Parentage Analysis

DNA parentage testing is a valuable tool which allows breeders to select elite animals within their stud with confidence, knowing that their ancestry is correct. Breeders can use this information to help fast track genetic progress and confirm parentage when selling elite animals. It increases the validity and value of a pedigree and is essential if estimated breeding values (EBVs) are being used as a basis for selection.

The first year of DNA parentage testing requires the testing of all the dams and sires as well as the progeny, however Genomnz™ recognises the large outlay involved and offers very competitive prices. In the subsequent years only calves and any bought in dams will need to be tested. All DNA profiles are stored on the Genomnz™ database and can be used in at any time for parentage analysis.

The accurate information and production gains that can be achieved will certainly offset the price of DNA testing.

Examples of the benefits of DNA testing

The long term benefits are considerable. A deer farmer for instance, could use the information to:

Identify which hinds are producing the best progeny for venison and velvet production.
Accurately work out hind efficiency in terms of Kg’s of fawn produced to the live weight of breeding hinds. This enables the farmer to collect data from carcass weight and date of slaughter, which is important if you want to know which hinds are producing stock that can be culled early.
A farmer could request a sire match only through DNA if they mob mate their hinds. This means the farmer can determine which stag has been the most active and will also be able to compare the live weight of the progeny. If you can identify the best performing sire, then the following year that sire may be worth using for single sire mating. If you can identify such a sire then the cost of DNA testing is very economical.

How does it work?

Pedigree testing works on the knowledge that every offspring inherits half their genetic information (genes) from their sire and half from their dam. A DNA profile is made up of a panel of highly informative microsatellite markers. These markers are regions of DNA that have a wide variation in length between individuals. By taking a “snapshot” of the offspring’s DNA at these markers (the DNA profile), we can compare it with the DNA profiles of the parents. If a variation of one of these markers (genotype) is present in the offspring but absent in the parents then they cannot be the true parents and they are said to be ‘excluded’.

Genomnz™, using a proprietary pedigree analysis program, checks the DNA profile of the progeny against all potential parents and determines whether the progeny is excluded from the sire and/or dam. The probabilities of parentage are also calculated if no markers from the panel exclude either parent.

Below is a result from one of the microsatellite markers that make up a Genomnz™ DNA-profile. In this case the dam was known but there were two possible sires. By comparing the progeny’s DNA with that of the possible parents we see that the progeny gets the “D allele” from Sire 1 and the “H allele” from the dam. This means Sire 2 does not contribute any genetic information so he is excluded as the sire at this marker.

The progeny inherits the “H peak” from the dam and the “D peak” from Sire 1. Sire 2 is excluded from the calf.

What is the accuracy of the test?

Parentage analysis is an exclusion test, that is, it is 99% accurate if a potential parent is excluded from the progeny. However, DNA alone can not necessarily determine the true parents. The accuracy of the test therefore refers to its ability to exclude an incorrect parent.

Because parentage analysis is an exclusion test, it is possible to get false matches. A false match is where we fail to exclude an incorrect parent, so the progeny either matches more than one pedigree or matches a parent that is not its true parent. Although rare, there are a number of steps you can take to reduce the chance of a false match including using diverse genetics in your herd and supplying Genomnz™ with all relevant information.

If you try and match a calf against all the DNA profiles on the Genomnz™ database there could be several matches. An increase in the number of markers used could help determine a unique match however the cost would also increase proportionately. On farm records such as mating or calving groups, AI and ET records, a complete list of sires used (including backup sires), and a complete list of possible dams will narrow down the number of potential combinations for analysis and will keep the numbers of markers necessary to an affordable cost.

There are a variety of factors that can affect the outcome of the analysis:

Diversity of the genetic pool – if the sires used are half sibs or the dams are closely related there is an increased likelihood of false matches.
Missing animals – if the Genomnz™ database does not hold a DNA profile of all animals involved in the matings a false match may occur where a calf matches a dam that is related to the true dam.
Sire Match only – a full pedigree test is more powerful than a sire and/or dam match.

While DNA testing is the most accurate tool for parentage recording it is necessary to also provide accurate on farm records.

Pedigree Verification
Confirms the breeder’s own pedigree records

Provides full parentage verification, using DNA profiles, for progeny from putative (supposed) pedigrees supplied by the client.
Particularly beneficial to stud breeders who can achieve premium sale prices for animals with certified pedigrees.
Important in ET or AI programs where elite animals are used for genetic gain and therefore accurate records are necessary. DNA pedigree verification is needed to determine if the AI sire or backup sire is the correct sire, or if the calf born to the recipient hind is from the ET program.
Detects over 99 percent of incorrect pedigrees.
Parentage certificates are provided for qualified pedigrees at the client’s request.

Sire/Dam Match
Confirms a sire or dam is matched to an offspring

Determines which sires qualify to be the sire of any individual progeny.
Allows multiple mating for commercial breeders and lowers the cost by not having to test the dam.
For stud breeders where the dam is recorded it can valuable in AI programmes where multiple sires are used.
Can determine which stag has been the most active and allows you to identify the best performing sire.
Good for solving cases of mis-mothering.
Is not as powerful as full pedigrees and sometimes more than one sire can qualify as a match – providing a sample of the dam in these cases can resolve the problem.

DNA-Match
Matches up sires and dams to offspring using only mating and birthing mob records

Used where the client does not provide supposed (putative) pedigrees and Genomnz™ must match progeny to parents from whole mating or birthing groups.
Genomnz™ can test multiple pedigree combinations against multiple progeny to establish true parents.
Invaluable for all types of mix-ups, particularly involving AI or multiple mating.
Allows farmers to leave animals alone at birthing, spend fewer hours matching progeny to dams and use multiple sire mating.

The power of this test relies largely on the extent and accuracy of the information the client provides to Genomnz™. The information required includes mating and birthing groups, dams involved in the ET programme and information on any complicating circumstances (for example, mix-ups at mating or birthing). It is also important to send in samples of all animals involved in the matching including the backup sire and dry dams.

Identity
Proves a sample came from a particular animal
A DNA sample is collected from the animal and a profile is generated and stored on the database. The profile (which may also have been used for pedigree testing) can then be recalled at any stage and used to match to a subsequent sample from the animal.

Used to identify that a DNA sample belongs to a particular animal.
Applications include, providing missing tag numbers, insurance of valuable animals, forensic testing where animals have been stolen, product tracing, and resolving identity disputes.

For information about sample types and sampling instructions please see our sample types page. For information about submitting samples for parentage analysis services please see our sample submission page or download a submission form (Dairy Cattle, Deer, Other Species).