Population genomics of American mink using genotype data

Guoyu Hu; Duy Ngoc Do; Ghader Manafiazar; Alyson A Kelvin; Mehdi Sargolzaei; Graham Plastow; Zhiquan Wang; Younes Miar

doi:10.3389/fgene.2023.1175408

Population genomics of American mink using genotype data

Front Genet. 2023 May 9:14:1175408. doi: 10.3389/fgene.2023.1175408. eCollection 2023.

Authors

Guoyu Hu¹, Duy Ngoc Do¹, Ghader Manafiazar¹, Alyson A Kelvin², Mehdi Sargolzaei^{3

4}, Graham Plastow⁵, Zhiquan Wang⁵, Younes Miar¹

Affiliations

¹ Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
² Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.
³ Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
⁴ Select Sires Inc, Plain City, OH, United States.
⁵ Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.

Abstract

Understanding the genetic structure of the target population is critically important to develop an efficient genomic selection program in domestic animals. In this study, 2,973 American mink of six color types from two farms (Canadian Centre for Fur Animal Research (CCFAR), Truro, NS and Millbank Fur Farm (MFF), Rockwood, ON) were genotyped with the Affymetrix Mink 70K panel to compute their linkage disequilibrium (LD) patterns, effective population size (Ne), genetic diversity, genetic distances, and population differentiation and structure. The LD pattern represented by average r ², decreased to <0.2 when the inter-marker interval reached larger than 350 kb and 650 kb for CCFAR and MFF, respectively, and suggested at least 7,700 and 4,200 single nucleotide polymorphisms (SNPs) be used to obtain adequate accuracy for genomic selection programs in CCFAR and MFF respectively. The Ne for five generations ago was estimated to be 76 and 91 respectively. Our results from genetic distance and diversity analyses showed that American mink of the various color types had a close genetic relationship and low genetic diversity, with most of the genetic variation occurring within rather than between color types. Three ancestral genetic groups was considered the most appropriate number to delineate the genetic structure of these populations. Black (in both CCFAR and MFF) and pastel color types had their own ancestral clusters, while demi, mahogany, and stardust color types were admixed with the three ancestral genetic groups. This study provided essential information to utilize the first medium-density SNP panel for American mink in their genomic studies.

Keywords: American mink; effective population size; genotypes; linkage disequiblibrium; population genomics.

Grants and funding

Financial support was received from the Natural Sciences and Engineering Research Council of Canada (NSERC), Mitacs, Canada Mink Breeders Association, Nova Scotia Mink Breeders Association, Nova Scotia Department of Agriculture, and Mink Veterinary Consulting Research and Services.