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Improving Breeding Outcomes Through Alpaca Color Genotyping

This articles was last updated on 04/10/2024.

In our first year of breeding alpacas, we were at our farm with friends Dave and Kari. They are fellow alpaca breeders and they had brought over their herdsire Eddie to mate our female alpaca Vincentia. As we sat and discussed the breeding combination of Eddie and Vin, Dave made a joke that stuck with me. He compared alpaca breeding to a gumball machine. He said you cannot predict color outcomes of alpacas and you can only hope your preferred color pops out.

Gumball Machine

At the time I laughed because this funny comment felt so true to alpaca breeding. But the idea and the image it put in my head never left me. Dave hit is square on. While we can do our best to perform research and match up alpacas for the best possible outcomes, alpaca fiber color is still a guessing game. We cannot accurately predict outcomes because we simply lack the data to do so.

Or we did.

A lot of people assume if you mix a white alpaca with a brown alpaca you’ll end up with fawn alpaca. Well, that works in mixing frosting, but it doesn’t work in breeding alpacas. There is a lot more science that goes into the color outcomes of alpaca breeding.

This year my husband Jason has been working with Lynn Edens at Little Creek Farm Alpacas. They have been collaborating on a project to better understand the genetics behind alpaca fiber color.

This spring they took blood samples from both herds and sent them into NeoGen for analysis. Neogen operates Australia’s largest genomics lab in Gatton, Queensland. They also have a testing facility in Canada for North American livestock breeders. Their Alpaca Coat Color Test is genotyping that has been developed in collaboration with Dr. Kylie Munyard from Curtin University of Western Australia. Dr. Munyard is well known in the alpaca industry due to her extensive research in alpaca fiber color and genetics.

What is Color Genotyping?

Genotyping can sound rather scary, but it is simply the process of determining differences in the genotype of an alpaca by examining the individual’s DNA sequence and comparing it to another alpaca’s sequence or a reference sequence. It reveals the alleles an alpaca has inherited from its sire and dam.

I said early that breeding for specific alpaca colors doesn’t work like mixing two colors of frosting. This is because alpaca fiber color is complex. It includes two main genes responsible for base fiber color: AslP color alleles (A or a) and MCIR (E or e) which highlight dilution. It also includes an unknown number of genes involved with pattern fiber.

NeoGen Alpaca Coat Color Test Results Example
An example of the alpaca genotyping data received by our color testing with NeoGen.

In Lynn’s Parade of Champion’s presentation, Color Genotyping: What We Are Learning, she highlights the following key points of what the initial genotyping data is showing:

  • All alpaca base coat colors are produced by varying quantities of yellow/red and black pigment
  • The ASIP gene encodes a protein that regulates the production of yellow pigment, pheomelanin, by melanocytes
  • The MC1R gene encodes a protein that determines whether black pigment, eumelanin, will be produced by melanocytes
  • There appears to be no true white or light ASIP gene mutation, but instead just ASIP genotypes for brown and black
  • White phenotypes are produced by a dilution
  • All whites and lights carried two dilution mutations
  • We are seeing a relationship between depth of color and MC1R genotypes
  • Alpacas with zero dilutions are incapable of producing light fawn, beige, or white offspring

My husband is very focused on the dilution factor, as this provides a great deal of information and improves his pursuit of high-quality, dark-colored alpacas.

Why Do We Care About Color Genotyping?

As alpaca breeders of color, genotyping provides the following benefits:

  • Offers base color of an individual alpaca
  • Identifies mutations
  • Increase probability and predictability of expected fiber colors
  • Reduce probabilities for suboptimal alpaca combinations
  • Improves the chances of producing classic greys
  • Improves fiber quality of dark color offspring
  • Reduces chances of miscarriages in certain breeding combinations
  • Increase farm revenue through the production of higher-quality fiber and more predictable color outcomes

What Has the Initial Data Taught Us as Alpaca Breeders?

With the first round of genetic testing, we learned more detailed information on our herdsires, which has shifted an individual alpaca’s value to our program, and it altered how we would use this alpaca in future breeding.

We also now know we can improve the fiber quality of our dark program, by breeding color alpacas to high-quality white alpacas. We can do this because we know the genotype of each herdsire, and we have a better understanding of the potential of nonwhite crias.

There will be other data points to learn, but these will come in time, and we believe they will be a positive disrupter to the alpaca industy.

With more alpacas being added in to the testing process, the more we will learn from their results. We are encouraged with the findings to date and we are excited about the data to come. These next set of results will continue to help prove or disprove some of the hypotheses that have been cultivated in the research to date.

What Are Some Examples of Specific Animals?

OA’s XXXtreme Daredevil XXX is one of our herdsires who is a dark rose grey alpaca. Through this color testing, we learned he has no dilutions. This excited Jason because we now believe it is highly unlikely that Daredevil can produce a white alpaca. This new information opens up our color breeding program and it allows us to match Daredevil to white females. This will help us improve the fiber quality of our color herd, without compromising the pursuit of dark color crias.

Snowmass XXXtreme Tribute is a roan-colored herdsire whose test results showed he possessed two black alleles. This information allows us to breed him with greater confidence in producing black crias. We bought Tribute to complement our dark program and this genotype validates this was the right purchase.

Snowmass Coalition is a white herdsire we acquired to improve the fiber quality of our herd. He is in the top 1% and 5% for EPDs and he an outstanding male. We bought Coalition because of his fleece quality and the fact that his white sire, Snowmass Elite Legend, had a demonstrated ability to allow color to come through in breeding. Without genotype testing or years of offspring production, most would assume Coalition could only produce light-colored animals. Once we have his genotyping results, we will know the basis of his true color and we will have a better understanding of the probability of producing darker colored animals. While we did test Coalition, he showed some anomalies and we are still reviewing his data.

OAS Lady Liberty XX is a light brown female alpaca who has a small white and black spot in her fleece. She carries a black allele, which suggests she is capable of producing a black cria. This information influences our future breeding of her. With this new information, we can now match her to a black herdsire and have greater confidence that Lady could produce a black cria.

Lots of Bubbles is another female we tested. Her fiber looks like an Appaloosa alpaca. She has a dark grey (or light black) base color with lots of round white spots. She also has virtually every color of fiber mixed into her coat. Her test results show that she is a black alpaca who carries tuxedo grey. With this new information, we know we can breed her with the potential of producing a tuxedo grey alpaca. We also now know that we do not want to breed her to our herdsire Leviticus, who is a tuxedo grey. The combination of two tuxedo greys increases the likelihood of miscarriage.

September 2021 Update

There is still a lot we don’t know and there is still a lot we can learn about the color genetics of alpaca. Jason and Lynn have continued to perform testing on both herds and they have been comparing these results to the crias that were born throughout the summer.

The duo has had over 50+ crias delivered this year that were sired by males that did not carry a dilution. All 50 crias are colored animals, and many of the dams were white or light colors. The current testing of over 200+ white alpacas has provided strong evidence that there is no white gene among them, and a white fleeced animal is instead produced by a full dilution.

Jason is also investigating alternate testing options with academic intuitions here in the states. These new testing options would potentially expand the testing details and provide even more information for advancing color breeding and the overall quality of alpaca herds.

Use the Alpaca Color Genotype Calculator

4 thoughts on “Improving Breeding Outcomes Through Alpaca Color Genotyping”

  1. This was a fantastic read! I look forward to learning the outcome of your ongoing studies and hope the presentation will be shared widely. Congratulation and good luck!

  2. This article was very informative and I enjoyed reading it. Thank you for putting this information out to the world.

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