Genomics has been introduced in 2021 for the first Small Stock breed in South Africa. This made accurate parentage verification based on SNP-markers, as well as testing for single gene traits a reality for all Small Stock breeds.
For inclusion of genomic information in the estimation of genomically enhanced breeding values (GEBVs), a representative number of animals with high impact in the breed and therefore that have highly accurate breeding values, first need to be genotyped. These animals form the Reference Population from which the genetic code is interpreted, an essential foundation for the implementation of Genomic Selection. It is therefore strongly recommended that biological material of high impact animals is collected and preserved with the purpose to create a strong representative Reference Population for future application of Genomic Selection in a breed.
Why is participation in Genomic Selection important?
Inclusion of genomic information in a breed’s Genetic Evaluation has the following benefits:
- Serves as evidence of the identity of the animal (traceability).
- Accurate parentage and offspring authentication with more than 20 000 markers, also in cases of closely related multiple sires (brothers or father-son combinations) and highly inbred animals, provided both parents have also been genotyped.
- More accurate selection of young and unmeasured rams. This is especially beneficial for traits that are measured late in the animal’s life, in one of the sexes or only in daughters, for example, milk, fertility and longevity.
- Enhancement of genetic linkages between flocks, especially for flocks with weak linkage or that have many animals of unknown parentage.
- Tests for carriers of several lethal, semi-lethal, desirable or unwanted traits.
- Genomic relationships between genotyped animals are determined.
- Establishment of a genomic database of the breed which will enable precious, breed-specific genomic research in future. It can therefore be seen as an investment in the flock and population.
- Genotyping adds value to the animal, as more information and more accurate breeding values become available.
Which animals should be genotyped?
- Animals whose parents need to be verified, or where unknown parents need to be identified.
- Animals that have already made an impact in your flock: All sires that were used. This will ensure that future young genotyped animals are genomically linked to animals with highly accurate breeding values and it will aid in enhancing the linkage of the flock within the breed.
- Animals that have the potential to have many offspring.
- Young animals: This will ensure more accurate EBVs, selection will be more efficient, resulting in faster genetic gain.
- New rams that are considered for use in the flock.
How should the biological samples be taken?
Due to an insufficient amount of DNA that can be obtained from hair samples of Small Stock, laboratories only accept tissue-, semen- and blood samples as biological material for genotyping. Some laboratories do accept the roots of tail hair for goats, but for sheep breeds these are problematic and are not accepted by the laboratories.
Following discussions with the laboratories, it is recommended that one of the following procedures should be followed for sampling of biological material:
- Blood cards which can be obtained free of charge from the laboratories or SA Stud Book. A drop of blood of the animal should be dripped on the card. Blood cards are made of special paper created for the taking of blood samples.
- A tissue sample of the animal’s ear can be taken and preserved in a tube with preservation solution. The Allflex applicator can be used with the accompanying tubes containing the solution for preservation. Alternatively, the RFID ear-tag applicator can be used, with automatic collection of the sample in a preservation tube when the animal receives its ear-tag. The Allflex applicator costs around R1 100, which is a once-off payment, with R24/tube/animal. Click on this link for more information on the Allflex applicator: https://www.allflexsa.com/products/dna-sampling/tissue-sampling-tag/
- Semen straws of rams can be sent in paper envelopes.
- Blood samples in glass tubes (those with the purple lids), kept at a temperature of 4˚C, can be sent. However, SA Stud Book cannot handle these samples. It should therefore be arranged with and send directly to the laboratory.
Utmost care should be taken to prevent cross-contamination when sampling is done.
Where should the samples be sent to?
Biological samples for genotyping should be send to the following address:
Small Stock Genomic Testing
118 Henry Street
Contact Person : Elsa van den Bergh
If the samples are sent for conservation in SA Stud Book’s biobank and not for genotyping, it should clearly be indicated and send to the following address:
Small Stock Biobank Conservation
118 Henry Street
Contact Person : Elsa van den Bergh
The SA registration number, ID and sex of the animal, as well as the breeder’s information should accompany the sample.
What is the cost for participation?
For conservation of the samples in SA Stud Book’s Biobank, a once-only fee of R30/sample (VAT excluded) applies.
The cost of genotyping and participation in Genomic Selection, is R730/animal (VAT excluded). Please note that for semen and blood samples the lab will charge an additional fee of R95 per sample.
How long for release of the genomic results?
It takes around 6 weeks from when the samples were received at SA Stud Book, until the release of the genomic information to the breeder.