Genomics

However, bulls are at least 5 to 6 years of age before they can achieve moderate reliability for traits such as direct calving performance and carcass traits; the duration is considerably longer for lower heritability traits and maternal traits. Imagine the increase in genetic gain achievable if one could accurately predict the genetic merit of an animal at birth. Theoretically, one could increase annual genetic gain by 500%. This is the basis behind using genomics in animal breeding: more accurate predictions of genetic merit at a younger age. 

Genomics is a scientific discipline involved in research at the DNA level. Every individual, including humans and cattle, has DNA and every cell in the body of a given individual has identical DNA. In other words a cell from a hair follicle will have the same DNA as a red blood cell from the same individual. DNA is the building blocks of genes and it is the genes that determine the characteristics of an animal such as its stature, muscularity, and growth rate. Because DNA does not change over the lifetime of an individual, it is possible to measure the DNA underpinning adult performance (e.g., carcass weight) from the hair follicles of the animal as a calf. The limitation is that we currently don’t know which pieces of DNA underpin adult performance. There are two main forms of using genomics in animal breeding: 1) marker assisted selection, and 2) genomic selection.

Marker Assisted Selection

Marker assisted selection involves identifying a small number of DNA segments, called genetic markers, and using these to identify genetically elite animals. An example of this is the myostatin gene which causes double muscling and is present in Belgian Blue cattle. Screening for the double muscle variant of the myostatin gene in Belgian Blue cattle is of limited use because of its high prevalence but it may be of interest to other breeds. Similarly, genetic markers associated with feed efficiency, meat tenderness as well as other characteristics have been reportedly identified and these could be used in Belgian Blue breeding programs. Such marker panels are commercially available from companies such as Merial (IGENITY®), Pfizers (GeneSTAR®) and Cargill (Metamorphix Inc). However, the effectiveness of these markers in Irish cattle has never been tested and therefore it is not clear how these tests perform in Irish cattle under Irish production conditions. International studies evaluating these marker panels do not yield consistent results. Their effectiveness in Ireland could however be tested by using the marker panel on several hundred bulls with progeny in Ireland.

Genomic Selection

The second application of genomics in animal breeding, which is receiving ever-increasing attention is genomic selection. Genomic selection is essentially a large scale version of the previously described marker assisted selection. However, rather than focusing on individual genetic markers with apparent associations with performance, genomic selection uses many thousands of genetic markers to identify the best DNA signature of an animal for a range of traits. The technology is currently available to measure the DNA signature of an individual at over 54,000 locations along the DNA and in early 2010 this is likely to have increased to 660,000 locations. Ireland was the second country in the world to launch genomic selection for Holstein-Friesian dairy cattle in Spring 2009. Research from the Irish Holstein-Friesian population suggests that the reliability of animals with only parental information would increase from an average of 32% to an average of 50%. This
means a greater accuracy of selection of genetically elite animals, or in other words, a lower probability of fluctuations in genetic merit as animals accumulate more information.

The main difficulty in operating genomic selection breeding programs is to estimate the best DNA signature for Belgian Blue cattle in Irish production systems. It is of fundamental importance that the best DNA signature for Ireland is estimated using Irish production data. Although the DNA of a bull taken in another country like Belgium will be the same as if taken in Ireland the best DNA signature for Belgium will not be the same as the best DNA signature for Ireland, although there will be similarities. This is identical to the differences in best bulls in Ireland compared to other European countries using the current methodology.

Genomic Selection in Ireland

To undertake genomic selection in Ireland, DNA from at least 1,000 Belgian Blue animals with high reliability is required. This sample population of bulls is commonly referred to as the training population and is used to estimate the best DNA signature for Ireland. Identifying 1,000 high reiability Belgian Blue bulls is probably not achievable in the near future and therefore the possibilities of undertaking genomic selection across breedsb will be investigated. If successful, DNA from at least 1,000 beef animals of high reliability will be required. However, a good representation of Belgian Blue bloodlines in that population will improve the benefit of genomic selection in the Belgian Blue breed. Although almost 1,500 AI beef bulls suitable for determining the best DNA signature have been identified, it is unlikely that semen from all sires will be acquired. Therefore, blood samples from stock bulls of moderate to high reliability are also being sought. More DNA can be extracted from blood and therefore blood is preferred to hair follicles, for the moment at least.

Once the training population is developed and the best DNA signature for Ireland determined, genomic selection can be used by pedigree and commercial farmers. Extracted DNA, from hair, blood or tissue of a newborn calf, is sent to a laboratory to determine the animal’s DNA signature, commonly referred to as its genotype. Currently the cost is approximately Û230 per animal although the cost is continuously declining; the same approach would have cost many thousands of euros some years ago. The ICBF can compare the DNA signature of the calf to the best DNA signature for Ireland and the genetic merit of the animal can be estimated. This can be done for male and female animals of any age. Genetic evaluation information published by the ICBF will not differ with the exception of maybe an additional column in sire lists that state whether or not the animal has been genomically selected.

To maximise the benefit of genomic selection for an individual farmer or breeder, the pedigree of any animal being genomically selected should be genotyped and in the training population. Also, a large representation of Belgian Blue bloodlines should be in the training population. The more animals in the training population the greater the benefit of genomic selection. Genetically inferior as well as genetically elite animals must be included in the training population; it’s as important to identify the bad DNA signatures as it is to identify the good DNA signatures. Although difficult to ascertain at this stage, genomic selection should be available for beef cattle in Spring 2011