Match-A-Yak: a tool to minimize inbreeding in North American Yaks
Jeff Lehmkuhler, Darrh Bullock, Mary McCarty, Les Anderson
The domesticated yak (Bos grunniens) arrived in North America in the late 1890’s. A few animals were imported into Canada and North American zoos which became the foundation of the North American genetic pool. Research was conducted in Alaska hybridizing them with Highland cattle in the early 1900’s. A very limited number of yaks were imported into the United States in the early 1900’s and again later in the 1980’s. However, the genetic diversity of the North American yak is limited necessitating a need to manage breeding programs to reduce inbreeding.
Figure 1. First yak at the National Zoo in the United States. Reported to be taken December 23, 1898 with the bull dying January 14, 1912. Source: posted on Yak History Channel Facebook from William Bartels of New York City.
Organized breeding associations of Bos grunniens recognized the importance of maintaining genetic diversity. Most of the yak associations now require DNA testing for registration of animals which reveals the degree of cattle introgression as well as the genetic coefficient of inbreeding (COI) based on the estimated degree of heterozygosity. This information, along with pedigree, can assist in reducing .
The next step to assist in conserving genetic diversity was the development of an online software tool which is available to members of the US Yaks association (USYAKS). The program is called Match-A-Yak. Users enter a proposed mating between a sire and dam. The software then calculates an average COI and the number of heterozygous SNPs for the progeny. These results are based on a subset of single nucleotide polymorphisms (SNPs) currently being reported for the animals registered in USYAKS.
Using the software, a breeder seeking to replace a bull for mating with their current herd of females can run each female and potential replacement bull to identify the bull that would provide the greatest degree of heterozygosity in the SNPs monitored. In this situation, heterozygosity refers to SNPs having differing alleles (ie. G/C, A/T, G/T, etc.) while having the same alleles (ie. A/A, G/G, T/T, C/C) at the SNP is referred to as homozygous. An example report for an individual yak SNP profile and calculated COI is shown in Figure 2. As inbreeding increases, heterozygosity will decrease and homozygosity will increase at these SNPs. A scenario using cows representing a small herd was modeled using different bulls. The outcome of these matings with the estimated COI and number of heterozygous SNPs of the progeny are shown in Table 1.
Figure 2. Example of the single nucleotide polymorphism (SNP) profile reported for a yak registered in with United States Yaks association.
Running the model for the five bulls in this group of females, Duke would be estimated to yield the fewest homozygotes of the SNPs and lowest COI an average. However, the amount of heterozygosity in individual matings varies across the herd, as would be expected. Some individuals mated to the overall “best” bull are likely to have similar alleles for several of the SNPs reported and may have less heterozygosity than if they were mated to a different bull. In this scenario, Audry mated to Duke is estimated to yield progeny with greater homozygosity than if she were mated to any of the other bulls. Looking at the pedigrees for these two individuals, a common ancestor SBR Dreadlock is found. Further investigating the estimated number of heterozygous SNPs, the mating of Dr. Who and Smash is observed to yield the fewest heterozygous SNPs and highest COI at 0.301. Again, investigating the pedigrees, these two are half-siblings sharing the same dam.
Table 1. Results of Match A Yak for five different bulls mated to 14 female yaks and the resulting estimated Coefficient of Inbreeding and the number of heterozygous SNP’s. Scaled color coding for ease of viewing where green results in the greatest and red is the fewest heterozygous SNPs within each mating.
To use the Match A Yak tool, one must be a registered member of USYAKS. After logging in with one’s username and password, scrolling under “Membership” and hovering over “Membership Benefits” the “Match A Yak” tool becomes accessible.
Clicking on Match a Yak, takes one to the tool landing page. On this page, one can enter the registration number of the sire and dam registered in USYAKS to obtain estimated COI and number of heterogeneous SNPs. Each mating must be conducted for each animal of interest. If the DNA information has not been added to the registry database, the computation cannot be performed.
Once the sire and dam numbers are entered, click the “Run Match” button. The predicted heterozygous SNPs or “hetsites” are shown. The Number of useable sites refers to the number of SNPs that were used in the analysis as some animals may not have the full 95 SNPs reported. The Expected Heterozygote proportion is a constant based on animals assessed when the initial DNA tests were assembled. A coefficient of inbreeding (COI) is calculated. In theory, COI ranges between -1.0 and +1.0 where 0 is the average level of inbreeding. The actual observed COI lies between -0.45 and +0.45. The more positive the calculated COI, the greater the degree of inbreeding while a more negative number would indicate less inbreeding than the average. The estimated number of cattle alleles are also calculated for the progeny.
The alleles passed on are random and the software generates a bell-shaped curve. This provides a degree of confidence for the actual number of hetsites and COI of the mating.
Yak breeders are increasing their ability to make improved breeding decisions with increased registration of animals. Having access to tools such as Match a Yak has the potential to reduce the level of homozygosity and aid in managing the genetic diversity of the narrow gene pool of the North American yak population.
In an effort to maintain genetic diversity and limit inbreeding, the Match A Yak tool can assist breeders in making mating decisions to reduce the degree of homozygosity. Granted, the number of SNPs currently being monitored is limited. Even with the few SNPs reported, the tool can still be used to quickly determine an estimated COI outcome. As new bulls are sought to be introduced to herds, the Match A Yak program is another tool in the toolbox to assist in selection decisions to increase genetic diversity, or at least minimize homozygosity.
Acknowledgement
The authors wish to thank Mr. Gregor Dike of Shi-bah Shing-ga Yaks for permitting us to use the females in the simulations run in the Match A Yak program.