Crossbred Wagyu Test

WagyuContentTestdec2016

New test identifies black wagyu content

The Australian Wagyu Association (AWA) has developed a genomic test to determine the level of Japanese Black (Black Wagyu) in non-pedigreed crossbred animals. This ground breaking development, known as the Crossbred Wagyu Test (CWT) will help the supply chain determine feeding regimes and the propensity of cattle to produce a genuine Wagyu eating experience.

AWA’s Carel Teseling explains the purposes of the test, how it works and delves into the prefectural nuances of the breed in Japan.

Purpose

  • To assist the beef industry in identifying the approximate level of Black Wagyu content from a non-pedigree crossbred animal’s DNA sample.
  • Assist in selecting a new class of breeding animals to purchase or to register with the AWA. Animals with tested Black Wagyu content can be registered into the Wagyu Content Register and used for breeding purposes.
  • The AWA board is reviewing the Bylaws to determine the appropriate level at which animals with tested Black Wagyu content can enter the Herdbook as a Purebred animal.
  • Supply chain verification of non-pedigree, crossbred animals. Testing may be particularly valuable before feedlot entry, offering a new cost-effective means for producers, cattle buyers, and processors to determine the Black Wagyu content in commercial crossbred cattle mobs. The results could, for instance, facilitate categorising crossbreds into the progeny of the Black Wagyu bull or a mickey bull. This knowledge would significantly influence the choice of optimum feeding regimes, processing, and marketing.

Introduction

The Australian Wagyu Association has developed a genomic test to determine the level of Japanese Black (Black Wagyu) content in a DNA sample from a crossbred animal. The test measures Black Wagyu content in terms of the animal’s relationship to the mainstream Black Wagyu sub-population available in Australia. While some Australian fullblood animals will return lower CWT values, this needs to be recognised as an indication of their importance as “outliers” within the local gene pool, and the valuable contribution they can make to maintaining genetic diversity and providing future selection flexibility. Further development work will endeavour to measure better and define these outlier populations, which have already been identified as descendants of specific, original Japanese Black prefectural herds.

How the test works

Essentially the CWT measures the genomic “distance” between the genotype of a particular animal being tested and the “clouds” or reference sets of genotypes available for other breeds and delivers the estimated breed content level of each breed within that animal.

The CWT software has been developed by the Animal Genetics & Breeding Unit (AGBU) at the University of New England. It uses a reference dataset for each breed type whose genotypes are currently available. At least 100 individual animal genotypes, representing the genetic variation in the breed, are required to form an accurate representation of a particular breed, so only the major breeds have sufficient genotypes to enable them to be included at this stage.  Each animal in the reference set requires a genotype of sufficient SNP (Single Nucleotide Polymorphism) density to enable accurate breed determination, with the Low-Density GeneSeek Genomic Profiler (GGPLD) of some 34,000 SNPS currently the minimum (previous GGPLD SNP levels were 10K, then 20K and these have also been used).  The breed genotypes have been provided by a range of industry contributors including AWA through its Wagyu Collaborative Genetics Research Project, Meat & Livestock Australia through the various Beef Cooperative Research Centre projects and other breed associations.

Figure one – principle component analysis illustrating the genomic distance between breeds.

content-test-figureOne

The CWT uses a two-step process to calculate the breed content:

  • Firstly, the software calculates the unique allele frequencies for each breed in the reference dataset. An allele is one of a pair of genes that appear at a particular location on a particular chromosome and control the same characteristic, such as blood type or coat colour.
  • Secondly, it calculates the correlations between the allele frequencies of the test animal’s genotype and those of the other breeds, and this represents the breed percentages.

Breeds in the reference dataset

The reference dataset currently has more than 10,000 genotypes representing 11 of the most prominent Australian beef breeds and consists of:

  • Approximately 1,600 Wagyu and Crossbred Wagyu genotypes ranging from Fullblood Wagyu 100% (almost exclusively Japanese Black) to Crossbred Wagyu F1 50% provided by AWA derived from its Wagyu Collaborative Genetics Research Project co-funded through the MLA Donor Company.
  • Approximately 7,000 genotypes from 10 other beef breeds largely provided from the Beef Co-operative Research Centres (Beef CRC’s) I, II and III co-funded by the beef industry and the MLA Donor Company.
  • The 11 breeds currently having genotypes in the reference dataset are Angus, Brahman, Charolais, Droughtmaster, Hereford, Limousin, Murray Grey, Santa Gertrudis, Simmental, Shorthorn and Wagyu.

This reference dataset of the various breeds in their genomic “clouds” is graphically represented in Figure one, showing the distance between each breed “cloud”.

The Wagyu reference dataset

The term Wagyu is a general term for about five breeds of cattle bred in Japan.  The Japanese word is ‘our’ (wa) and ‘cattle’ (gyu).   The CWT measures only content from the dominant Japanese Black breed. There are three major Japanese Black bloodlines well represented in the Australian sub-population:

  • Kumanami and Tajima from the Hyogo Prefecture
  • Itozakura & Fujiyoshi from the  Shimane Prefecture
  • Kedaka and Eikou from the Tottori Prefecture

Two major red (Japanese Brown) sub-populations (Akaushi) are also represented in Australia, but are not covered by the CWT.  These are:

  • Kochi; and
  • Kumamoto

Modern Wagyu cattle breeds are the result of crossing of the native cattle in Japan with imported breeds. Systematic crossing began in 1868 during the Meiji restoration. Brown Swiss, Devon, Shorthorn, Simmental, Angus, Ayrshire and Korean cattle were imported during this period. The infusions of these British, European and Asian breeds ceased about 1910.  However, it can be expected that some evidence of these breeds still exists in some prefectural Fullblood Wagyu cattle herds in Japan.  The red population was strongly influenced by Korean and European breeds, particularly Simmental.

The Australian herd is descended from a foundation Black Wagyu population exported to the USA and Australia from Japan between 1976 and 2001. This comprised some 300 animals.

The Crossbred Wagyu Test results

Fullblood results

An animal is regarded as a Fullblood Wagyu whose forebears originate from Japan. Registered Fullbloods require DNA parent verification to both the sire and dam to ensure complete pedigree accuracy. Over 300 registered Black Fullblood Wagyus were represented in the reference dataset with their test results shown in figure two.

Figure two – frequency distribution of registered black Fullblood animals. 

The results highlight the genetic diversity available in the registered black Australian Fullblood population. The Fullblood animals with lower CWT results are highly valuable to the future of the Black Wagyu population in Australia as they provide the only current opportunities available to retain genetic diversity and deliver enhanced selection options for traits such as superior conformation, growth and maternal capability, with retained marbling.

Crossbred results

Initially, it was expected that the Black Wagyu content in crossbred Wagyu animals would follow the traditional genetic norm of:

  • F1 or first Wagyu cross delivering 50% Wagyu
  • F2 or second cross Wagyu delivering 75% Wagyu
  • F3 or third cross Wagyu delivering 87% Wagyu
  • F4 or Purebred Wagyu delivering 93% Wagyu

However, the genomic variation identified in the genotyped registered Black Fullblood animals was reflected in their crossbred progeny resulting in a range for any given crossbred grade as shown in figure three.

Figure three – frequency distribution of F3 Wagyu cross animals. content-test-figurethree

Note: It is expected that F3 animals with higher than 92% were out of cows that already had some Black Wagyu influence.

Therefore, crossbred progeny of a high scoring Black Fullblood sire can be expected to have content close to the expected genetic norm, while progeny from sires with other prefectural genomic content may show less than the expected genetic norm. Providing the sire is registered with known performance through its Estimated Breeding Values (EBVs), this will not pose a problem and indeed may be a distinct advantage if the sire has higher growth and other attributes.

How the CWT  may be used

Wagyu Content Register

There are many animals with Wagyu content in member herds where pedigree cannot be proven through DNA parent verification and so cannot be registered as Fullbloods or Purebreds.  However, they are of considerable value to the Wagyu gene pool.  These animals can now be registered in the Wagyu Content Register and their performance data input for analysis through Wagyu BREEDPLAN.  The Crossbred Wagyu Test can provide the Black Wagyu breed percentage required by the Content Register Bylaws:

Content register

  1. The Content Register makes provision for the registration of Wagyu influenced animals not eligible for registration in the fullblood or purebred registers.
  2. It shall be a requirement for the registration of a Content Register calf that its sire has a DNA profile recorded with AWA at a minimum level to be specified by AWA.
  3. Prior to registration a hair sample of the animal will be provided to AWA.
  4. Parent verification of calves will not be required.
  5. Random parent verification of calves will be conducted at a frequency determined by the board at no cost to the animal owners.  Animals found to have an incorrect sire will be deregistered if the correct sire is not identified by the owner at the owner’s cost.
  6. If no Wagyu content is claimed for a base animal, the breed (or breed combination) of the base animal shall be recorded.
  7. If Wagyu content is claimed for a base animal, a breed content test will be required for the animal. Animals registered in the content register shall be assigned a percentage breed content calculated from the percentage Wagyu of the sire and dam or results from the Crossbred Wagyu Test.

Registration of animals with Wagyu content is expected to significantly increase the animal’s sale and therefore capital value as buyers can have greater confidence in the claimed Wagyu content.

Testing Animals with the CWT

An animal can be tested to determine its Black Wagyu content using the Crossbred Wagyu Test. This may be of value in:

  • Assisting in selecting breeding animals to purchase or to register with the AWA. Animals with tested Black Wagyu content can be registered in the Wagyu Content Register and used for breeding purposes.
  • Upgrading an animal into the Herdbook. The AWA board is reviewing the Bylaws to determine the appropriate level at which animals with tested Wagyu content can enter the Herdbook as a Purebred animal.
  • Supply chain verification of animals.  Testing may be particularly valuable before feedlot entry, offering a new cost-effective means for producers, cattle buyers, and processors to determine the Black Wagyu content in commercial crossbred cattle mobs. The results could, for instance, facilitate categorising crossbreds into the progeny of the Black Wagyu bull or a mickey bull. This knowledge would significantly influence the choice of optimum feeding regimes, processing, and marketing.

How to order the CWT

Producers who wish to do a Crossbred Wagyu Test on animals should contact AWA staff or download a DNA test request form from the AWA website. The form contains the instructions for the collection of the sample and testing as follows:

  1. Take a DNA hair or ear notch (using the Allflex Tissue Sampling Unit) sample from the test
    Text
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    animal
  2. Send the DNA sample to the University of Queensland Animal Genetics Laboratory (UQAGL)
  3. Email the order form requesting a Crossbred Wagyu Test to regos@wagyu.org.au.
  4. UQAGL will make the GGPLD genotype available to AWA.
  5. AWA will use the GGPLD genotype to conduct the Crossbred Wagyu Test analysis and return the result to you.

The CWT will cost $79.00 (inc. GST) per animal.

Download information

This information is available as a PDF – click here to download

FAQs and further information

Frequently asked questions about the Crossbred Wagyu Test (CWT) are listed below. If you need more information, please contact us.

Q. What is the key objective of the CWT?

The primary objective of the CWT is the provision of an accurate, easily deployed quality assurance tool for the commercial crossbred Wagyu industry in Australia, and possibly other Wagyu producers outside Japan. Most Australian commercial production involves crossbreeding from Japanese Black sires and occurs without subsequent formal parent verification of the Wagyu calf crop, which requires a complex DNA-based process in multi-sire commercial environments. The CWT will offer a new inexpensive tool to allow producers, buyers, and processors to sample Wagyu content in commercial cattle mobs to determine optimum feeding regimes, processing, and marketing.

A similar Quality Assurance sampling opportunity might be available to boxed beef processors, who may be packaging and promoting Wagyu beef by ‘Percentage Wagyu’ guidelines.

Finally, AWA has also created the Wagyu Content Register, which enables high-performance animals with unknown pedigree but CWT-proven Japanese Black percentage to be registered. The Content Register will facilitate the registration of Black Wagyu animals that were previously ‘lost’ as breeding animals. Content Register animals may in future qualify for enhanced value sales or the commencement of new pedigree trees.

Q. Who will manage the use of the CWT in the Australian market?

The Australian Wagyu Association is a not-for-profit member organisation, and the CWT is a commercial product. To effectively manage this AWA has created a new legal entity and wholly owned subsidiary, called Wagyu Services Pty Ltd, which will manage licensing, risk and other commercial market facets of the CWT. Wagyu Services Pty Ltd will reside with AWA in Armidale, NSW.

Q. Does the CWT challenge the need for Herdbook pedigree recording and or/the veracity of existing pedigree records?

The CWT will have no impact on historical or future DNA parent verified pedigree recording of Herdbook registered Wagyu cattle in Australia. No existing Herdbook pedigree records will be revisited purely as a result of an ‘unexpected’ CWT percentage. As explained previously, the inherent genetic diversity of the Japanese Black, arising from prefectural breeding, is expected to create an ongoing minor deviation in CWT percentages of commercial cattle at a low but commercially acceptable level. These should not be considered as ‘errors’ and have no ramifications for pedigrees.

The lack of sufficient representation of the complete suite of Japanese Black prefectural bloodlines is a constraint in the development of a ‘truly representative’ Japanese Black content test. If all prefectures were sufficiently represented in the reference dataset, it would have enabled a definitive assessment of all Australian Wagyu animals. However, the Australian Wagyu population (and the reference dataset) is skewed towards the Hyogo prefecture and Itozakura bloodlines.

Q. What impact does the CWT have on the AWA pedigree registrations of Herdbook animals with less than 100% CWT Content?

None.

The strict DNA parent verification for the Australian Wagyu Fullblood and Purebred registered animals will ensure ongoing Herdbook accuracy. As discussed, genetic variation with registered Australian Fullblood Black Wagyu has been identified as based on differing prefectural herd ancestries. Pedigrees alone continue to define Fullblood status in the AWA Fullblood Wagyu Herdbook.

Q. Are registered Fullblood animals with higher CWT scores “better” than those with lower scores?

No. The lower score Fullblood animals are critically important because they are different. When compared to other beef breeds, the Australian Wagyu population is very closely related. A lower CWT score is an indication that the Fullblood animal is genomically different from the majority of Black Wagyu animals used in the reference dataset. Those registered Fullblood animals with ‘different’ CWT scores are extremely valuable to the Black Australian Wagyu population because they offer the mainstream registered herd the opportunity to extend genetic diversity, enhance selection flexibility and counter inbreeding.

Q. Will CWT- assessed Content Register animals be able to transfer to other AWA registries, such as breeding up grades within the Purebred grade?

Not at this stage. However, given that many are likely to show content considerably over the current <50% Base grade, AWA is examining methods for enabling such transitions.

No. Employers can continue salary for Wagyu Fellows while they are on their Fellowship or if you are a student this Fellowship is considered an ongoing part of your studies.

Q. Will the CWT be useful in differentiating non-pedigree, commercial Fullblood slaughter cattle from registered Purebreds or similarly high content crossbred cattle?

Due to constraints discussed previously, the CWT will not accurately identify the Fullbloods within such a group. Where Fullblood Black Wagyu content requires formal Herdbook level of verification, a full DNA parent verification process would remain necessary from an AWA perspective, meaning the animal will have full ancestral and individual breeder traceability. However, individual processors have well-established QA mechanisms in the Fullblood area, which is an established slaughter market segment. AWA believes this segment will continue to grow as high-end consumers demand ever-greater supply chain transparency.

Q. Does AWA expect the CWT will be used in support of litigation in disputes over the Wagyu content of either livestock or retail/food service beef?

Definitely NO. ‘100% certainty’ of a sample’s relationship to a specified Wagyu category (Fullblood, Purebred or other crossbred) is not a deliverable. The CWT cannot be used as a foundation for litigation on the basis of percentage Wagyu Content. The variation in the results and known genetic variation within the Black Wagyu breed means the use of the CWT should be limited to quality assurance programs.

Q. How does the CWT apply to Fullblood red and Fullblood composite (black X red) cattle?

The reference dataset used to develop the CWT contains very few red Wagyu animals. The CWT should not be used to test red Wagyu animals.

Q. What about breeds not represented in the reference dataset?

The CWT isn’t able to calculate accurately the breed percentage of breeds not represented in the reference dataset. Breeds like Brown Swiss, Ayrshire, and Devon don’t have genotypes in the reference dataset but contributed genes to the development of Wagyu in Japan.

Q. Why do we use an Australian and not a Japanese breed content benchmark?

The Japanese Black (Black Wagyu) is a genetically diverse, international breed derived from numerous ancient prefectural herds in Japan with (historically) several breeds contributing to its genetic makeup. The Australian herd does not currently include the full range of Japanese prefectural bloodlines and it is unlikely we will get access to sufficient genetic material to represent the Japanese genetic makeup accurately. The Australian Fullblood herd is a closed sub-population consisting of a subset of the overall Japanese Black genome. Using a test developed using Australian Fullblood sub-population genotypes is the best method for accurately benchmarking the local population.

Q. Does Japan have a similar Wagyu Content Test?

We are not aware of the existence of a similar test in Japan. The Japanese Wagyu industry and JMGA grading system includes a strict ‘whole of life’ separation of Fullblood and crossbred or ‘infused cattle’. There is also no ‘purebred’ category, so the issue of ‘percentage content’ does not arise. At the Fullblood Black level, Japan has unique traceability systems starting at calf birth recording and culminating in government level maintenance of national carcass databases. However, there is no DNA parent verification in Japanese registration. Mechanisms like Japan’s are unavailable in Australia, but we believe with our strict DNA parent verification for Herdbook registered animals, and with the addition of the CWT to our Quality Assurance (QA) toolkit, Australian Wagyu production offers very high levels of QA.