Aleutian disease (AD) is the most significant health issue for farmed American mink. The objective of this study was to identify the genomic regions subjected to selection for response to infection with Aleutian mink disease virus (AMDV) in American mink using genotyping by sequencing (GBS) data. A total of 225 black mink were inoculated with AMDV and genotyped using a GBS assay based on the sequencing of ApeKI-digested libraries. Five AD-characterized phenotypes were used to assign animals to pairwise groups. Signatures of selection were detected using integrated measurement of fixation index (FST) and nucleotide diversity (θπ), that were validated by haplotype-based (hap-FLK) test. The total of 99 putatively selected regions harbouring 63 genes were detected in different groups. The gene ontology revealed numerous genes related to immune response (e.g. TRAF3IP2, WDR7, SWAP70, CBFB, and GPR65), liver development (e.g. SULF2, SRSF5) and reproduction process (e.g. FBXO5, CatSperβ, CATSPER4, and IGF2R). The hapFLK test supported two strongly selected regions that contained five candidate genes related to immune response, virus–host interaction, reproduction and liver regeneration. This study provided the first map of putative selection signals of response to AMDV infection in American mink, bringing new insights into genomic regions controlling the AD phenotypes.

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink 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) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

BackgroundTwo separate domestication events gave rise to humped zebu cattle in India and humpless taurine cattle in the Fertile Crescent of the Near and Middle East. Iran covers the Eastern side of the Fertile Crescent and exhibits a variety of native cattle breeds, however, only little is known about the admixture patterns of Iranian cattle and their contribution to the formation of modern cattle breeds.ResultsGenome-wide data (700 k chip) of eight Iranian cattle breeds (Sarabi N = 19, Kurdi N = 7, Taleshi N = 7, Mazandarani N = 10, Najdi N = 7, Pars N = 7, Kermani N = 9, and Sistani N = 9) were collected from across Iran. For a local assessment, taurine (Holstein and Jersey) and indicine (Brahman) outgroup samples were used. For the global perspective, 134 world-wide cattle breeds were included. Between breed variation amongst Iranian cattle explained 60 % (p < 0.001) of the total molecular variation and 82.88 % (p < 0.001) when outgroups were included. Several migration edges were observed within the Iranian cattle breeds. The highest indicine proportion was found in Sistani. All Iranian breeds with higher indicine ancestry were more admixed with a complex migration pattern. Nineteen founder populations most accurately explained the admixture of 44 selected representative cattle breeds (standard error 0.4617). Low levels of African ancestry were identified in Iranian cattle breeds (on average 7.5 %); however, the signal did not persist through all analyses. Admixture and migration analyses revealed minimal introgression from Iranian cattle into other taurine cattle (Holstein, Hanwoo, Anatolian breeds).ConclusionThe eight Iranian cattle breeds feature a discrete genetic composition which should be considered in conservation programs aimed at preserving unique species and genetic diversity. Despite a complex admixture pattern among Iranian cattle breeds, there was no strong introgression from other world-wide cattle breeds into Iranian cattle and vice versa. Considering Iran’s central location of cattle domestication, Iranian cattle might represent a local domestication event that remained contained and did not contribute to the formation of modern breeds, or genetics of the ancestral population that gave rise to modern cattle is too diluted to be linked directly to any current cattle breeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0416-z) contains supplementary material, which is available to authorized users.

The economic efficiency of mink production is greatly influenced by reproductive performance. Therefore, the objective of this study was to estimate phenotypic and genetic parameters for reproduction traits including total number of kits born (TB), number of live kits at birth (LB), number of live kits at weaning (LW), survival rate at birth (SB), survival rate at weaning (SW), gestation length (GL), average kit weight per litter at birth (AWB), average kit weight per litter at week 3 (AW3), and average kit weight per litter at weaning (AWW) in American mink. Data included records of 3,046 litters collected by the Canadian Centre for Fur Animal Research at Dalhousie Faculty of Agriculture between 2002 and 2016. Significance (P < 0.05) of fixed effects (year, number of matings, color type, age of dam, origin of dam, sex ratio, and number of live kits) and random effects of permanent environment were determined using univariate repeatability models. A significant effect of permanent environment was only found for survival rate traits (P < 0.05). Subsequently, genetic and phenotypic parameters for all traits were estimated by fitting a set of bivariate models using ASREML 4.0. Heritabilities (± SE) were estimated to be 0.07 ± 0.03 for TB, 0.07 ± 0.02 for LB, 0.09 ± 0.04 for LW, 0.13 ± 0.03 for SB, 0.10 ± 0.02 for SW, 0.29 ± 0.03 for GL, 0.28 ± 0.05 for AWB, 0.19 ± 0.04 for AW3, and 0.10 ± 0.04 for AWW. Moderate positive genetic correlation was observed between AWB with SB (0.66 ± 0.10) and SW (0.61 ± 0.13). Furthermore, genetic correlations of LB with SW and AWB were 0.55 ± 0.16 and 0.53 ± 0.18, respectively. On the other hand, negative and moderate genetic correlations were observed between GL and survival rates at birth (-0.43 ± 0.14) and at weaning (-0.37 ± 0.15). These results indicated that selection for higher litter weights at birth can effectively improve survival rate and number of live kits in mink farms. It was suggested to incorporate litter weight traits as a selection criterion to increase maternal ability in mink breeding programs. Unfavorable genetic trends were observed for the studied traits indicating that phenotypic selection with low selection intensity had not been an efficient method to improve them over the last 10 yr. It was recommended to use genetic or genomic evaluation methods for mink selection.

Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-bysequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (F HOM ) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r 2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r 2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of F HOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.