Questions and answers for the Texel Sheep Society-SRUC sire genotyping project using the 700K SNP chip
Genomics is the study of genes. In sheep breeding, we use genomics to understand which genes are influencing certain traits. We do this by using SNPs to detect tiny variations in DNA sequences, and it is these tiny variations that might explain which particular sequence of DNA is responsible for a trait of interest./p>
Genomics is an incredible tool that has the potential to change the nature of sheep breeding. Genomic breeding values are a much more informed way of predicting the genetic merit of individual sheep as you are directly analysing whether that animal carries a known gene or set of genes which have been found to influence a particular trait. The areas where genomics will be of most use will be in the traits which are hardest to measure, such as disease resistance, meat quality or traits which are sex linked such as milk yield. We must, however, continue to take measurements of the existing traits as well as start measuring new traits, especially those involving disease.
The British Texel Sheep Society will be sampling and testing 1000-1300 pedigree rams. The tests will be on the very latest genomic bead chip which contains 700k SNPs of the sheep genome. The 700k SNP chip is the very latest high density SNP chip that can genotype over 700,000 loci (positions along the genome). Over the next few months, we will be sourcing1000 suitable rams from farms across the UK that can be genotyped and have their genotypes stored in our BTSS DNA bank.
This is a fantastic chance to collect vast amounts of genotypes from across the Texel breed that can be stored and used for research purposes. Having such a large bank of information gives us a very detailed insight into the genetics of the Texel breed and, if for example we decided to undertake a genetic research project, we have a great quantity of high density genotypes to refer to and ultimately make the research more accurate and reliable. This information will be directly used in the Agri-Tech Catalyst project on mastitis in Texels in 2015/16 which will hopefully aid the finding of resistance genes to mastitis and the creation of GEBVs for mastitis and footrot.
We will not just simply test any sire. We need to test sires that are significant within the breed and provide an accurate representation of the rest of the breed. Every ram we test needs to be performance recorded in five or more traits and have an accuracy of 60% or over for at least five traits. This ensures that all animals have a sufficient pedigree history and phenotypic records behind them. In addition we will be trying to target animals that have also been CT scanned. We will consider lowering the accuracy for ram lambs which will have lambs born in 2015. This is because many ram lambs will not have a very high accuracy until they have progeny born.
The reason we are only sampling accurately performance recorded sires is because the previously collected measurements made on the progeny of these sires provides essential information to develop GEBVS. These measurements are called phenotypes and are important in genomic wide association studies.
We will use our breed data in our co owned BASCO data base to find suitable animals that meet our criteria. We will then contact the breeder/owner to ensure that the ram/s are alive and present. If so, with the owner's permission, we will then send out nasal sampling kits for the owner to take the samples and send them back to the lab to be genotyped. This is already a standard practice and familiar to many members for our Genetex parentage system launched in 2013.
When we contact you to see if you still own the given rams, we might also ask you if you have any other rams in your possession that might meet our criteria. With your permission, we would also probably like to test those animals as well. This can be clarified when we contact you.
We would ask the owner to carry out the nasal sampling. This is a very simple procedure, however, there is a correct procedure which must be followed to ensure the sample is taken correctly (we will provide instructions on this procedure). We would also ask the owner to take time to make sure eartags are read correctly and the right nasal swabs go into the right package already with the rams eartag number printed on it. We would then ask you to post the samples as promptly as possible, again following the instructions provided.
Once received by us the samples will be sent to our chosen laboratory where they will be genotyped. The samples will have the DNA extracted which will be stored along with the genotypes. These genotypes will be used as part of the Texel breed’s genomic development studies.