Horse Genetics Explained

Horse Genetics Explained

Learn what outcross, line cross and "percent of blood" means in a pedigree and for a breeding program.

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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 comes 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.

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

Percent Blood Is Only an Estimate

“My old horse genetics professor stressed that percent of blood is not an absolute number, it’s only an estimate,” Larry says. “The reason 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.”

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.

Types of Pedigree Crosses

  • 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.

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 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.

The Importance of Numbers

“I learned a lot from studying the King Ranch and its early inbreeding and line breeding program to Old Sorrel,” Larry says. “As the ranch's 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 the ranch 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 who 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.”