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Reading Your IYAK Genetic Registration Report

IYAK Genetic Pedigree Analysis: Codes and Interpretation 

The International Yak Association (IYAK) is genetically impressive! Our registered animals are out-performing the Tibetan domestic and wild-type yak on several genetic and phenotypic fronts. Its a very special population in the world. IYAK is a truly unique and valuable herd. UINC estimates indicate Tibetan wild yak are "Vulnerable" and dropping 2% per year (2014), and new counts suggest wild yak are already endangered. IYAK may soon be the last strong hold of the original, ancient and pure genetics (if we continue to protect it)!  

 
 
 

 
 

GeneSeek Sample Status: Call Sample Rate

Pass: “Pass” means the sample quality was sufficient to report reliable test results.

Fail: A “Fail” indicates that the sample quality was poor and retesting with a new sample is required to obtain reliable test results.

Call Count for 95 SNPs: This number is a count of the genetic markers successfully tested (ie. Single Nucleotide Polymorphisms or “SNiPs”). The threshold to “Pass” is a minimum of 90 out of 95 SNPs (95%). 

Sample Status (threshold 0.95): This reports the percentage of markers in this sample successfully tested. Less than 95% (90 of 95 SNPs) will result in a “Fail.” 

 
 

 
 

IYAK Parental Verification

DAM AND SIRE PARENTAL MATCHING AND RESULTS INTERPRETATION

Verification (>.95): This sentence is based on a count of the genetic markers (ie. Single Nucleotide Polymorphisms or “SNiPs”) that match the parents. If the offspring has 95% of the SNPs in common with the proposed parents, it considered to be a match.

Example: “LDR Brandyberry SO61 qualifies as an offspring of LDR Appleberry P012 and FW Jette P021.”

Probability Match (.901 - .949): A sample falling below threshold is reported as a probability match and may be referred to RegComm for a review. 

Example: “LDR Brandyberry SO61 is a 93% match to parents of LDR Appleberry Twist and FW Jette P021. 

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Example of Failure of Verification (<.90): If the percentage of markers in common with the parent are less than 90% this test will result in a “Fail.” In this case, alternate dam and sire options may be submitted for retesting.

Example: “LDR Brandyberry SO61 is not a match to parents of LDR Appleberry P012 and FW Jette P021.”

Lack of Pedigree Information: If no prospective parents were submitted, they are unknown, or they are not linked to registered yak in the database this will be reflected on the report.

Example: “No pedigree information provided for Sire or Dam to test for parentage.” 

Whole-Herd Comparison and Additional Testing: In these cases where parentage is unknown, IYAK has several additional tests available to seek out the correct parent. Including Multiple Matches and Full-herd Comparison. Please contact our Registrar or search “Tests of Parentage” at www.iyak.org for details and pricing. 

 
 
 

 
 

IYAK Genotypic Species Indicated

Reported Species Indicators

Bos mutus grunniens Yak with 3 or fewer cattle alleles are eligible for IYAK foundation registration.  

Introgression Indicated Animals with between 4 and 10 cattle alleles are flagged for suspected cattle introgression.

Bovinae Undetermined Bovinae Family confirmed, species determination can’t be made with ambiguous cattle allele counts (11- 142).

Bos taurus hybrid Alleles indicate the animals is at or above 75% Bos taurus (142 -166).

Bos taurus Greater than 166 cattle alleles (less than 12.5% yak) meets threshold for species determination (USDA, 2018).

 
 

 
 

IYAK BOVINE INTROGRESSION

CATTLE ALLELES AND RESULTS INTERPRETATION

1-3 cattle alleles

The IYAK average for the foundation herd based on current data is a mean of fewer than 1 cattle alleles out of 180, or less than 1% introgression. This means that the majority of yak in our registry will have no statistically significant cattle introgression (p=.01), a few will have 1% cattle alleles, and a small minority will have 3 or more alleles (1.5%). 

4 cattle alleles

Animals with 4 cattle alleles are flagged. This animal is at threshold for Cattle Introgression and undergoes review for consideration of additional genetic and phenotypic evidence, as well as pedigree history. 

5-10 cattle alleles

Animals with greater than 5 alleles that do not meet requirements for registration and are sent to RegComm for review. If RegComm does not upgrade this yak, and it is believed that a hybrid determination was made in error, owners of animals with between 5-10 cattle alleles may request further review by IYAK RegComm. For example, it is possible that a cow and sire, each with 4 alleles produce a calf with 8. In these cases, it may be helpful for IYAK to review pedigree history and additional information to evaluate introgression.

* Animals may also be flagged for a variety of reasons other than the number of Cattle Alleles (ie. ownership by professed Intentional Hybridizers, phenotypic/trait characteristics, alleles indicating recent introgression, multiple alternate Bovine genetic mutations, etc.)

 
 
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IYAK Coefficient of Inbreeding (COI)

COEFFICIENT OF INBREEDING  (COI)

COI stands for Coefficient of Inbreeding. Essentially, it measures the common ancestors of a dam and sire, and indicates the probability of how genetically similar they are. While many bovine breeds are extremely inbred due to Artificial Insemination, the IYAK herd is not. The goal of COI reporting is to continue to our quality breeding practices and mitigate inbreeding. 

Breeding Programs / Line Breeding: IYAK breeders can continue to facilitate and improve the transmission of desirable yak traits, while minimizing the transmission of undesirable consequence

What is Line Breeding? Breeding Programs are Linebreeding, and this is an attempt to increase outstanding ancestral traits and decrease and/or minimize inbreeding.

Linebreeding a Conservation Effort: Done properly, linebreeding can preserve the genotype and phenotype of an exceptional, wild-type ancestor. It’s really the only way to preserve ancestral genetic heritabilit

Who should Attempt a Breeding Program? Linebreeding should only be used by foundation, seedstock breeders who have the genetic resources, as well as a clear understanding of its purpose. It should be used only in herds that are superior, and only those bulls that are clearly outstanding should be the object of a linebreeding program. Mating of close relatives, such as brothers with sisters or parents with offspring, should be avoided. Pedigree lines and COI should be continually monitored and evaluated, substandard calves should be rigorously culled.

Match A Yak: Genomic help is available through IYAK.

IYAK IS LESS INBRED THAN MOST BRED ANIMALS 

A few lines of beef cattle and swine that have undergone intense inbreeding for 40 to 50 years have average inbreeding coefficients of .5 to .6 (50-60%). This is accomplished by many generations of brother-sister or parent-offspring matings; therefore, an inbreeding coefficient over .5 is unlikely in a seedstock herd of beef cattle. The Line 1 Hereford cattle developed at the Montana research station would be an example of an inbred line of cattle (David S. Buchanan Oklahoma State).

Holsteins: 26%

Ayrshires: 47% 

North American Bison: 36% 

IYAK IS LESS INBRED THAN BOTH DOMESTIC AND WILD TIBETAN YAKS 

International Yak Association (2015) foundation yak (n=200): 5.3% 

International Yak Association (2018) IYAK registered animals (n=365): 1.3%

Wild-type yak in  the Himalayas (2017): 1.7%

Qinghai Tibetan Plateau (QTP) domestic yak: 4.4%

(Hendrick, P., 2009, Qiu, Q, 2015)

Average inbreeding coefficient levels of less than 5% within a breeding program are considered low, with inbreeding levels of 5 – 10% generally considered more moderate levels of inbreeding and warranting more careful management (Burrow, H.M, (1993).

In most beef cattle breed societies, the vast majority of animals have an inbreeding coefficient of less than 10%, inbreeding coefficients over 30% are unusual.

In a comparison with COI in other breeds, 5 - 6.5% is the commonly accepted ideal COI for transmission of good traits without deleterious effects. The UK Kennel Club breed target COI is 6.5%, with a much higher average in many breeds (9.6% in registered Yorkies). It’s common for purebred cats to have COIs of 30%. Thoroughbreds are usually less than 5%, which is 4-5 generations between parents or the equivalent of first cousins. This is considered the ideal threshold to avoid Inbreeding Depression as recommended by the USDA, EU, and various breed associations worldwide.

The IYAK Population has a COI of the 5th Degree (.033 - .056). The average COI for the IYAK herd is 3.3%. The data from the IYAK population tested, demonstrates there is currently no “bottleneck” and currently no known clustering of inbreeding at a given ranch. It is a testament to the line-breeding practices of IYAK. These yakers have been skilled and diligent. It is important to continue successful line-breeding practices, which will allow a healthy and diverse IYAK population for many decades to come (see Successful Line-Breeding in Yak).

 
 
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IYAK Bovine Genetic Disease Mutations

Bovine Disease and Trait Mutants are often the result of cattle hybridization and increase the likelihood of hybrid variants. These additional markers will be used in conjunction with the markers for Cattle Introgression when hybridization is in question. This type of cross-species breeding, termed genetic pollution by some Conservation Biologists and activists, is a concern to those committed to preserving the genetic base of the wild-type species. Hybridization is also a concern to the breeders attempting to preserve a rare genome, particularly if the gene pool is small and if such crossbreeding or hybridization threatens the genetic base of the domesticated population.

The concern with the genetic integrity of a wild population is that hybridized animals or plants may not be as genetically strong as naturally evolved, region specific, wild ancestors, which may be better able to survive without human husbandry and may have higher immunity to natural diseases. The concern with hybridizing of domesticated species is that the process can degrade the specific wild-type qualities of a breed developed for a specific purpose. Thus, both foundation breeders and conservation biologists share a common interest in preventing accidental and/or intentional hybridization.

Mutation Bovine Disease StatuS

BVDV Bovine viral diarrhea virus not a gene carrier

PRNP Prion (Madcow) not a gene carrier

* These results should be taken as preliminary findings only, should be evaluated as informational, and are subject to change with additional data as we expand our dataset over time. Peer review publication and independent replication of findings will be necessary to scientifically verify these results. For example, PRNP has been scientifically verified in cattle. This is a subject for continued research, due to the severity of Prion disease and potential in cattle hybrids, this may become exclusionary for registration. No yak in the NAYR currently carries the PRNP gene, however if a yak is identified as a carrier they will be flagged, and there will be further consideration by RegComm, under recommendations from our research collaborators. 

 
 

 
 

IYAK Bovine Genetic Trait Mutations

Mutation Bovine Trait Status

KIT Colored points (spotted) not a gene carrier

Pmel 1 Pigmentation (coat color) not a gene carrier

SILV(MC1R) Silver (coat color) not a gene carrier

Pmel 2 Dilution (coat color) not a gene carrier

* These results should be taken as preliminary findings only, should be evaluated as informational, and are subject to change with additional data as we expand our dataset over time. Peer review publication and independent replication of findings will be necessary to scientifically verify these results.

 
 

 
 

IYAK Wild Type Genetic Traits

ALlele WILD-TYPE Trait Status

FGF5 Fiber type allele carrier

* These results should be taken as preliminary findings only, should be evaluated as informational, and are subject to change with additional data as we expand our dataset over time. Peer review publication and independent replication of findings will be necessary to scientifically verify these results.


Thanks to the hard work of the IYAK Genome Committee, the IYAK BOD, GeneSeek and the USDA for their hard work in developing this testing.

 

Nicole Porter-Salvato, PhD is one of the owners of Prairie Sky Sanctuary and Ranch, a horse and Tibetan yak ranch in South Western Wisconsin. She’s trained in epigenetics and epidemiology, an avid IYAK supporter, BOD member and yak lover. She and her husband, Dan, love to talk about yak and are always available to answer questions or provide resources.