Current system genetic evaluation
Most Limousin breeders are familiar with the term BLUP (Best Linear Unbiased Prediction) which is the current method of quantifying genetic merit of cattle in Ireland. This methodology is based on the statistical analysis of large quantities of data collected on many pedigree and commercial farms. The more information an animal has on either itself or its relatives, the greater will be the reliability of that animal’s predicted genetic merit. The greater the reliability, the narrower the range in which the proof may vary as the animal accumulates subsequent performance information on either itself or its relatives.
However, the current system of genetic evaluation is not without its shortcomings. The main obstacle to rapidly increase genetic gain is the long generation interval associated with current methodologies. A bull is at least 5 years of age before it reaches moderate to high reliability. In reality this is closer to 7 years and is considerably longer for maternal traits such as weanling weight or cow fertility.
Delaying the identification of the best animal per generation reduces annual genetic gain. Imagine the genetic gain that could be achieved if we could accurately identify the best animal at less than four weeks of age. This is the basis behind genomic selection!
DNA, genomics and all that stuff
Genomics is a discipline that investigates why differences in DNA among animals is associated with differences in performance. DNA is the building blocks of genes which, in turn, determine an animal’s characteristics such as its stature, growth rate and feed intake. DNA is present in all cells, both in cattle and humans, and is identical in all cells. Because DNA signatures are inherited from parents, DNA can and is used for parentage testing but can also use it to identify genetically elite animals. Furthermore, DNA does not change over the lifetime of an animal. DNA can be obtained from any biological sample such as blood, tissue, semen or hair follicles. Therefore, if somehow we could use an animal’s DNA to predict its genetic merit, then we could do so at a very young age without the necessity to wait for performance information from the animal itself or its progeny.
Genomic selection is a tool to help identify genetically elite animals from their DNA by: 1) determining the best DNA signature for Ireland, 2) screening the DNA all newborns, and 3) mating the animals with the best DNA signature, hoping with each generation to get closer and closer to the optimal DNA signature. Genomic selection should not be confused with marker assisted selection based on marker panels which are currently being sold by commercial companies. These marker panels contain tens or a few hundred of pieces of DNA, often called genetic markers. In my opinion, these marker panels have not delivered on promises. Genomic selection, on the other hand, uses many thousands of genetic markers; currently 54,000 markers are used and this will increase to over 500,000 in April 2010.
Genomic Selection in Ireland
Key to a successful genomic selection breeding program is knowledge of the best DNA signature for Limousin cattle producing under Irish production systems. The best DNA signature is determined for each trait separately. The optimal DNA signature for Ireland can be determined by obtaining the DNA signature of many thousands of moderate to high reliability Limousin cattle with performance data in the ICBF database. This group of animals is commonly referred to as the training population. The best animals for this training population are AI sires proven in Ireland because they have high reliability based on Irish data. Teagasc and the ICBF, in collaboration with Irish AI organisations, are mid-way through sourcing semen of proven bulls in Ireland. However, we don’t have thousands of Limousin AI bulls proven in Ireland and therefore DNA samples from older proven stock bulls are also useful. All animals must be proven in Ireland. Research is also currently underway at Moorepark to determine the usefulness of identifying the best DNA signature across breeds thereby facilitating the generation of a sufficiently large training population across all breeds. The biggest obstacle currently to the role out of genomic selection in Irish beef cattle is access to DNA from high reliability animals proven in Ireland.
When the best DNA signature is determined for each trait then genomic selection can be applied. DNA of a newborn animal may be extracted from any biological material of that animal (e.g., hair sample) at any age. This material is sent to a laboratory and the DNA signature determined; the animal is then said to be genotyped. The cost of this service is approximately ¤200 per animal but this ma y increase slightly with the improvement of the technology by the laboratories. This DNA signature of the newborn is compared to the optimal DNA signature previously determined for each trait and a prediction of the genetic merit of the animal for each trait estimated. This estimate based on the animal’s DNA signature is combined with its predicted genetic merit from the current BLUP evaluations. Presentation of breeding values by the ICBF estimated using genomic selection will be identical to what is currently published but the reliability is expected to be improved. Genomic selection of an animal could be complete within a few weeks. When the logistics are in place in Ireland to facilitate large throughput there should be no reason why a genomic breeding value should not be available before an animal is 4 weeks of age.
The increase in reliability achievable with genomic selection in Limousin cattle is difficult to quantify at this stage but will be a function of the number of Limousin animals included in the training population. The advantage of genomic selection on a per animal basis will also vary and will be greatest for animals whose pedigree is in the training population. Therefore, for breeders considering using genomic selection, it’s vital that the DNA signature of the back-pedigree of the animal is in the training population. In Dairy cattle, where genomic selection was launched in Ireland in February 2009, reliability of proofs of young bulls increased on average from 32% to 50%. This is based on a training population of 1,000 animals, albeit from the one breed. We should aim to achieve similar increases in reliability in beef but I suspect we may need more than 1,000 animals in the training population. Genomic selection will have no impact on proven bulls. ICBF currently have almost 6,000 DNA signatures from dairy cattle obtained mainly through swapping with other countries. Therefore, international colleagues in Limousin breeding should be informed that such work is underway in Ireland and that we are keen to develop collaborations. The DNA signature of an animal obtained in France is identical to the DNA signature of the same animal obtained in Ireland; what differs is the best DNA signature for Ireland and France. Therefore, there is no reason why both Ireland and France should obtain the DNA signature of the same animal separately. However, this is happening in dairy cattle and should be avoided in beef. A well as genomically selecting newborns in Ireland, genomic selection will provide a more accurate estimate of the genetic merit of Limousin calves (male or female) from around the world as long as we get access to their DNA signature (or hair sample). Similarly other countries could estimate the genetic merit of Irish born Limousin calves.
In conclusion, genomic selection which supplements current BLUP evaluations with information on the DNA of the animal may be used to increase the reliability of genetic evaluations. The greatest and most urgent requirement for implementation is the DNA signature of a large population (>1,000 animals) of animals proven in Ireland. Collaboration with international colleagues is vital to achieve this. We have set a target to have genomic selection available to Irish beef farmers for Spring 2011.
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