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

Abstract

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.

Figure 1

Graphical representation of identified CNVs: (A) Distribution of CNV sizes, (B) numbers of CNVs identified across autosomal chromosomes, (C) correlation between CNV numbers and chromosome length.

Figure 2

Manhattan plots for CNV regions across the 14 autosomal chromosomes associated with feed efficiency and growth traits. The horizontal line in each plot represents the threshold for significance (P < 0.0005) suggested by ParseCNV2 developers. HW: harvest weight; HL: harvest length; FBW: final body weight; FBL: final body length; ADG: average daily gain; DFI: daily feed intake; FCR: feed conversion ratio; KR: Kleiber ratio; RFI: residual feed intake; RG: residual gain; RIG: residual intake and gain.

Figure 3

Manhattan plots for CNV regions across the 14 autosomal chromosomes associated with reproduction traits. The horizontal line in each plot represents the threshold for significance ( P < 0.0005) suggested by ParseCNV2 developers. GL: gestation length; TB: total number of kits born; LB: number of kits alive at birth; LW: number of kits alive at weaning; SB: survival rate at birth; AWB: average kit weight per litter at birth; AWW: average kit weight per litter at weaning; SW: survival rate at weaning.

Figure 4

Manhattan plots for CNV regions across the 14 autosomal chromosomes associated with pelt quality traits. The horizontal line in each plot represents the threshold for significance (P < 0.0005) suggested by ParseCNV2 developers. DPS: dried pelt size; DQU: overall quality of dried pelt; DNAP: dried pelt nap size; LQU: live grading overall quality of fur; LNAP: live grading nap size.

Figure 5

Manhattan plots for CNV regions across the 14 autosomal chromosomes associated with Aleutian disease tests. The horizontal line in each plot represents the threshold for significance (P < 0.0005) suggested by ParseCNV2 developers. CIEP: counterimmunoelectrophoresis test; ELISA-P: VP2 based enzyme-linked immunosorbent assay test; ELISA-G: AMDV-G based enzyme-linked immunosorbent assay test.