great stallion, and I want to breed one of his daughters back to him. What am I going to get?’ Well, you can get both the good and the bad.”
“You have to be prepared, because there is a downside to inbreeding,” Larry says. “It’s going to be unsuccessful more than it’s going to be successful.
“King Ranch carried through inbreeding and line breeding to Old Sorrel and brought about great horses,” he says. “But they culled and got rid of the ones that didn’t work. That’s important to understand.
“If you’re going to have an inbreeding program, you need to have high numbers to make it work. King Ranch had those numbers: lots of individuals, lots of horses.
“It was the same with Hank Wiescamp. Hank had a lot of horses, and that allowed him to do what he wanted to do with his line breeding program.
“That’s largely why inbreeding is difficult for us to do today: We don’t typically have the ability to have hundreds of horses and maintain them and get rid of the individuals that don’t work.”
The Ultimate Goal
“Inbreeding a line of horses is only the path you take to get to where you can outcross that line,” Larry says.
In his opinion, the real “magic” to a successful breeding program is not reaching a high percent of blood for a particular great ancestor. It’s in knowing when to introduce the right amount of genetic diversity to a family of horses through an outcross.
“You don’t have true genetic improvement until you introduce hybrid vigor,” he says. “Introducing that outcross blood at strategic times to give you that hybrid vigor boost, that’s the key to it all. That’s the process that produces the better individuals.
“Hank Wiescamp was a genius at introducing outside blood at key times,” Larry says. “Bar Mount was one example. He also loved the mare Lena’s Bar (TB), the mother of Easy Jet, and he ended up using Double Dancer as an outcross because of her.
“King Ranch is another good example,” he says. “They came to the point in their program where they had a lot of great line bred mares to Old Sorrel, but there was no hybrid vigor when they crossed them back on their own stallions. They hit a plateau and leveled out.
“That’s when Mr San Peppy came in. He carried the King Ranch bloodlines, so he tied back into the mares, but he also had other outcross blood that put genetic diversity back into the King Ranch horses.
“Line breeding reaches a point where if the horses are going to continue to improve, you’ve got to outcross.”
Just One Tool
“The most important thing is to never use percent of blood without looking at the individual,” Larry says. “There are some people that go out and breed by pedigree alone, and that’s a mistake.
“Using percent of blood and pedigrees is only a part of what we do as breeders,” he says. “Conformation is so important, and performance and disposition.
“We have to remember that pedigree is only one of our selection tools.”
Correct ‘Crosses’
Cross-breed: When you cross two different breeds, as in breeding a Quarter Horse mare to a Thoroughbred stallion or vice versa.
Outcross: Crossing two unrelated individuals within the same breed.
Line cross: A type of outcross where you cross two specific families of horses. Example: If you took a mare line bred to King and bred her to a stallion line bred to Wimpy.
Approximate Percent Blood Influence per Generation
In pedigrees, the first generation is an individual’s parents.
If the ancestor appears in the ____ generation, then it contributes ____ blood to an individual
first generation = 50.00 percent
second generation = 25.00 percent
third generation = 12.50 percent
fourth generation = 6.25 percent
fifth generation = 3.125 percent
sixth generation = 1.5625 percent
seventh generation = 0.78125 percent
eighth generation = 0.390625 percent
Comments
17 Comments on “Horse Genetics Decoded”
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January 20th, 2012 at 1:54 pm
I AGREE
January 20th, 2012 at 2:46 pm
If Larry says it, it is true. He is the master. Always learn something when I read what he has written.
January 20th, 2012 at 8:17 pm
This is really interesting and informative. My late mare traced back to Old Sorrel and my late gelding went back to Skipper W. Now I understand their bloodlines. This article helped a great deal.
January 20th, 2012 at 9:16 pm
Larry is brilliant. I have a 4 yo stallion,Redeo Rex, that was bred by the late Fred Gist. Rex has homzygousity of 7.773 ( 8 matched pairs of chromosomes) and is 46.4% King P-234
January 20th, 2012 at 9:19 pm
Larry is brilliant. I have a 4 yo stallion,Redeo Rex, that was bred by the late Fred Gist. Rex has homzygousity of 7.773 ( 8 matched pairs of chromosomes) and is 46.4% King P-234. He is solid black and has the “King” conformation.
January 20th, 2012 at 9:41 pm
I have a dun gelding that is 9th generation from the great Man’O'War, plus 8th generation from Poco Bueno,6th generation from Three Bars, 4th generation from Dash For Cash, 5th generation from Rebel Cause, 8th geration from Leo, he is FQH. I have two geldings from these lines they are full brothers, one is a bay and has the Poco Bueno head and build, the other the dun has the Three Bars head and build. The bay likes to cut cattle, the dun likes to run. They are true to their heritage. Both have comfortable trots, canters.
January 20th, 2012 at 9:44 pm
Breaking down a pedigree in equal sections and attaching equal percentages to each position in a generation is fine, but to imply (even if unintentional) that each of those horses in a specific generation exerts equal influence is inaccurate.
One thing many people don’t realize is the fact that PERCENTAGE OF BLOOD does not equal PERCENTAGE OF INFLUENCE. All of the horses in any single generation do not exert equal influence on the subject horse. For example, mitochondrial DNA alone has shown that the influence of a tail female line on the subject horse can be much greater than an entire group of linebred horses elsewhere in a pedigree. There are other powerful influences that can be passed down based on the sibling relationships between certain ancestors, and their positions in a pedigree. It has nothing to do with blood percentages.
I agree with the advice to select a horse based on individual quality instead of selecting or breeding by pedigree. A good horse will have a good pedigree behind him, but a good pedigree doesn’t always guarantee a good horse. Roughly 50% of the horses from any given bloodline are not breeding quality. It is why there is no breed improvement taking place among those who breed horses by blood percentages alone.
I also agree about the necessity for genetic diversity in the Quarter Horse, although that’s a rare occurrence in today’s specialized world. Many people don’t want to risk breeding for hybrid vigor, if they even know what it is. The breeders mentioned (especially Wiescamp and I’ll add Walter Merrick to that group) were all about maintaining the versatility of the breed. There isn’t anyone out there doing this any more. The old masters of breeding are disappearing, and along with them, the knowledge gained from a lifetime of dedication to breeding horses capable of contributing to the breed in a positive way. A responsible breeder needs to know what a good horse is supposed to look like and they need to know the breed’s history and bloodlines, and they need to understand how pedigrees work.
January 20th, 2012 at 9:51 pm
Another thot, is both geldings have excellent conformations. Even tho they are full brothers, even tho they both have the same lines. They favor a different g-sire. Both are easy to train, very smart/intelligent guys.
January 20th, 2012 at 9:54 pm
Amen to that. I agree, alot can be told/said in a pedigree. I carefully selected the stallions I bred my mares to. Each time I got an excellent foal.
January 21st, 2012 at 10:31 am
Janet, the dissimilarity between your two full siblings makes me want to study their pedigree.
These are valuable things to know when breeding. It’s helpful to be familiar with the individual ancestors in a pedigree, where they are in the pedigree, how many times they are duplicated, and how many sibling relationships there are. Getting consistent results is the key to any breeding program. 
January 22nd, 2012 at 11:34 am
I agree with Susan’s comments and with the article when it talked about culling. Instead of culling these days, these horses are sold at auction to unknowledgeable buyers. There are horses sold at auction that have First Down Dash/Dash for Cash in each grandparent. Let us not forget that in-breeding and line-breeding have resulted in genetic abnormalities/diseases, i.e., HYPP and others. My personal opinion is that with AQHA allowing multiple embryos from mares (who knows how many is the maximum), the inbreeding is going to progress from bad to worst. AQHA is abrogating its responsibility to protect the integrity of the breed by allowing unlimited embryo transfers. It is my hope that AQHA will amend its rules to only allow limited embryo transfers, e.g. 3 maximum embryo transfers. What is going on right now is the elimination of the middle market of Quarter horses and limited diversity in breeding stallions/mares. This will be the ruination of the Quarter Horse.
January 22nd, 2012 at 11:54 pm
I really appreciated this article; it was very helpful to distinguish the different types of line breeding and inbreeding from each other. What the article fails to mention are some of the serious genetic problems that can occur because of these consanguineous breeding. Yes, with inbreeding, especially breeding a stallion back to his own daughter, you increase “the blood” and that the bad occurs more frequently than the good in the progeny. Let us consider HYPP (Hyperkalemic Periodic Paralysis) which has been traced back to Impressive. Impressive himself was not the problem: the inbreeding and line breeding that took place afterwards is what created those homozygous genes that authour talks so enthusiastically about. Also, HERDA (Hereditary Equine Region Dermal Asthenia) can be traced back to Poco Bueno and despite being only expressed when an individual has both copies of the recessive gene (versus HYPP where only one copy of the gene leads to symptoms as it is dominantly expressed) it too was caused by line breeding and inbreeding. These are serious and detrimental diseases, yet people still continue to line breed and inbreed. Think about it this way: you wouldn’t have kids with your cousin or brother or sister or parent? Most breeders tend to ignore this! The two examples mentioned in the article were insightful because they did manage to breed out, but I don’t think with all the smaller, scattered breeders active today that this practice is condonable. I am sure that easily in another 15-25 years there will be another genetic disorder affecting the Quarter Horse breed and unfortunately, it will be traced back to a single sire and it will most definitely be due to inbreeding and line breeding. Breeders need to be educated and potentially certified in some sort of program to mitigate this happening or else the Quarter Horse Breed will end up severely inbred. Just something more to consider.
January 23rd, 2012 at 7:49 am
Linebreeding/inbreeding do not CAUSE genetic defects…they only allow those defects to be seen and discovered. Linebreeding is one of the most valuable tools a breeder has at his disposal, as long as that breeder is knowledgeable about pedigrees and is familiar with the horses that are being linebred to.
Hank Wiescamp was a master at linebreeding. He was a master at achieving consistency without genetic defects. If you study his pedigrees, you will see that he always brought in an outcross (speed blood) every couple of generations, and he linebred to good MARES. People today aren’t linebreeding to ANY mares. There has to be a balance in the pedigree in order to get a good breeding horse and get consistent results.
For example, HERDA wasn’t even known back in the 50s and 60s, even though Poco Bueno and his descendants were very popular. Only when breeders started duplicating the carriers in a pedigree (through Doc O’Lena, Smart Little Lena, etc.), did symptoms appear and the disease surfaced. It was there all along from Poco Bueno forward, although only in heterozygous form (and non-symptomatic). Linebreeding didn’t CAUSE it – it allowed it to present itself.
Impressive had one copy of the genetic disorder, HYPP. Some of his foals were N/H and others were N/N. Linebreeding doesn’t have anything to do with this particular defect, in Impressive himself, or his descendants. HYPP didn’t increase through linebreeding to Impressive. In fact, you don’t need ANY linebreeding to get a horse with HYPP – only one line of uninterrupted carriers to Impressive is needed to get a symptomatic horse (N/H). The disorder was propagated after the fact by breeders breeding for the type who likely possessed the defective gene. You can linebreed to Impressive all day long, and as long as you use N/N stallions and mares, you won’t get the defective gene. It’s the same with HERDA.
If breeders continue to breed for specialized horses while constantly linebreeding without an outcross, the genetic problems will continue. Genetic diversity and breeding for versatility is the only way to preserve the integrity of the breed.
January 23rd, 2012 at 8:55 am
LEO was extremely inbred, yet when crossed with what was believed to be “outcross” blood of horses like Three Bars (TB), he saw his greatest success. There was never a more prominent, influential broodmare sire than LEO. There is a key element to discover with that cross when you study the pedigrees of Leo and Three Bars. They actually shared important ancestors whose mare line is duplicated in their pedigrees, and provides for even further linebreeding. That really wasn’t a true outcross, even if the horses were registered with two different associations. They may be two different “breeds” today, but they were one and the same at their origins. The majority of crosses between a QH and a TB are not true outcrosses; they have many common ancestors, sometimes up fairly close.
Many of the most prolific, influential sires of the breed were products of linebred ancestors. We could go all the way back to *Janus, whose influence on the speed of the Quarter Horse was guaranteed through the linebreeding and intense inbreeding of his sons and daughters. Peter McCue, arguably one of the most important sires in the early days of the QH, was linebred to *Janus, through sons AND daughters (there’s your balance in a pedigree). Again, the majority of the most successful horses bred by Hank Wiescamp were linebred to Peter McCue (also through sons AND daughters).
Today, we see foundation QH breeders linebreeding to Poco Bueno, King, etc., but the majority of those ancestors are through SONS only. There is no balance in their pedigrees. The result of pedigree only breeding like that is not breed improvement, or any semblance of consistency in excellence or type. Foundation associations don’t allow TB outcross blood (which was what created these great horses in the first place), and therein lies one of the problems with the future integrity of the breed.
The most successful stallions (and the majority of the TB influences on the QH) were from the tail female lines that were heavy in the linebreeding to *Janus. It is the origin of speed, which is a necessary ingredient to the integrity of Quarter Horse as a versatile breed.
January 23rd, 2012 at 9:04 pm
I agree with Susan and Gem. Impressive was a good example of a stud that has been only viewed for his connection to HYPP rather than his influence on the breed type. It was the breeders who continued to breed positive horses to get the breed type they wanted. This has continued today. I know several halter breeders with positive studs who continue to breed them and throw positive offspring so they can get the halter type they want. Rather than throw out the baby with the bathwater and marginalize the influence of a horse like Impressive, AQHA should refuse to register a positive horse and these unscrupulous breeders going for the money only will stop breeding positive horses for fear they can’t register or show them.
My mare is line bred Skipper W then her Impressive and Jimmy Mac Bee grandaughter dam was brought in for genetic diversity and I have a good looking mare that does well in halter, has a great disposition and is cowy enough to be a working ranch horse. That’s what genetic diversity does. It is a shame that one of the foundation associations won’t register a horse with Impressive blood because of HYPP. The National association will if they are negative because they recognize the impact Impressive had on the breed and consider him a foundation stud too. I don’t think Poco Bueno is omitted from their registrys!
January 28th, 2012 at 10:43 am
I am not sure why people continue to breed HYPP N/H horses if it will just continue the disease. I found a stallion I would love to get a foal by with my mare, but once I found out he is HYPP N/H I won’t be breeding my mare to him…. I came to this forum hoping to get a question answered. If a stallion carries the HYPP N/H gene, does that mean he will pass it on to everyone of his foals if he is bred to a NON HYPP Mare, or is it a 50% chance he would pass it on at all?
February 1st, 2012 at 11:50 am
My stud colt has excellent pedigree, great pedigree and amazing disposition