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Reading Your IYAK Genetic Registration Report

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)!  

 
 
 

 
 

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.” 

 
 

 
 

Parental Verification

Parental Verification:

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

This sentence is based on a count of the genetic markers (ie. Single Nucleotide Polymorphisms or “SNiPs”) that match the parents. If there are 95% of the SNPs in common, the parents are considered to be a match.

Example of Failure of Verification: If the percentage of markers in common with the parent are less than 95% will result in a “Fail.” You may have verification for one and failure for the other. In these cases the animal must be resubmitted to be tested against a different Sire and/or Dam.

Lack of Pedigree Information: If no prospective parents were submitted or they are not in the database, the results will read: “No pedigree information provided for any Sire to test for parentage. No pedigree information provided for any Dam to test for parentage.”

 
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Genotypic Species Indicated

Reported Species Indicators

Bos mutus grunniens Yak with 3 or fewer cattle alleles are considered IYAK foundation.  

Introgression Indicated Hybrids with between 4 and 10 cattle alleles, the animal is flagged for suspected cattle introgression

Bovinae Undetermined Bovinae Family confirmed. Species determination can not be made on hybrids with cattle allele counts from 11 TO 142.

Bos taurus hybrid 142 -166 indicates the animals is over 75% Bos taurus

Bos primigenius taurus Cattle with greater than 166 alleles (greater than 87.5% less than 12.5% yak) meet threshold for species determination (USDA, 2018).

 
 

 
 

Bovine Introgression

Cattle Alleles and Results Interpretation

1-3 cattle alleles

The IYAK average for the herd based current data is fewer than 1 cattle alleles, or less than 1%. This means that the majority of yak will have no cattle introgression, a few will have 1 cattle allele, and a small minority will have 2-3 alleles. 

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 evidence and pedigree history (see Bovine Genetic Mutations). 

5-10 cattle alleles

Animals with greater than 4 alleles do not meet requirements for registration. If it is believed that the “Hybrid” determination was made in error, owners of animals with between 5-10 cattle alleles may request a Review of the genetic report and pedigree history by the IYAK RegCom.

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

 
 
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Coefficient of Inbreeding (COI)

COI stands for Coefficient of Inbreeding. Essentially, it measures the common ancestors of dam and sire, and indicates the probability of how genetically similar they are. While many bovine breeds are extremely inbred due to Artificial Insemination, IYAK is not. The goal of COI reporting is to continue to transmission of desirable yak traits in the IYAK, while minimizing the transmission of undesirable consequences of Inbreeding Depression.

YAK LESS INBRED THAN TIBETAN YAKS (Hendrick, P., 2009, Qiu, Q, 2015)

North American Bison: 36% 

International Yak Association (iYAK): 3.3% 

Qinghai Tibetan Plateau (QTP): 4.4%

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).

Holsteins 26% and for Ayrshires 47% 

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).

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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Bovine Genetic Disease Mutations

All Bovine Disease and Trait Mutants are 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 those who are concerned about preserving the genetic base of the wild species, has become a major concern. Hybridization is also a concern to the breeders of purebred species as well, particularly if the gene pool is small and if such crossbreeding or hybridization threatens the genetic base of the domesticated purebred population.

The concern with genetic pollution of a wild population is that hybridized animals and plants may not be as genetically strong as naturally evolved region specific wild ancestors wildlife which can survive without human husbandry and have high immunity to natural diseases. The concern of purebred breeders with wildlife hybridizing a domesticated species is that it can coarsen or degrade the specific qualities of a breed developed for a specific purpose, sometimes over many generations. Thus, both purebred breeders and wildlife biologists share a common interest in preventing accidental hybridization.

Mutation Bovine Disease StatuS

ATP6 Neuropathy, Ataxia gene carrier

BVDV Bovine viral diarrhea virus not a gene carrier

*PRNP Prion (Madcow) not a gene carrier

* Due to the severity of Prion disease, this is exclusionary for registration. No yak in the NAYR currently carries the PRNP gene. If a yak is identified as a carrier they will be flagged, they are not eligible for admission to the breed book and should not be bred. 

 
 

 
 

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

 
 

 
 

Wild Type Genetic Traits

ALlele WILD-TYPE Trait Status

FGF5 Fiber type allele carrier


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.