Using triallelic SNPs for determining parentage in North American yak (Bos grunniens) and estimating cattle (B. taurus) introgression

Authors: KALBFLEISCH, TED - University Of Kentucky; PETERSEN, JESSICA - University Of Nebraska; TAIT, RICHARD - Geneseek Inc, A Neogen Company; QIU, JIANSHENG - Geneseek Inc, A Neogen Company; BASNAYAKE, VERONICA - Geneseek Inc, A Neogen Company; HACKETT, PETER - Usyaks; Heaton, Michael - Mike

Submitted to: F1000Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/4/2020
Publication Date: 9/4/2020
Citation: Kalbfleisch, T., Petersen, J.L., Tait, R.G., Qiu, J., Basnayake, V., Hackett, P.H., Heaton, M.P. 2020. Using triallelic SNPs for determining parentage in North American yak (Bos grunniens) and estimating cattle (B. taurus) introgression. F1000Research. 9:1096. https://doi.org/10.12688/f1000research.25803.1.
DOI: https://doi.org/10.12688/f1000research.25803.1

Interpretive Summary: Yaks are valued around the world for meat, fiber, milk, fuel, transportation, predator protection, and as pets. Although originally from the Qinghai-Tibet Plateau, a few zoological park records suggest that maybe a dozen or two yaks were imported from Europe around the turn of the 20th century for display in North America (NA). Surplus yaks from successful breedings were eventually sold to ranches and the NA yak herd expanded to its current size, estimated to be between 2000 and 5000 animals. Strict federal regulations on the importation of live yak, embryos, and semen to NA have prevented the introduction of new bloodlines that would increase genetic diversity. This has created a critical need to preserve the existing genetic diversity in NA yaks through careful breeding. In addition, yaks may hybridize with beef cattle, further accelerating the loss of NA yak germplasm. New platforms for high resolution genetic testing can verify the accuracy of pedigrees and thereby help manage genetic diversity among registered animals. DNA testing can also detect the unwanted introduction of beef cattle germplasm in NA yaks. This report describes the development of a specialized set of triallelic yak markers (tySNPs) for determining yak parentage and cattle introgression. A key feature of these genetic markers is their dual purpose which reduces the total number of markers needed to do both jobs. This in turn can reduce the total cost. These markers can facilitate more precise genetic management of NA yak and may be useful for livestock species whose breeders do not currently have access to higher-density genome-wide SNPs and other high-throughput genotyping technologies. In principle, a similar triallelic SNP approach could be used with other bottlenecked species that hybridize with cattle, such as North American plains bison.

Technical Abstract: Background: Genetic testing for pedigree accuracy is critical for managing genetic diversity in North American (NA) yak (Bos grunniens), a population expanded mostly from imported zoological park specimens. DNA testing also enhances species conservation by identifying recent B. taurus F1 hybrid ancestors (within three generations). Biallelic single nucleotide polymorphisms (SNPs) can accomplish either task, but increases the marker count and costs necessary to achieve both. Our aim was to identify novel, multifunctional, triallelic yak SNPs (tySNPs), with each having two alleles for yak parentage testing, and a third allele for identifying recent cattle introgression. Methods: Genome sequences were aligned to the cattle UMD3.1 assembly and SNPs were screened for 1) heterozygosity in a NA and a Chinese yak, 2) a third allele at high frequency in cattle, and 3) flanking sequences conserved in both species. Subsequently, tySNPs were filtered for unique alignment to the haplotype-resolved F1 yak assembly. Allele frequencies were estimated in a subset of 87 tySNPs by genotyping 170 NA yak. Results: We identified 610 autosomal tySNPs, distributed in 441 clusters with 5 Mb average genome spacing. The average NA yak minor allele frequency was high (0.296), while average introgressed cattle alleles were low (0.004). In simulations with tySNPs, 28 were sufficient for globally-unique animal identification (PI=5.81x10-12), 87 were able to exclude 19 random bulls from parentage at the 99% level without using the dam’s genotype (PE=5.3x10-4), and 87 were able to detect F1 hybridization events after three generations of yak backcrosses (1/16th B. taurus germplasm). Conclusions: Identifying animals, determining parentage and detecting recent hybridization events was efficient with as few as 87 tySNPs. A similar triallelic approach could be used with other bottlenecked Bos species that hybridize with cattle, such as NA plains bison (B. bison).