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BBR DNA Tests for Cattle Breeds
white paper report

Breed Base Representation (BBR) is a DNA test to establish relative genetic purity of an animal. "Since the 1800s, breed registries have been established for livestock species to maintain the purity of breeds and to document the ancestry of animals. However, a significant number of animals are unregistered with no or incomplete pedigree data and uncertain ancestral breed origin. Although many heritage livestock breeds are “at risk” on the basis of the number of fullblood breeding females in a breed registry, there is often also a reservoir of unregistered animals that may belong to the same breed. However, due to the missing pedigree it is not possible for breed societies or herd books to include those animals in their closed herd books for pure animals." In 2018 a genetic SNP test was developed to unequivocally determine the breed origin of cattle without pedigree data. This test opens up the possibility to incorporate animals without pedigree data in the breed registry that turn out to be purebred based on the test results. ~ BBR test developers in the Netherlands

Purebred Dairy Cattle Association
Purebred Dairy Cattle Association, member, CDCB

BBR Dairy DNA test. There is currently a BBR test available for 5 dairy breeds; Ayrshire (AY), Brown Swiss (BS), Guernsey (GU), Holstein (HO) and Jersey (JE). The Council of Dairy Cattle Breeding (CDCB) owns these proprietary BBR tests. They had them developed to assess the degree to which alleles in one individual dairy animal's genome are in common with the allele frequency of any of the 5 reference breed groups. CDCB made the decision that animals with a BBR score of greater than or equal to 94 for 1 of the 5 testing dairy breeds are considered to have one-breed background and will be categorized as 100% for that breed, and other possible breed percentages will be set to zero. BBRs below 94 are reported at the % calculated. Precise percentages of breed sources are not possible because of genetic variations that exist within the same breed. And although there are common alleles within breeds, there are also common alleles across breeds. The genetic contribution from a primary breed could be off by 5% or even more. If any breeds other than those 5 are part of the animalís ancestry then the BBR crossbred test will not be accurate. A BBR score of lower than 90 however, usually indicates crossbreeding. (~ CDCB tools for the improvement of the Jersey breed, 06-2018, worldjerseycattle.com.) The CDCB BBR DNA test is available to the public, at the time of this report, costing owners approximately $25 /cow, $135 /young bull, or close to $1600 /bull over 14 mos.




More about the CDCB BBR test:
There is evidence that BBR DNA testing results are impacted by the chip used for genotyping. Animals with alleles coming from other breeds (e.g., BBR of the primary breed around 87%) often receive a BBR about 4% higher if re-genotyped using a higher density chip. However if the BBR is above 97% for the primary breed (common for pure animals) there is no consistent change when re-genotyped with a higher density chip. ~ (Documenting changes in dairy breeds in the United States including genomic examination using breed base representation, 2018; H.D. Norman, J.M. Megonigal, G.R. Wiggans, and João Dürr) ~ ICAR

The CDCB BBR test uses 2 approaches, one for purebreds and one for crossbred dairy cattle. The BBR test for a single breed is used on animals that are identified by a breed SNP-based check. The BBR test approach for crossbreeds is designed to determine the % of DNA contributed to the animal by each of the 5 breeds, in order to provide more accurate genomic production evaluation of crossbred dairy animals. If a crossbred animal carries genetics from a breed other than the primary 5 dairy breeds, the results may not be reliable. In April 2019, an updated BBR procedure was developed to lend more accuracy in determining the composition of the 5 dairy breed makeup of crossbreeds. (~CDCB BBRs & Crossbred Dairy Cattle).


BBR scores: presentation & distribution


The Accuracy of a BBR Test: We get lots of inquiries about the BBR test, that usually boil down to these questions:

Q: Does a BBR test prove my animal is pure?
The short answer is, while a BBR test establishes relative purity, it can not absolutely prove an animal is 100% pure. But if a BBR shows a high enough score for the breed being tested, it provides genetic corroboration for an animal with evidence of purity. Other indications that an animal is pure may include:

  1. the animal has an extended pedigree tracing all the way back to the breed's foundation (herdbooks began forming in UK in the early 1800s)
  2. the animal displays a phenotype consistent with the history of its breed (irregardless of selection)
  3. the animal DNA tests with a genotype consistent with the history of its breed (irregardless of selection)
  4. the animal DNA tests with no genotypic traits inconsistent with its history, and known to originate in other breeds

Q: Can I BBR test my cow to find out what breed(s) she is?
The short answer is yes and no.
Yes, if she is a purebred or a crossbred of the 5 primary dairy breeds, and does not carry additional genetics of other breeds, and is tested with the CDCB BBR dairy breed test.
No, not if she is tested with a BBR test formulated for breed(s) other than what she is. A BBR test formulated for one breed does not work for another breed. Each breed needs its own BBR test to determine the percentage of that breed's DNA in an animal. If an animal had an unknown pedigree, we could only guess which BBR test(s) to use. As we know, the proprietary CDCB BBR test is formulated for 5 major dairy breeds only. All other breeds of cattle will have to formulate a BBR test of their own.

Q: When formulating a BBR test, how are animals selected to represent a breed?
The short answer is, for any existing BBR test we would not know unless we were involved. But when planning a new BBR test for a breed, we know how they should be selected:

  1. People entrusted to select a breed base reference population must be experienced with the breed and sufficiently knowledgeable about genetics.
  2. People entrusted to select a breed base reference population must be completely objective and free of prejudice or personal agenda regarding purity.
  3. Animals selected to represent a breed must be reasonably believed to be 100% pure, with genotype & phenotype consistent with the breed's history.
  4. Animals selected to represent a breed should have extended pedigrees indicating stacked generations of purity as far back as the breed has been recorded.
  5. Animals selected to represent a breed should be taken from as many diverse populations of pure animals that can be found across the globe.
  6. Animals selected to represent a breed base reference population should total in the highest number possible. The more animals used, the more accurate a BBR test should be.

BBR DNA tests made for more breeds of cattle will certainly be developed. There is another one or two that have been developed or are in development for rare heritage breeds. Rare breeds would benefit with added genetic diversity, if found among additional pure (unregistered) cattle identified and included for preservation. There are also mainstream breeds that are no longer believed to be pure, with purity issues debated about animals registered as fullbloods in their main herdbooks. BBR presents a solution to will help protect old pure lines or rare breeds of cattle. However developing the initial BBR test for a breed, could be a major undertaking.


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(more of the research I gathered)

Breed registries usually offer:
SNP panel (SeekSire for example), parentage included
STR panel for parentage, old technology but can be used to verify older parents

That said...

Breed Identification for Purity, etc...

It is expensive, prohibitely so, to do this kind of DNA research in depth, at this time, when searching for as many markers as possible in a breed or population.

Identification of breed-specific SNP panel in nine different cattle genomes. .. [Biomedical Research (2019) Volume 30, Issue 1]. Single nucleotide polymorphism (SNP) high-density chips are now serving as important bioinformatics tools for improvement and development of various livestock species. Major constraint being the high cost of protocol which is not feasible at the population level. Hence, in the present study, we have tried to reduce the SNP panel to a fewer number of informative markers which will be very much cost-effective. Single nucleotide polymorphism (SNP) high-density chips are now serving as important bioinformatics tools for improvement and development of various livestock species. Major constraint being the high cost of protocol which is not feasible at the population level. Hence, in the present study, we have tried to reduce the SNP panel to a fewer number of informative markers which will be very much cost-effective.

It is still in development:... (and how accurate (how PURE) is the choice of the reference animals chosen for the reference population, in YOUR breed?)... Who chooses them?

Assessing SNP markers for assigning individuals to cattlepopulations
SummaryThe effectiveness of single nucleotide polymorphisms (SNPs) for the assignment of cattle totheir source breeds was investigated by analysing a panel of 90 SNPs assayed on 24 European breeds. Breed assignment was performed by comparing the Bayesian and frequentist methods implemented in the STRUCTURE 2.2 and GENECLASS 2 software programs. The useof SNPs for the reallocation of known individuals to their breeds of origin and the assignment of unknown individuals was tested. In the reallocation tests, the methods implemented in STRUCTURE 2.2 performed better than those in GENECLASS 2, with 96% vs. 85% correct assignments respectively. In contrast, the methods implemented in GENECLASS 2 showed a greater correct assignment rate in allocating animals treated as unknowns to a reference data set (62% vs. 51% and 80% vs. 65% in field tests 1 and 2 respectively). These results demonstrate that SNPs are suitable for the assignment of individuals to reference breeds.The results also indicate that STRUCTURE 2.2 and GENECLASS 2 can be complementary tools to assess breed integrity and assignment. Our findings also stress the importance of a high-quality reference dataset in allocation studies.

The older way...
Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd.
During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent years single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E-42, respectively. Generally 2–3 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ~ 10-11). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording).
Genetics & Molecular Biology; Genet Mol Biol. 2013 Jul; 36(2): 185–191., Published online 2013 Jun 22. doi: 10.1590/S1415-47572013000200008


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BBR Estimation of genomic breed composition of individual animals in composite beef cattle -- Three statistical models (an admixture model, linear regression, and ridge-regression BLUP) and two strategies for selecting SNP panels (uniformly spaced vs. maximum Euclidean distance of SNP allele frequencies between ancestral breeds) were compared for estimating genomic-estimated breed composition (GBC) in Brangus and Santa Gertrudis cattle, respectively. Animals were genotyped with a GeneSeek Genomic Profiler bovine low-density version 4 SNP chip. by: Z Li, X-L Wu, W Guo, J He, H Li, G J M Rosa, D Gianola, R G Tait, J Parham, J Genho, T Schultz, S Bauck. Animal Genetics 2020 April 2.

Development of a genetic tool for determining breed purity of cattle: BBR Original Research Paper. Genotype data (50k SNP array) were used to compose reference populations for six local Dutch cattle breeds. Such a test will open up the possibility to incorporate animals without pedigree data in the breed registry that turn out to be purebred based on the test results. In this study we developed and validated such a test. Received 18 October 2018, Revised 28 January 2019, Accepted 06 March 2019, Available online 08 March 2019, Livestock Science Volume 223, May 2019, Pages 60-67sciencedirect.com/science/article/pii/S1871141318305341

The Global Standard for Livestock Data on dairy crossbreeding & BBR: Documenting changes in dairy breeds in the United States including genomic examination using breed base representation; ICAR: 2018, H.D. Norman, J.M. Megonigal, G.R. Wiggans, and João Dürr

A test to include unregistered rare Dutch cattle in the herd book: In December 2018 the Centre for Genetic Resources the Netherlands (CGN) and the Dutch Rare Breed Survival Trust (SZH) introduced a DNA test to help identify rare Dutch breeds of cattle to help preserve the breed.

Council on Dairy Cattle Breeding (CDCB) Council on Dairy Cattle Breeding, One Town Center, 4201 Northview Drive, Suite 302, Bowie, MD 20716 USA. CDCB provides dairy genetic information services through industry collaboration centered around a mission to help optimize cow health and productivity in herds worldwide. This non-profit organization is responsible for calculating and distributing the genetic evaluations and genomic predictions, for managing the national cooperator database, and for analyzing and distributing dairy cattle data in the United States. The CDCB drives continuous improvement and maintains the integrity of the world’s largest animal database, building on a quality foundation with more than eight decades of recorded U.S. dairy animal performance. The CDCB is a collaboration between four sectors of the U.S. dairy industry: Dairy Records Providers (DRP), Dairy Records Processing Centers (DRPC), National Association of Animal Breeders (NAAB) and Purebred Dairy Cattle Association (PDCA).

US to be the first country to genotype cross-bred animals, by Emma Gilsenan, Apr 15, 2019, Agriland, Ireland's largest farming news portal

Genetics research verifies purity of the Mexican Wolf, by Stacy Pigott, University of Arizona June 21, 2018. Are the genetics pure, or had the Mexican wolf, on its path to near-extinction, cross-bred with domestic dogs? Using Genome-Wide Analysis of SNPs allows researchers to use genomic data from one species, such as domestic dogs, to study a similar species, such as Mexican wolves. This study confirmed the genetic purity of the Mexican wolf, information that is important to conservation efforts.

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