Development of a 70k Snp Genotyping Array for American Mink (Neogale vison)

Abstract Mink is an important fur animal species; however, little is known about the genomics of complex traits in mink. The development of single nucleotide polymorphism (SNP) array has accelerated genomics application in animal breeding by facilitating genotyping and associated analyses. The current project aimed to design a medium-density SNP array in American mink for genomic studies and selection in this species. For this purpose, whole genome sequence with 30x coverage was generated for 100 individuals from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada). Variant calling was done using Samtools and GATK pipelines. A total of 8,373,854 bi-allelic SNPs identified by both pipelines were used for an initial selection of 91K SNPs for submission to the Affymetrix scoring system. After filtering, 62,375 SNPs were selected for probe design and production of an Axiom Mink Genotyping Array 70K. This 70K SNP array was used to genotype 2,973 mink for validation. After quality control of genotypes, 47,159 SNPs were classified as high-resolution SNPs, and among them 24,237 were polymorphic. A preliminary genome-wide association study of 1,356 mink for body length at harvest identified a SNP (AX-647623051) significantly associated (P < 1.26 × 10-5) with the trait. In conclusion, this 70K mink SNP array could be used for genomic studies and potentially as a starting point for genomic selection programs in American mink.