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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #336107
Title: Triallelic SNPs for estimating cattle introgression, inbreeding, and determining parentage in North American yak

Author
item KALBFLEISCH, THEODORE - University Of Louisville
item PETERSEN, JESSICA - University Of Nebraska
item HACKETT, PETER - Institute For Altitude Medicine
item BASNAYAKE, VERONICA - Geneseek Inc, A Neogen Company
item QIU, JIANSHENG - Geneseek Inc, A Neogen Company
item SIMPSON, E - Geneseek Inc, A Neogen Company
item Heaton, Michael - Mike

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/15/2016
Publication Date: 1/14/2017
Citation: Kalbfleisch, T.S., Petersen, J.L., Hackett, P., Basnayake, V., Qiu, J., Simpson, E.B., Heaton, M.P. 2017. Triallelic SNPs for estimating cattle introgression, inbreeding, and determining parentage in North American Yak [abstract]. International Plant & Animal Genome XXV Conference, January 14-18, 2017, San Diego, CA. Poster #P0111.

Interpretive Summary:

Technical Abstract: The current population of yaks in the U.S. is estimated to exceed 5,000 and was derived from about 150 animals imported in the 20th Century. During the expansion of the U.S. herd, some yaks were allowed to hybridize with cattle, although it is not clear to what extent. Our aim was to use next generation whole genome sequencing (WGS) data to identify a multi-purpose set of single nucleotide polymorphism (SNP) markers for estimating a yak’s heterozygosity, percent hybridization with cattle, and proportion of ancestral germplasm, while also being able to determine parentage and provide a DNA-based record of identity. WGS produced from a female yak founder of the U.S. population (Queen Allante), and that reported from a Chinese domestic yak, were aligned to the bovine reference assembly (UMD3.1). Rare, triallelic SNP markers (n = 538) were identified that were heterozygous in both yak while being “fixed” for a third allele in WGS from 96 U.S. cattle from 19 breeds (average minor allele frequency less than 0.05). Of the two yak alleles, the ancestral allele was identified by comparison to WGS of the gaur, banteng, and a bison. These triallelic SNPs were grouped in 135 bins, evenly distributed across the genome, and used to design multiplex assays for a matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry genotyping platform. If successful, this all-purpose marker panel would enable producers to identify animals with minimal cattle introgression, manage inbreeding, determine parentage, and provide a unique genetic fingerprint for each animal.