The Importance of Alpaca Parentage Validation for AOA Registration | Updated 2012
At Alpaca Owners Association, Inc., we want to insure that new and established breeders alike develop a clear understanding of this important aspect of the alpaca industry — one that is the basis for the strength of alpaca breeding stock — that all pedigrees are supported by robust scientific methods to validate parentage.
In order to be an AOA-registered alpaca, an animal must be validated as the offspring of two AOA registered alpacas using DNA testing (genotyping). Microsatellite markers have been used for many years in animals and humans as DNA markers for individual identification. Microsatellite markers are anonymous stretches of repetitive DNA — which means that they are not genes that code for physical traits, but they are quite useful in being able to identify individual animals and compare them to each other.
AOA utilizes a set of 18 microsatellite markers that have been shown by molecular genetics research to have a high “polymorphism information content” or PIC value. Basically, this means that each microsatellite has a number of different alleles that are distributed fairly evenly across the entire population. An allele is a slightly different version of a piece of DNA. In the case of microsatellite markers, the alleles are simply different sizes — different numbers of base pairs of DNA within a specific area on a chromosome. Each animal has only two alleles for each marker, but in the overall alpaca population there may be several different alleles for each marker. The more different alleles there are with a fairly even frequency of occurrence in the population, the higher that marker’s “information content,” making it useful for parentage validation purposes. We have selected from among the hundreds of microsatellite markers that have been identified in alpacas to get the set of markers currently used in AOA’s primary and secondary panels.
The fact that there are many different microsatellite markers, each with a number of different alleles in a population, and that each cria inherits one allele from each parent, allows us to compare the cria to the parents and determine whether or not there is a statistically significant chance that the reported parent is NOT a possible parent of the cria. This is known as the Exclusion Probability. Statistical calculations allow us to determine an Exclusion Probability for a specific number of markers of known PIC value.
What this means is that we know how many markers we must have to be able to say with assurance that an animal can or cannot be validated as a parent of the cria. You will note that I say ‘validate’ a parent rather than ‘verify’ — an important distinction. The DNA analysis allows us to say that with a very high statistical certainty we cannot EXCLUDE an animal as a parent.
So, why is all of this important to each of you? It is important because, in order for AOA to validate the parentage of your cria, we must have a sufficient number of markers in common between the reported dam, cria, and reported sire. We must have enough data to compare the cria to the reported dam (first) and if she validates then to the reported sire. If there are not enough markers in common between the three animals, we cannot accurately assess the putative parentage. The dam is assessed first — if she is validated, then we assess whether or not the sire can be validated as well. If the dam does not check out, we do not analyze the sire, because we cannot be sure which alleles came from him.
Some of you may have encountered a situation where you have had a herdsire which has already been validated as the sire of one or more crias. Then AOA tells you that you need to have a re-test on this herdsire’s DNA, because he cannot be validated as the sire of a new cria. More rarely, a female cannot be validated as the dam of a new cria. The issue is that animals registered between 1998 and September 2005 used a 10‑marker panel. Many have not been updated to the 14-marker panel that was in use from September 2005 until 2010. In May of 2010, AOA selected a new DNA testing vendor. This vendor was able to combine more markers into a single test, so we began using an 18-marker panel (14 from the earlier primary panel and 4 from our secondary panel) to increase the Exclusion Probability and improve the validation capability of our process. Making the 18-marker panel our primary panel has drastically reduced the need to re-test using the remaining markers of the secondary panel.
Table 1 is an example of a Parentage Validation Analysis — this is a graphical depiction of what AOA’s software does to validate parentage. First the cria’s marker alleles are compared to the reported dam and ‘assigned’ to the dam (for illustration — in pink). If there is a full match, then the remaining allele sizes for the cria are compared to the reported sire. If they all match, then we can validate the sire (for illustration — in blue). These two cria are validated as the offspring of the reported parents.
As breeding practices change and population genetics change, AOA is at the forefront of the science of parentage validation. We have expanded the microsatellite marker system and incorporated more markers into the primary panel — at no increase in cost — in order to provide accurate parentage validation with minimal testing and cost. AOA provides the most up to date and robust genotyping and parentage validation process for our members to assure the validity of our pedigrees — the basis for the strength of the alpaca industry in North America.
Without DNA validated pedigrees, the accuracy of the pedigree database would be a fraction of what it is. AOA’s data shows that at least 15 percent of initially reported sires are incorrect! You can see that, if these errors are not caught through validation, in a few generations virtually none of the recorded pedigree would be correct — making improvements in important traits virtually impossible. AOA strives to make testing and registration of one of the most robust livestock databases in the world as affordable as possible.