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

Ted Kalbfleisch, Jessica L. Petersen, R. G. Tait, Jiansheng Qiu, Veronica Basnayake, Peter H. Hackett, Michael P. Heaton

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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 (P I=5.81x10 -12), 87 were able to exclude 19 random bulls from parentage at the 99% level without using the dam's genotype (P E=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).

Original languageEnglish
Article number1096
JournalF1000Research
Volume9
DOIs
StatePublished - 2020

Bibliographical note

Funding Information:
We thank J. Carnahan and H. Sadd for outstanding technical assistance. This work was conducted in part using the resources of the University of Louisville's Research Computing Group and the Cardinal Research Cluster. TK would like to acknowledge specifically the support of Mr. Harrison Simrall of the University of Louisville Research Computing Group. We would also like to thank the University of Kentucky Center for Computational Sciences and Information Technology Services Research Computing for their support and use of the Lipscomb Compute Cluster and associated research computing resources. TK would like to acknowledge specifically the support of Mr. Vikram Gazula. We thank Dr. E. Bailey thoughtful discussions and improvements to the manuscript; Drs. D. Armstrong and E. Louis from Omaha's Henry Doorly Zoo for providing gaur blood samples, Ms. L. Chemnick and Dr. O. Ryder from the San Diego Zoo's Beckman Center for Conservation Research for providing banteng DNA samples; the late Dianne Latona for historical research in 'Out of Tibet-Highlights of the Yak's Journey to the New World' and her passion for preserving the genetic health and welfare NA yaks, and members from the International Yak Association and USYAKS for donating yak tissues samples. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer.

Publisher Copyright:
© 2020 Kalbfleisch T et al.

Keywords

  • Introgression
  • Parentage Testing
  • SNP test
  • Yak

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (all)
  • Immunology and Microbiology (all)
  • Pharmacology, Toxicology and Pharmaceutics (all)

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