INTRODUCTION OF SNP SERVICES
Shorthorn Beef is moving to the use of SNP services, gradually replacing the old Micro-satellite services (MiP). The University of Queensland has been contracted to provide these services.
Micro Satellite (MiP) testing has been a tremendous benefit to the industry, however as DNA technology evolves, SNPs have emerged as the dominant technology for future DNA testing and Genetic analysis.
SNP testing provides two key opportunities
- The technology is significantly cheaper than Micro-satellites (MiP)
- SNPs allow for storing Panels for future genomic evaluation
It is important to note the animal and its parent/s must have been tested using the same technology to allow Parent Verification.
Therefore, individual animals requiring Parent Verification from parents with Micro-satellite DNA records will still be required to be tested using the Micro-satellite test.
Members will still be able to have DNA profiles completed using Micro-satellite (MiP) and should request the service they require when filling out the DNA Profile Test request form.
SNP for Parent Verification
There are 3 options for SNP Parent Verification services.
SEQ–1. The primary panel for parent verification and consists of 140 markers.
SEQ-2. A panel of 190 markers for parent verification, which contains the SEQ-1 markers, plus an additional 50 markers.
SEQ-3. Similar to the Micro-satellite service, extra markers may be required for difficult (multiple sets of qualifying parents) or disputed cases. In this case the SEQ-3 test provides additional markers. These additional markers will be run free of charge if a full parentage analysis has been undertaken. If only one parent is used in the verification, then the additional marker set will incur a charge and will only be performed at members request.
If members request an SEQ-2 test, it will prevent the need to use the SEQ-3 test and the SEQ-2 test is also comparable between laboratories.
SNP for Genomic Evaluation
Utilising Genomics for increasing accurate EBV predictions is continuing to gain momentum. Members will have the opportunity to have SNP marker panels stored for use in future genomic evaluation programs.
There are currently two GeneSeek Genomic Profiler (GGP) tests available through UQ-AGL.
GGP-LD. Low Density chip which contains around 20,000 markers, suitable for imputation up to 800K and will fulfil most requirements.
GGP-HD. High Density chip which contains around 80,000 markers, suitable for imputation up to 800K and is recommended for particularly influential animals.
GGP-LD and GGP-HD both contain the SEQ-1 markers, which means that if an animal is genotyped with a GGP, it does not need to be genotyped with SEQ-1/ SEQ-2 to be included in a parent verification analysis.
Pricing for these services are contained in the fee schedule available on the Shorthorn Beef website.
Prices are for hair samples and a surcharge of $14.30 per sample is applicable to semen or tissue samples.
Members who require tail hair kits should contact the Shorthorn Beef office and they will be sent free of charge.