Wagyu Collaborative Genetic Research Project

This unique and innovative project will radically increase the rate of genetic improvement in the Wagyu breed. The project is being delivered by the Australian Wagyu Association, with matched funding collaboration from Meat & Livestock Australia.

Project Aim

To increase the rate of genetic gain of Australian Fullblood/Purebred Wagyu at a faster rate than any other Australian beef breed over the next ten years, by developing a low-cost, whole of Wagyu industry genetic advancement model.

This project is delivering a novel approach to the Beef Information Nucleus concept. It is utilising the Australian Wagyu industry’s unique commercially focused structure, combining its large volumes of phenotypic production data from the vertically integrated commercial producer base, and the latest advances in genomic technology to rapidly increase the breed’s rate of genetic gain.

Two Stage Delivery

The project will be delivered in a two-stage approach:

Stage 1:

This initial stage was completed in September 2014. Data was “mined” from large cohorts of Fullblood Wagyu progeny from large commercial Wagyu producer operations, delivering some 2-3000 phenotypes depending of the trait considered. Digital camera imaging and carcase analysis, AUS-MEAT kill sheet data and MSA grading data have delivered new research Estimated Breeding Values (EBVs) for Rib Eye Area, Marbling Percentage and Fineness of Marbling from the camera imaging; and Carcase weight, Marbling Score and P8 Fat from the AUS-MEAT and MSA data. Genotypes for 2147 samples were generated by University of Queensland Genotyping Laboratory with 258, 1287, 378 and 224 samples genotyped with Illumina Bovine LD(10K), 20K, 50K, 80K and HD 800K SNP panels, respectively. The results were analysed using the traditional pedigree methodology (Phase 1 analysis). Phase 2 analysis used the Genomic Relationship Matrix approach by the Animal Genetics & Breeding Unit (AGBU) in the new “single step” BREEDPLAN analysis, utilising the SNP genotypes to more accurately establish pedigree relationships. Digital carcase imaging has enabled accurate scoring of marbling attributes at extreme levels ie. 9+ AUS-MEAT Marble Score, with some 17% of the Fullbloods/Purebreds analysed exceeding Marble Score 9. While the camera imaging data was very valuable it was expensive to collect and more invasive on the highly valuable Wagyu carcases. AUS-MEAT (and MSA data) is more readily available and Marble Score has been found to be highly correlated with the more accurate Camera Marbling Percentage at 0.9. The result is a research based genomically enhanced Wagyu BREEDPLAN analysis which will much more accurately represent the true Wagyu carcase, which is the primary focus of the breed.

Stage 2:

This second stage will implement research results obtained in Stage 1. The Wagyu Genetic Analysis will be customised using new Wagyu genetic parameters (heritability’s and trait correlations, and the new research carcass EBVs moved into Wagyu BREEDPLAN production. Also the genomically enhanced EBVs and the single step genomic BREEDPLAN analysis produced in Stage 1 will be incorporated in the production Wagyu BREEDPLAN analysis. Predictive genomic performance tests will be developed and commercialised for breeding and commercial feedlot slaughter animals. A new Business Model will be developed to enable collection of the large numbers of genomic and phenotypic records needed to build and maintain the accuracy of the genomically enhanced EBVs. Promising young sires will be identified annually and their widespread use encouraged across Wagyu breeding herds supplying performance data, reducing generation interval and further increasing genetic gain. 

R&D Stage 1

Stage 1 was established to achieve the following objectives:

1. Develop Wagyu specific carcass EBV’s based on real carcass data;

2. Develop genomically enhanced EBV’s to increase accuracy and predict performance of animals with little or no known pedigree; and

3. Identify new high performing sires.

Over 3000 Wagyu Fullblood and Crossbred Wagyu carcasses have been analysed using Japanese digital camera and AUS-MEAT data. Accurate heritability’s and trait correlations have been determined for a wide range of new research carcass traits including the level Marbling (Marbling Percentage), Fineness of Marbling, Carcass Weight and Rib Eye Area (Eye Muscle Area).

New Research Estimated Breeding Values (EBVs) have been determined for the following carcass traits:

  • CWT: Genetic differences in AUS-MEAT carcase weight – Hot Standard Carcase weight (kgs). This EBV describes genetic differences in weight at a constant age. A higher value indicates that the animal has genes for faster growth than average.
  • CMAU: Genetic differences in AUS-MEAT Marble Score (range 1 – 9 score) in a 420 kg Wagyu carcase (research data set average CWT was 417 kg). A higher value indicates the animal has genes to produce more marbling.
  • CCMP: Camera Image – Genetic differences in Carcase Marbling Percent in a 420 kg Wagyu carcase. (Percentage of Rib Eye Area which is marbling fat).
  • CCRA: Camera Image – Genetic differences in Carcase Rib Eye Area (square cm) in a 420 kg Wagyu carcase.
  • CCFI: Camera Image – Genetic differences in Carcase Fineness of Marbling Index in a 420 kg Wagyu carcase (degree of fineness of marbling fat.) A higher value indicates finer marbling (smaller fat particles).

Final Report

The Final Report for the Wagyu Collaborative Genetic Research Project Stage 1 is available for download here .

Sire & Dam Research EBV Lists

Wagyu Collaborative Genetic Research Project – Sire & Dam Research EBV Lists October 2014 are available for download here.

These provide the Research Carcass EBVs for the sires involved in the Stage 1 which had at least 6 progeny recorded and dams with at least 3 progeny recorded.

The project involved collection of performance, pedigree and genotype data on approximately 2-3,000 Wagyu animals, including data collected using the Japanese Digital Camera Image Analysis methodology.

While the vast majority of progeny performance data used to produce these Research EBVs was from Fullblood animals, 225 Crossbred Wagyu F1 50% carcasses were included in the analysis. Some animals in the Sire & Dam Lists may have their Research EBVs affected by this Crossbred data.

The Stage 2 implementation of the Research EBVs into the production Wagyu BREEDPLAN analysis will not include the Crossbred Wagyu F1 50% data.

Disclaimer: The research EBVs listed in the Wagyu Collaborative genetics Research Project Sire and Dam Research EBV Lists October 2014 are based on data collected from commercial feedlots and abattoirs, in which some harvesting of animals is likely to have occurred. This can cause errors in the results. All care has been taken to minimise this risk. The research EBVs were calculated from field data collected from carcases in commercial kills of Wagyu cattle. Information on the sires and dams (where available) of these cattle as well as the Wagyu purity was supplied by the breeders of these cattle. The Australian Wagyu Association accepts no responsibility for any outcomes arising from their use.

R&D Stage 2

Stage 2 will achieve the following objectives:

  1. Develop a new business model for AWA to enable rapid genetic improvement in the Wagyu breed
  2. Tailor Wagyu Group BREEDPLAN to best meet the needs of Australian Wagyu production; and
  3. Increase the accuracy of genomically enhanced Wagyu EBVs.

Stage 2 outcomes will be delivered in three Phases:

  1. A new business model for AWA which involves:

1.1.  Capture and recording of large volumes of commercial progeny performance data from birth to carcase to enhance the accuracy of genomically enhanced EBVs. Under the current BREEDPLAN business model the seedstock breeders input the performance data and recover the costs through bull sales. However, in the Wagyu supply chain, the commercial animals and their carcass data are not usually owned by seedstock breeders, so a new data access and revenue model is needed to enable AWA to recover the cost of commercial data capture. This model could well be used by other breeds in future.

1.2.  Registration and performance recording of “unknown” Purebred animals with no sire/dam pedigree as “base” animals in a performance register. These animals are currently excluded from Herdbook registration due to un-verifiable pedigree, and so their bloodline progeny are also excluded. Their level of Wagyu content will be verified using the Percentage Wagyu Content genomic test delivered by Stage 1.

1.3.  Commercial use of the digital carcase cross-section imaging and analysis – to obtain large volumes of carcase data at low cost for research purposes.

1.4.  Establish SNP genomic test service to predict performance of un-phenotyped Fullblood/Purebred breeding animals.

1.5.  Establish SNP genomic test service to predict Estimated Feedlot Profitability of un-phenotyped Fullblood/Purebred commercial feeder slaughter animals.

1.6.  Establish a TGRM/MateSel service using SNP based relationships and genomically enhanced EBV performance prediction.

1.7.  Establish a SNP genomic test using principle component analysis to estimate the percentage of Wagyu breed content in an individual animal.

1.8.  Establish a Young Sire Program to identify a new group of potentially high performing young Fullblood/Purebred bulls each year and encourage their widespread use in commercial herds willing to provide performance data for use in Wagyu GROUP BREEDPLAN. This will involve use of the FBMI and F1TI to identify potential young sires and genomically testing them as un-phenotyped breeding animals to increase their EBV accuracy.

  1. Wagyu Group BREEDPLAN tailored to best meet the needs of Australian Wagyu production through:

2.1.  Incorporation of AUS-MEAT and camera imaging data as captured in Stage 1 into the Wagyu GROUP BREEDPLAN production analysis to produce and communicate the new carcass EBVs based on real carcass data.

2.2.  Incorporation of the Genomic Relationship Matrix and “single step” inclusion of genomic data linked to phenotypic data into Wagyu GROUP BREEDPLAN to deliver genomically enhanced EBVs in the production analysis.

2.3.  Develop a Fullblood Maternal Index (FBMI) and an F1 Terminal Index (F1TI) including the new carcass EBVs.

  1. Increasing the accuracy of genomically enhanced EBVs by 20K SNP genotyping, carcass image analysing and registering 1000 commercial progeny per year.