Population genomics of American mink using genotype data

Genomic Regions Associated with Growth and Reproduction Traits in Pink-Eyed White Mink

In mink breeding, balanced selection for growth and reproductive features is essential because these traits are contradictory. The variables of total number born (TNB), number born alive (NBA), and body weight (BW) are highly valuable in terms of their importance in mink production. A comprehensive understanding of the molecular mechanisms that drive these features could offer vital insights into their genetic compositions. In the present study, the single-nucleotide polymorphism (SNP) genotypes of 219 minks were obtained via double digest restriction-site associated DNA sequencing (ddRAD-seq). Following several rounds of screening, about 2,415,121 high-quality SNPs were selected for a genome-wide association study (GWAS). The GWAS was used to determine BW and reproductive traits in pink-eyed white mink. It was suggested that SLC26A36, STXBP5L, and RPS 29 serve as potential genes for the total number of kits born (TNB), while FSCB, PDPN, NKX 2-1, NFKB 1, NFKBIA, and GABBR1 are key genes for the number born alive (NBA). Moreover, RTTN, PRPF31, MACROD1, and KYAT1 are possible BW genes based on association results and available functional data from gene and mammalian phenotype databases. These results offer essential information about the variety of mink and theoretical principles for applying mink breeds.

Identifying selection signatures for immune response and resilience to Aleutian disease in mink using genotype data

Aleutian disease (AD) brings tremendous financial losses to the mink industry. Selecting AD-resilient mink has been conducted to control AD. Such selections could have altered the patterns of genetic variation responding to selection pressures. This study aimed to identify selection signatures for immune response (IRE) and resilience to AD. A total of 1,411 mink from an AD-positive facility were used. For IRE, 264 animals were categorized according to the combined results of enzyme-linked immunosorbent assay (ELISA) and counterimmunoelectrophoresis (CIEP). For resilience, two grouping methods were used: 1) general resilience performance (GRP, n = 30) was evaluated based on the feed conversion ratio, Kleiber ratio, and pelt quality; and 2) female reproductive performance (FRP, n = 36) was measured based on the number of kits alive 24 h after birth. Detection methods were the pairwise fixation index, nucleotide diversity, and cross-population extended haplotype homozygosity. A total of 619, 569, and 526 SNPs were identified as candidates for IRE, GRP, and FRP, respectively. The annotated genes were involved in immune system process, growth, reproduction, and pigmentation. Two olfactory-related Gene Ontology (GO) terms were significant (q < 0.05) for all traits, suggesting the impact of AD on the sense of smell of infected mink. Differences in detected genes and GO terms among different color types for IRE indicated variations in immune response to AD among color types. The mitogen-activated protein kinase (MAPK) signaling pathway was significant (q < 0.05) for FRP, suggesting that AD may disrupt MAPK signaling and affect FRP. The findings of this research contribute to our knowledge of the genomic architecture and biological mechanisms underlying AD resilience in mink.

Genome-wide association studies for economically important traits in mink using copy number variation

Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.