Genomics
There is a lot of talk about genomics in the dairy industry at the moment, and two conferences have recently been held regarding the 'shiniest new tool in the breeding toolbox'.
What is genomics?
Genomics is a new technology which aims to understand the information contained in an animal's DNA. By understanding how genes interact with themselves, each other and the location of certain genes for specific traits within DNA sequences, genomic predictions can be made for individual animals. On the basis of desirable traits, these genomic predictions identify animals that are genetically superior to the rest of the population based on the DNA markers that they contain. DNA markers are recognisable 'flags' that identify the presence of desired genes which make up traits.
What it looks like
Understanding the DNA sequence of an animal or its genomic information (in relation to desired traits) allows predictions of its genetic merit and performance to be made. Breeding values based on genomics and pedigree information are now being calculated by the Australian Dairy Herd Improvement Scheme (ADHIS) for bulls that have little or no daughter information. This information appears in a bull's Australian Breeding Value (ABV) as an ABV(g), the g represents the genomic information. Proven bulls may also have genomic information in addition to their daughter information, although once a bull has daughters, his genomic information becomes less important.
What it means to farmers
Genomics fast tracks genetic gain (the annual improvement in herd performance that is attributable to genetics) by allowing sire selection decisions based on desired traits such as milk production to be made on younger animals. To genomically test an animal a DNA sample is extracted from a small amount of body tissue, such as tail hair roots, ear-tag punches or nasal swabs. Genomic testing of an animal can be done at any age, which means that breeding values can be estimated for young calves, heifers and bulls long before performance data is available. In the future it will be possible for a bull to have progeny on the ground a lot sooner and at a younger age.
Screening bulls for the DNA markers that they have, for traits such as milk production, enables testing of large numbers of potential progeny test sires. The advantage of genomic testing is that breeding companies can have more confidence in an animal's future breeding value based on their genomic data, rather than only using their pedigree information. This will result in a significant reduction in the need for the number of bulls entering progeny test programs.
The dairy industry is already seeing a change in the way semen companies select bull teams. Semen companies have previously selected bulls on pedigree and visual assessments only. Using the new genomics technology, the DNA marker information will identify bulls that are genetically superior (which is not identifiable by visual assessment of the animal). Some bulls now entering sire programs would possibly not have been selected based on their pedigree alone, however with genomic testing they have been identified as genetically superior animals and have now been included in the sire programs.
A good example of how genomic technology works can be seen in the comparison of a set of four or five embryo transfer (ET) brothers. Semen companies can genomically test the bulls to determine which of the brothers is genetically superior and place that bull into a progeny test program. Before this technology was available all 5 brothers could have entered a progeny testing program, as they would have had exactly the same genetic merit based solely on their pedigree information.
It is even possible to look at the genetic merit of embryos and determine which are likely to be superior to others. This could change the way in which the industry uses ET programs in the future. If a breeder can compare the DNA genetic merit of cows and embryos, then they can make decisions on which cows will be placed into ET programs.
In France, the dairy industry no longer progeny test bulls. Bulls are selected solely on their genetic merit using genomic testing. The French dairy industry screen more than 10,000 bulls each year to work out which bulls are genetically superior to the rest of France's bull population.
Cow ABV(g)s will also allow farmers to compare animals between herds more confidently. It is initially expected that stud breeders will take up this technology. Commercial farms may consider testing heifers if they have surplus stock and are looking at selling some. As the genetic potential of the heifers can not be physically seen, genomic testing allows breeders to make a more informed decision about which heifers to keep and which to sell based on their genetic potential.
Using bulls with genomic proofs
It is recommended by ADHIS and semen companies to use a team of bulls that is a combination of proven, progeny tested and genomically tested sires to spread breeding risk. A Dairy Futures CRC research project being carried out by DPI scientists, suggests that when using genomically tested bulls in bull teams, one progeny tested bull should be replaced by two genomically tested bulls. This is because genomically tested bulls have reliabilities of around 60 per cent (for a trait with a heritability of 0.3) which is approximately equal to a bull having a daughter proof with 20 daughters.
Cost
The cost of genomic testing is being reduced with advancements in technology and the increased number of samples being processed. At the moment costs vary depending on how many DNA markers you screen for, with tests ranging from $90 to $275.
The sampling process is relatively simple; all you need to do is to take a tail hair root, ear-tag punch or nasal swab sample and send it away to the testing laboratory. A sampling kit can be acquired from Holstein Australia who coordinates the testing. The results from the genomics test are then sent to Australian Dairy Herd Improvement Scheme (ADHIS) for analysis and interpretation.
Currently there is a long turn around time for the analysis and interpretation of the genomic testing. This is being improved and it is hoped that in the near future breeders will receive the results more promptly.
Concerns for the future
It is fair to assume that breeders will demand a premium price for genomically tested animals and one concern in the industry is that it will become a marketing strategy. Genomic testing does not ensure superiority of the stock, but it may become a factor in influencing purchasing decisions. It has been suggested that in the future a grading or scoring system may need to be developed so that purchasers can see how well or how poorly animals rate genomically. It could become a case of buyer beware, with potential buyers needing to keep in mind that while stock may be in the bottom section of one particular herd, they may still be superior to the purchaser's herd.
Summary
Genomics is a new tool which has the potential to help dairy farmers and breeders make more informed decisions about the selection of young animals. It is also particularly useful for semen companies. Semen companies can now identify genetically superior bulls at a much younger age and offer these bulls to farmers. This has the potential to accelerate the rate of genetic gain in commercial dairy farms and result in more profitable dairying.
It is important to remember that when using genomically tested sires in a breeding program, to use a mixture of proven, progeny tested and genomically tested sires to spread the breeding risk. As it is a new tool it would be wise to consult a semen salesman or the ADHIS in regards to any questions about using genomically tested sires within a herd.
For DNA sampling kits, contact Matt Shaffer from Holstein Australia, phone (03) 9835 7600 or email mshaffer@holstein.com.au.
