Genome-wide detection of copy number variation in American mink using whole-genome sequencing

Abstract

Background Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. Results A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). Conclusions This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.

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

“…The TOX gene, located in the duplication CNVR75 (Chr4:75,332,844,330–75,473,471), which overlapped with the identified CNVR in our previous study in American mink 64 , was significantly associated with FBW and ADG. The TOX gene is a family member of high‐mobility group box proteins and serves as a regulator of gene expression, mostly through modifying the density of the chromatin structure 65 .…”

“…Regarding the female reproduction traits, we found 168 significant CNVRs, overlapping with several functional genes, among which GRM1, RNASE10, WNT3, WNT3A, and WNT9B might be the candidate genes related to female reproduction in mink. The GRM1 gene, which was previously identified in a CNV study in American mink 64 , was located within the duplication CNVR15 (Chr1: 56,870,177–56,925,961), associated with AWB trait. The GRM1 was a gene of interest reported in several studies to be associated with female reproduction in different livestock species, such as seasonal reproduction in sheep 79 , litter size in goats 80 , number of teats and litter traits in pig 81 , and fertility-related traits in cattle 82 .…”

“…Notably, it was shown that the MYO10 gene mutation altered the coat color pigmentation pattern in mice, further supporting its role in facilitating melanoblast migration 95 . Interestingly, another member of the myosin superfamily, the MYO5A gene, has been widely documented for its impact on coat color phenotype in different species 96 – 98 , and specifically in American mink 64 , 99 .…”

Rosemary extract improves egg quality by altering gut barrier function, intestinal microbiota, and oviductal gene expressions in late-phase laying hens

“…The increased gene expressions in the oviductal magnum indicated that they actively participated in the synthesis of egg albumen in laying hens fed with RE. According to KEGG enrichment analysis, four pathways were signi cantly enriched in the RE200 group, which were closely associated with immune response (relaxin signaling pathway) [46], albumen formation and secretion (focal adhesion and ECM-receptor interaction) [43], and behavior (circadian entrainment) [47]. Collectively, RNA-seq data showed that RE improved gene expressions and functional pathways related to immune function and albumen formation in the oviductal magnum, which provided a direct molecular mechanism for improvements in egg albumen of laying hens induced by RE supplementation.…”

Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs

“…Previous studies in humans with about 69 detection algorithms for SV revealed that Manta is better than most software [ 40 ]. Pourya et al found characteristics-related genes in mink by using Manta [ 41 ]. A total of 15,972 and 20,774 CNVs were identified in WBP and AWB, separately.…”