SUCKLER DAM BREED
FOR CURRENT SLAUGHTER GENERATION
Prime cattle slaughter data from abattoirs across Great Britain between 2010 and 2019 shows the Simmental breed is currently the 3rd most popular dam breed for suckler producers, behind the Limousin and Aberdeen Angus breeds, and running neck and neck with Angus for the number two position. Simmental dams accounted for 9.2% of prime cattle slaughtered during this time period.
Showing the importance of the Simmental breed in the national suckler herd it is reasonable to assume a significant percentage of Simmental genetics in the non-Simmental sired females.
STEPPING IT UP WITH SNPs
DNA parentage testing has traditionally been done with microsatellite markers. These markers are simple repeats in the DNA sequence, and the number of repeats present is highly variable. This high level of variability is what allows us to correctly assign DNA-based parentage using a relatively small number of markers.
Single Nucleotide Polymorphisms (SNPs) occur when there is a high amount of variation amongst individuals at a single position in the DNA sequence. There are millions of SNPs present across the cattle genome. Genotyping using SNP ‘chips’ can provide data on many thousands of SNPs at once, as opposed to the small 16 marker panel for microsatellites.
As well being used for parentage verification, genotype data from SNP chips can be used to assess animal status for many single gene traits, such as myostatin status, or carriers of disease mutations such as arachnomelia and curly calf syndrome. They are also the technology that underpins genomic selection, which uses phenotype and genotype information on a reference population of animals to predict genetic merit in cattle at an early age.
Historically, the cost of SNP genotyping has been higher than that of microsatellite genotyping, however these costs have significantly decreased over time, and are now much more comparable. Moving from microsatellites to SNP-based parentage verification will provide many opportunities to accelerate breed development.
BRITISH SIMMENTAL MOVING ITS DNA SERVICE PROVISION TO SINGLE NUCLEOTIDE POLYMORPHISM (SNP) TECHNOLOGY IN 2021
In a progressive step, the British Simmental Cattle Society will move its DNA services in 2021 from the presently used Microsatellite (MS) technology to Single Nucleotide Polymorphism (SNP) technology.
The work to make the transition has commenced with the aim being that the new service will fully commence from 1st March 2021. To explain this change as clearly and simply as possible, please see the following Q&A where we have anticipated what we think may be the most relevant and helpful questions:
Q: Why is the Society moving to using SNPs (Single Nucleotide Polymorphism technology)?
A: There are a few reasons but the first thing to say is that SNP technology provides an improved and robust parent verification test that is internationally accredited. The technology has been used in the livestock industry for almost a decade now and with most of the principle herdbooks, that work with Weatherbys, already having moved over.
Q: What other reasons are there to move to this new technology.
A: Importantly, the increasing use of SNP technology at an industry wide level has seen a significant drop off in the use of Microsatellites (MS) for parentage verification purposes. Weatherbys have made clear that the use of MS technology will be phased out and possibly as early as 2022. As use across the industry diminishes then costs for MS may also increase. Given this, it is important and sensible to make the transition to SNP technology in a good time prior to the phase out of MS.
Q: Are there any other advantages or benefits that moving to the SNP technology may bring members?
A: Yes. As above, the SNP technology will bring improved and more robust sire and parentage verification and is a move forward in technology. The SNP technology will also give the ability to add more to a single test, a parentage plus polled test would be an example of this. Both could be done at one test and as opposed to two separate tests at a greater cost. Members will therefore, in such an instance, make a considerable saving.
SNP technology will also give the platform from which, if the Society chose to do so, major gene testing can be carried out for a range of such as health traits, traits of economic importance, and for work in genomics generally.
Q: What will the cost of DNA testing for parentage verification be to members?
A: The base cost of SNP DNA testing is higher. After full consideration Council have set the cost of a DNA test for parentage verification at £27.50. This increase is unavoidable but prices are in line with other principle breed society herdbooks. The set price has a small margin on top of the cost price to the Society from Weatherbys. This margin allows the Society to absorb some costs where additional DNA testing is required with regards to sale matters, general herdbook work, and for herd inspection work. As above, where you are requesting a further test such as polled at the same time the overall cost will be significantly lower. For example Parentage + Polled will be £33.00 (£27.50 + £5.50) + VAT which is a considerable saving.
As noted in the second question, Weatherbys have made clear that the use of MS technology will be phased out and possibly as early as 2022. As use across the industry diminishes then costs for MS may also have to increase.
Q: What work is required from here for the Society to make this transition?
A: At present we are testing and SNP genotyping the most commonly used Simmental sires. SNP genotyping these breeding bulls means the bull SNP profiles will be available in the parentage testing data base in advance of the offspring presenting for sire verification. So it is in effect a library of bulls to check progeny against and that has to be established prior to 1st March.
Q: How many bulls will require to be tested and who will pay for the SNP genotype testing of the most commonly used sires.
A: The Society, in discussion with Weatherbys, are compiling a list of all Simmental sires that have had at least one calf registered to them in the last three years. This will come to approximately 1500 sires. These sires will require to be SNP genotyped with the total cost likely to be £25 – £30k. Again, it’s an unavoidable cost and one which the Society will pay.
Q: Why is the ‘new’ service provisionally set to commence from 1st March?
A: We want to make the transition quickly to ensure that members are getting the best value by using the best technology. Continuing to use a technology that is getting phased out is not practical or sensible. As noted, work has already started to make the transition. If the hair samples are in the British Simmental sample archive, held in Weatherbys Scientific bio-bank, then these samples can be retrieved and SNP genotyped reducing the necessity to re-collect from animals. There will inevitably be some samples from storage that may not be good enough to use and some bulls where we will have to request further hair samples from breeders. We are taking aim at an eight-week working period to test these bulls and to make the transition from microsatellites to SNP’s.
Q: What will happen to the Society’s DNA testing between January 2021 and the 1st March?
A: We are asking members to continue to submit DNA samples for testing as would be required. The DNA samples received from now until 1st March will be logged and held, and then tested beyond the commencement date. All samples received up to the 1st March will
be tested at the present prices. The new pricing schedule will be applicable from 1st March and for samples received after that date.
If there are sale or ‘special’ situations where DNA testing is required then consideration will be given to this prior to March but it would be using the existing and in effect ‘old’ MS technology.
Q: What challenges might the transition bring?
A: We hope of course for the transition itself from MS to SNPs, and the DNA service provision thereafter, to be as smooth as possible. It is likely, if not inevitable, that challenges will arise from time to time regarding such as ‘older animals’ and embryos in storage. We hope that these will be at a minimum and each will have to be considered on their merits and as they arise. Weatherbys have faced and successfully met similar challenges in other transitions, and whilst we are closer to the MS technology being phased out, we trust that this will also be the case during and beyond the Simmental transition also.
Q: What about testing turn round times for SNPs
This is an important point. The turn round time for DNA testing should be largely the same as at present i.e. from receipt of the sample, members should have results back within 4-6 weeks. However, please note that the SNP process in itself takes 3 weeks from the time Weatherbys receive that sample, for samples to have DNA extracted and parentage tests carried out thereafter. Therefore, particularly with reference to sale animals, samples will be required in plenty of time in advance of sale dates. Where there are any problems or need for retesting following the initial sample being tested, then at least three weeks is required for a second test beyond receipt of the sample at the lab.
Q: Are there any other suggestions for members in collecting samples?
A: Yes. If a member is selling/disposing of a bull that has had, or is due to have, progeny registered to him, then it would be good practise to collect a hair sample from the bull. Identify the sample on the bag it’s put in, and keep in a drawer out of sunshine. This could be very important in case the sample held and retrieved from Weatherbys is not good enough to be SNP profiled, or where a bull is having his first calves registered to him. It would be sensible to take a hair sample in this manner from any pedigree breeding animal, male or female, that is being sold or disposed of, just in case there is a requirement for a DNA purpose, now or in the future.
Please note, hairs should be collected by plucking (not cutting) from the animal’s tail. This is preferable to hairs from the neck as the root follicles are bigger. It is recommended that 20-30 hairs are required per sample collected.
Q: Will the Society be able to help with member queries around this transition now and beyond 1st March?
Absolutely. The Society’s staff will be working hard to ensure the ‘new’ service is rolled out as smoothly as is possible and to help members with queries and problems. Many members will remember Bloodtyping being the standard technology. The livestock industry then transitioned to Microsatellites. This move to SNP technology is the next and further step forward in the provision of DNA services.