15 May The use and value of genomics in improving the accuracy of breeding values in the Australian lamb industry
US Trip Report by Harriet Moss
Genomics is the study of genes, made up of DNA, and their function in the body. The sequence of nucleotides in DNA determines what and how genes are expressed by the animal, in turn dictating the differences within and between species. The entire sheep genome has not yet been sequenced, however there are a number of places along the DNA strand for which a short section of the nucleotide sequence has been mapped (Sheep CRC n.d.). Within these sequences a variation has been identified at a particular nucleotide known as a Single Nucleotide Polymorphism (SNP). These SNPs are then used in what is known as a genome-wide SNP assay, which involves the correlation of known SNPs to the pedigree information and performance data (for example lean meat yield, eye muscle depth and loin eye fat depth used in sheep) of an animal population. The SNP results are analysed to identify which variations are present and whether or not these correspond to significant differences in the phenotypic (or observable) traits of the animals (Sheep CRC n.d.). Any SNP identified as having a significant correlation to the phenotypic traits of the species in question can then be utilised to predict the genetic potential of an animal outside of this original sample population, based on the variations it expresses at these known SNPs. This is the basis for the use of genomic testing in production animal breeding as a means of selecting animals with the greatest genetic potential, in turn yielding a higher quality product. This report will focus on the comparison of utilisation of genomics in the American and Australian livestock industries and the expected benefits to producers using genomics technologies.
Genomics in the US
Genomics are currently being utilised by American Breed societies such as the American Angus Association (AAA) and the American International Charolais Association as a means of enhancing the accuracies of their Expected Progeny Differences (EPD), equivalent to Australian Sheep Breeding Values (ASBVs) currently in use here in Australia (American Angus Association 2018, American International Charolais Association 2013). Genomic-enhanced EPDs (GE-EPDs) combine SNP data (genomic results) with pedigree information and performance and progeny data, providing a figure from which producers can select animals of greater genetic merit to use in their breeding programs. The genomics test results of an animal are analysed for their relationship to other animals’ genomic test results of which a performance trait is known. If a close relationship is detected between the new animal and an animal known to perform well for a particular trait, then the EPD for that trait is adjusted accordingly to reflect this superior genetic potential (American Angus Association 2018, American International Charolais Association n.d.). For example, if the newly tested animal is shown to have a strong genomic relationship to one that is known to excel in its marbling characteristics, then the marbling EPD for the newly tested animal will increase (American Angus Association 2018). GE-EPDs are reported to not only have an increase in accuracy compared to standard EPDs, but also improve the accuracy of EPDs in younger animals by reducing the reliance of EPDs on progeny data. In a report by the AAA (2018) on Genomic Enhanced EPDs it stated that “Depending on the trait, GE-EPD on unproven bulls have the same amount of accuracy as if they had already sired 8-33 calves”. This allows producers to not only select their animals with greater confidence, but to do so at a younger age allowing for faster genetic progress within their animals.
The use of genomics in the American Angus and Charolais beef industries is a great example of the utilisation of such technologies in production animal breeding however as EPDs have been developed by individual breed societies, the ability to compare animals between breeds is lacking in the US system (Spangler and Kuehn 2017). This is however, a defining characteristic of the Australian Sheep Breeding Value. With across breed comparison possible through a number of common traits analysed and stored in the Sheep Genetics database, the Australian sheep industry is positioned ahead of its US counterparts in this respect and is in turn likely to reap an even greater reward from the use of genomic-enhanced breeding values (Sheep Genetics 2012).
Where the Australian lamb industry would benefit from genomics
Australian Sheep Breeding Values employed by producers here in Australia have enabled the genetic evaluation of individual animals for over 20 years (Barnett 2006 and Swan et al. 2011). However, the greatest value of these technologies for the sheep meat industry have been limited to a number of easy to measure traits with moderate to high accuracies (Daetwyler, et al. 2010). These include live weight, growth rate, eye muscle area and fat depth, measured using ultrasound scanning at around 8-12 months of age (Stockscan Australia 2018). Harder to measure traits such as Lean Meat Yield (LMY) and eating quality traits, rely on post-slaughter data collection and in the case of Intramuscular Fat measurement, through technologies only available in a research setting (Brito, et al. 2011, Hayes Daetwyler and van der Werf 2012, Craigie 2016). For example, hot carcase weight and GR tissue depth measurements are combined to estimate the lean meat yield of a carcase and the majority of the sheep meat industry still relies on this measurement modality to describe LMY (Pearce 2016). More recently, Dual Energy X-ray Absorptiometry or DEXA technologies have been developed that are capable of more accurately and precisely measuring the lean meat yield, however this is not yet widely available (Meat and Livestock Australia 2017). As these breeding values are reliant on post-slaughter data, the accuracy of the value is in part determined by whether or not the animal in question has slaughtered progeny and if the traits are able to be measured in these animals. This is where genomics will have the most benefit. By reducing the reliance on progeny data to achieve adequate accuracies for these breeding values, genomics will increase their accuracy at a younger age. This will allow for the selection of genetically superior animals at a younger age resulting in a faster rate of genetic gain and in turn yield a superior product (Daetwyler et al. 2010, Swan et al. 2011, Brito et al. 2017, Lee and van der Werf 2014).
Research into current genomics testing in Australia
Analysis of the use of genomics testing in the American industry highlights the importance of an appropriate sample population as a reference point in the implementation of these technologies into the Australian sheep industry. This concept is supported by Swan et. al (2011) where the need for a sample flock that accurately represents the wider sheep population, which also represents the major breeds of interest in the Australian industry, is discussed. The Sheep Cooperative Research Centre (CRC) has since begun research using high density SNP tests as well as full genome sequencing of animals with relevant performance data, in a program involving producers across Australia (Lee and van der Werf 2014). By opening up the project to producers throughout the country the resultant increase in genomic information available to researchers is predicted to allow for a better understanding of the relationship between genes and performance traits. In turn investigating the ability of genomics tests in improving breeding value accuracies through the prediction of an animals phenotypic potential (Van der Werf n.d.).
An improvement in accuracies has already been reported for weight and carcase traits (5-7% increase) and post weaning worm egg counts (30-40% increase). A set of Research Breeding Values being provided to producers using the Sheep Genomics testing have also shown improvements for eating quality traits with an average accuracy of between 40 and 50% (Lee and van der Werf 2014). This research program will allow the Sheep CRC to work closely with producers to develop a cost effective and reliable DNA analysis system which can be implemented with the potential for genetic improvement and faster genetic gain (Van der Werf n.d.). As more research such as this is conducted into the development of genomics testing and its use within the industry, we are likely to see an improvement in the accuracy of genomics and its value in Australian lamb production (Swan, et al. 2011).
The predicted value of genomics in a commercial setting
With the potential of genomics testing to increase the accuracy of ASBVs and allow producers to select animals at a younger age and therefore increase the rate of genetic gain, the value of the technology in a commercial setting is likely to be high. Horton et. al (2014) explored the potential benefits of genomic testing taking into account the proportion of rams tested, the age at which rams were first used and the breeding system adopted. An increase in financial gain of between 12-22% was reported in those systems adopting genomics testing for the selection of animals. The highest increase (20-22%) was seen in the system involving stud producers utilising rams between 6-7 months of age (Horton, Banks and van der Werf 2014). Horton et. al (2014) also considered the optimal number of rams that should be tested in order to achieve the highest value from the genomics testing, finding that the top 20% of rams should be tested in order to maintain a low-cost system while also achieving desirable genetic gains.
The future for the use of genomics in the Australian lamb industry is promising, however a significant amount of research and development is required to ensure its validity as an accurate means of predicting the genetic potential of an animal. Through nation-wide research projects currently being conducted by the Sheep CRC, an increase in understanding of the relationship between the sheep genome and the performance traits important to lamb production is predicted. Furthermore, the development of an adequate sample population to which future genomic test results can be referenced, will allow for an increase in the accuracy of breeding values as well as providing accurate breeding values for animals at a younger age. Genomic testing has already been implemented successfully in the US beef industry, providing a good example from which the Australian sheep industry can learn. Finally, the potential for this technology to enable producers to achieve an increase in genetic gain and progress has been shown experimentally to be of economic benefit, yet another incentive for the development of this technology in the Australian lamb industry.
American Angus Association. (2018, January 25). American Angus Association Genomic Enhanced EPDs. Retrieved March 2018 from Angus Genetics Incorporated: http://www.angus.org/AGI/GenomicEnhancedEPDs.pdf
American International Charolais Association. (n.d.). Genetic Evaluation. Retrieved March 2018 from Charolais USA: http://charolaisusa.com/members/genetic_evaluation.html
American International Charolais Association. (2013, August 22). Genomics. Retrieved March 2018 from Charolais USA: http://charolaisusa.com/members/genomics.html
Barnett, R. (2006). LAMBPLAN – Review of adoption by the Australian meat sheep breeding industry. Sydney: Meat & Livestock Australia Limited.
Brito, L. F., Clarke, S. M., McEwan, J. C., Miller, S. P., Pickering, N. K., Bain, W. E., et al. (2017). Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip. BioMed Central Genetics , 18 (7), 1-17.
Craigie, C. (2016). In-plant measurement of Intramuscular fat (IMF). Retrieved March 2018 from Beef and Lamb New Zealand Genetics: http://www.blnzgenetics.com/files/1475005747_In%20plant%20IMF_Craigie.pdf
Daetwyler, H. D., Hickey, J. M., Henshall, J. M., Dominik, S., Gredler, B., van der Werf, J. H., et al. (2010). Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population. Annimal Production Science , 50 (12), 1004-1010.
Hayes, B., Daetwyler, H., & Van Der Werf, J. (2012). How well is the sheep industry positioned to capture the benefits of genomic technologies? Genomics Breaktfast Workshop – LambEx 2012 (pp. 6-10). Armidale: Sheep CRC.
Horton, B. J., Banks, R. G., & van der Werf, J. H. (2014). Industry benefits from using genomic information in two- and three-tier sheep breeding systems. Animal Production Science , 55 (4), 437-446.
Lee, S., & van der Werf, J. (2014). Sheep CRC genomic test for terminal breeds – what are the benefits? Armidale: Sheep CRC.
Meat and Livestock Australia. (2017). DEXA technology. Retrieved February 2018 from Meat & Livestock Australia: https://www.mla.com.au/globalassets/mla-corporate/news-and-events/documents/dexa-factsheet-lr.pdf
Pearce, D. K. (2016). Improving Lamb Lean Meat Yield. Sheep CRC and Meat & Livestock Australia.
Sheep CRC. (n.d.). Genomics – The Basics. Retrieved February 2018 from https://www.sheepcrc.org.au/industry/genetics-genomics/genomics-the-basics.php
Sheep Genetics. (2012, August 10). How to use the databases (LAMBPLAN and MERINOSELECT). Retrieved March 2018 from Sheep Genetics: http://www.sheepgenetics.org.au/Getting-started/How-to-use-the-databases
Spangler, M., & Kuehn, L. (2017, February 01). Can I Compare EPDs Across Preeds. Retrieved March 2018 from University of Nebraska Lincoln Announce: http://newsroom.unl.edu/announce/beef/6178/35135
Stockscan Australia. (2018). About Us – Australian Stockscan Services PTY LTD. Retrieved March 2018 from http://www.stockscanservices.com.au/about-us/
Swan, A. A., Johnston, D. J., Brown, D. J., Tier, B., & Graser, H.-U. (2011). Integration of genomic information into beef cattle and sheep genetic evaluations in Australia. Animal Production Science , 52 (3), 126-132.