DNA Markers for multiple applications
DNA Markers for multiple applications - Beef CRC - Beef Genetic Technologies
 The Beef CRC plans to discover DNA markers or Single Nucleotide Polymorphisms (SNP) that are associated with a range of economically important traits such as carcase and beef quality (beef tenderness, marbling and retail beef yield), feed efficiency, parasite resistance and other adaptive traits, and female reproductive performance (age at puberty, postpartum reconception and lifetime reproductive performance).The markers associated with each trait are most likely to be marketed as part of a larger panel of markers. Current thinking is that panels may be marketed as SNP panels with up to 384 markers, with applications including parentage identification, diagnostic testing and markers for production traits that allow drafting of animals to best meet particular market specifications. A larger panel of 1500-2000 markers could be used for the same management applications but in addition it could be used to identify genetically superior animals for the traits outlined in the breeding objective. The Beef CRC envisages the DNA markers discovered will account for up to 50 per cent of the genetic variation for each of the traits targeted. The Beef CRC also aims to develop diagnostic DNA based tests for conditions such as the poll, scur and African horn genes. |
| Why does industry want these DNA markers? |
| Prior to the development of the Beef CRCIII, a 3-day externally-facilitated workshop was conducted for around 60 beef industry leaders from all sectors of the beef industry and from across Australia and New Zealand. These leaders highlighted the need for producers to have a set of specific tools which will help them identify cattle which best meet particular market specifications, be most suited to particular production/marketing systems or which are genetically superior for particular attributes and should therefore be used for breeding purposes. The beef industry needs to have confidence that the DNA markers discovered by the Beef CRC are reliable and cost effective. This requires very rigorous confirmation and validation in industry-representative cattle of the DNA markers prior to commercial release. DNA marker technologies potentially offer solutions to all these needs and potentially also secure national and international market access for Australian beef through use of ethical, ‘clean and green’ production systems. |
| How will DNA markers be used? |
| Businesses from all sectors of the beef industry (commercial and seedstock breeders, feedlotters and beef processors) will use DNA markers by collecting biological samples (blood, hair, tissue etc) from cattle and sending the samples to commercial genotyping companies for DNA extraction and genotyping. Genotypes derived from the DNA will then be returned to the businesses or service provider companies for the very wide range of different applications to value-add their businesses. |
| How will DNA markers be delivered to industry? |
| There are numerous applications for the Beef CRC’s DNA markers. Marker-assisted EBVs (EBVM) and genomic selection will be delivered through genetic evaluation schemes such as BREEDPLAN to identify genetically superior animals for economically important traits for use in breeding herds. BREEDPLAN is Australia’s national beef genetic evaluation system. It produces Estimated Breeding Values (EBVs) of recorded cattle for a range of economically important productive traits. Information used to calculate EBVs includes knowledge of the animal’s own performance, the performance of its known relatives, the heritability of each trait and the estimated relationships between all the different traits. BREEDPLAN offers all breeders the potential to accelerate genetic progress in their herds and to provide objective information on stock they sell. Including DNA Markers in BREEDPLAN represents a very powerful opportunity to deliver DNA Markers to a large number and broad range of beef industry end-users, nationally and internationally. DNA markers will be incorporated into commercial or phenotypic values, where DNA markers are used as a management tool to draft animals into groups of cattle that will best meet particular market specifications or specific production/marketing systems. They will be used as diagnostic tests for single traits such as the polled and scurred condition and causative mutations or QTL of large effect that do not fit a quantitative inheritance model. In these cases, the genotypic information will be used as a “yes/no” solution to make breeding selections, perhaps in addition to using Estimated Breeding Values (EBV) to make breeding decisions on complex productive and adaptive traits. Genotypic information associated with carcase and beef quality traits (beef tenderness, marbling and yield) will be included in the Meat Standards Australia (MSA) meat grading scheme to predict and provide increased assurance about the quality and palatability of Australian beef. MSA is a beef eating quality program that labels beef with a guaranteed grade and recommended cooking method to identify eating quality according to consumer perceptions. By integrating the Beef CRC’s meat quality DNA marker technology into the MSA grading system there is the potential to achieve significant uptake and adoption of the technology. Because there is a premium associated with carcases that are graded under MSA, incorporation of DNA markers into the model will provide a premium for herds with a high frequency of the favourable DNA markers. It will also provide a pullthrough effect to increase uptake of the technology that is difficult to achieve for example from BREEDPLAN technologies without the premiums associated with meeting market specifications. To integrate DNA markers into the MSA grading system, Beef CRC is working with MLA, MSA and Pfizer Animal Genetics. DNA markers will also be included into decision support systems such as Total Genetic Resource Management (TGRM) and Beef CRC’s ‘Beef Specs’ calculator. Information on DNA markers and their application will need to be included in training material and information packages delivered through educational institutions, supply chains and the CRC’s “Beef Profit Partnerships”. If DNA markers associated with animal welfare or feed efficiency/methane reduction traits are validated by Beef CRC, they may be included in policy and regulatory frameworks to improve compliance with animal welfare standards or reduce greenhouse gas emissions by cattle. |
| Progress |
| DNA markers for a very wide range of conditions and associations with productive and adaptive traits are being, and will continue to be, discovered, confirmed and validated by Beef CRC in industry relevant cattle populations. They will be commercialised in conjunction with genotyping companies such as Pfizer Animal Genetics (GeneSTAR) and Merial (Igenity) over the life of Beef CRC. CRC scientists are now using Illumina’s 50k SNP panel to discover large numbers of new DNA markers associated with the traits of interest. This research is being undertaken in conjunction with key international collaborators, primarily the United States Department of Agriculture – Agricultural Research Service (USDA-ARS), the Universities of Guelph and Alberta in Canada and the US National Beef Cattle Evaluation Consortium(NBCEC). This new collaboration will have far-reaching impacts. Ultimately impacting on the way the global beef industries use genomics technologies to benefit individual beef businesses at every level of the breeding, growing, finishing and processing sectors in future. The collaboration will significantly increase industry and scientific confidence in the accuracy of DNA markers and their ability to identify animals that will better meet market specifications or are genetically superior for economically important traits and therefore suitable for use in breeding herds. It will at least halve the time it would take the Beef CRC to undertake the research and it will provide additional information about the value of the markers in different environments. Finally, the collaboration will transform the way industry uses the markers across the collaborating countries, where a uniform model of DNA marker commercialisation is being implemented to promote more effective sharing of germ-plasm and technologies across the countries. The uniform commercialisation model will also include an ability to demonstrate the economic impact of DNA markers in industry, thereby greatly assisting uptake of the technology in all countries. It is likely Beef CRC will deliver its first fully-validated DNA markers for carcase and beef quality and feed efficiency traits by 2010. Additional markers for carcase and beef quality and feed efficiency and new markers for reproduction and adaptive traits will be commercialised and delivered to industry as they are validated between 2010 and 2012. |
