SNP markers associated with body size and pelt length in American mink (Neovison vison)

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

BACKGROUND

Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group.

RESULTS

After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations.

CONCLUSIONS

Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison)

Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.

Genetic and Phenotypic Parameters for Pelt Quality and Body Length and Weight Traits in American Mink

Understanding the genetics of fur characteristics and skin size is important for developing effective breeding programs in the mink industry. Therefore, the objectives of this study were to estimate the genetic and phenotypic parameters for pelt quality traits including live grading overall quality (LQU), live grading nap size (LNAP), dried pelt size (DPS), dried pelt nap size (DNAP) and overall quality of dried pelt (DQU), and body length and weight traits, including November body weight (Nov_BW), November body length (Nov_BL), harvest weight (HW) and harvest length (HL) in American mink. Dried pelt quality traits on 1195 mink and pelt quality traits on live animals on 1680 were collected from mink raised at two farms, in Nova Scotia and Ontario. A series of univariate analyses were implemented in ASReml 4.1 software to identify the significance (p < 0.05) of random effects (maternal genetic effects, and common litter effects) and fixed effects (farm, sex, color type, year, and age) for each trait. Subsequently, bivariate models were used to estimate the genetic and phenotypic parameters using ASReml 4.1. Heritability (±SE) estimates were 0.41 ± 0.06 for DPS, 0.23 ± 0.10 for DNAP, 0.12 ± 0.04 for DQU, 0.28 ± 0.06 for LQU, 0.44 ± 0.07 for LNAP, 0.29 ± 0.10 for Nov_BW, 0.28 ± 0.09 for Nov_BL, 0.41 ± 0.07 for HW and 0.31 ± 0.06 for HL. DPS had high positive genetic correlations (±SE) with Nov_BW (0.89 ± 0.10), Nov_BL (0.81 ± 0.07), HW (0.85 ± 0.05) and HL (0.85 ± 0.06). These results suggested that body weight and length measured on live animals in November of the first year were reliable indicators of dried pelt size. DQU had favorable genetic correlations with Nov_BL (0.55 ± 0.24) and HL (0.46 ± 0.20), and nonsignificant genetic correlations with DNAP (0.13 ± 0.25), Nov_BW (0.25 ± 0.25) and HW (0.06 ± 0.20), which made body length traits an appealing trait for selection for increased pelt size. High positive genetic correlation (±SE) was observed between LNAP and DNAP (0.82 ± 0.22), which revealed that nap size measurement on live animals is a reliable indicator trait for dried pelt nap size. However, nonsignificant (p > 0.05) low genetic correlation (±SE) was obtained between LQU and DQU (0.08 ± 0.45), showing that indirect selection based on live grading might not lead to the satisfactory improvement of dried pelt overall quality. The estimated genetic parameters for live grading, dried pelt quality, and body weight and body length traits may be incorporated into breeding programs to improve fur characteristics in Canadian mink populations.

Amino Acid Solute Carrier Transporters in Inflammation and Autoimmunity

The past decade exposed the importance of many homeostasis and metabolism related proteins in autoimmunity disease and inflammation. Solute carriers (SLCs) are a group of membrane channels that can transport amino acids, the building blocks of proteins, nutrients, and neurotransmitters. This review summarizes the role of SLCs amino acid transporters in inflammation and autoimmunity disease. In detail, the importance of Glutamate transporters SLC1A1, SLC1A2, and SLC1A3, mainly expressed in the brain where they help prevent glutamate excitotoxicity, is discussed in the context of central nervous system disorders such as multiple sclerosis. Similarly, the cationic amino acid transporter SLC7A1 (CAT1), which is an important arginine transporter for T cells, and SLC7A2 (CAT2), essential for innate immunity. SLC3 family proteins, which bind with light chains from the SLC7 family (SLC7A5, SLC7A7 and SLC7A11) to form heteromeric amino acid transporters, are also explored to describe their roles in T cells, NK cells, macrophages and tumor immunotherapies. Altogether, the link between SLC amino acid transporters with inflammation and autoimmunity may contribute to a better understanding of underlying mechanism of disease and provide novel potential therapeutic avenues. Significance Statement SIGNIFICANCE STATEMENT In this review, we summarize the link between SLC amino acid transporters and inflammation and immune responses, specially SLC1 family members and SLC7 members. Studying the link may contribute to a better understanding of related diseases and provide potential therapeutic targets and useful to the researchers who have interest in the involvement of amino acids in immunity.

Population Genomics of American Mink Using Whole Genome Sequencing Data

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.

Detection of selection signatures for response to Aleutian mink disease virus infection in American mink

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 (F_ST) 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.

How Selective Breeding Has Changed the Morphology of the American Mink (Neovison vison)-A Comparative Analysis of Farm and Feral Animals

In this study, we performed a comparative analysis of the morphological traits between feral (n = 43) and farm (n = 200) individuals of the American mink in Poland to address the question of how multigenerational intensive selective breeding has morphologically differentiated these two populations. Nine body measurements and two proportion coefficients were obtained using adult individuals. The significance of differences between population means was assessed using the Wilcoxon test for independent samples, while the Kruskal-Wallis test was used to compare sex-population groups. Spearman's correlation coefficients between measurements were estimated for each population. We also performed Principal Component Analysis (PCA) to identify the variables that were most closely correlated with variation in the trait measurements and to investigate the morphological differences between farm and feral minks. We found that the farm minks exhibited significantly higher mean values for eight out of eleven studied traits. Moreover, significant changes in forelimb length, with no concomitant changes in hindlimb length, were accompanied by differences in body shape: trapezoidal in feral minks and rectangular in farm minks. The PCA suggested an almost complete separation of the two populations and indicated that sexes were quite separate; farm males in particular constitute a wholly discrete cluster. Such a clear differentiation between the two populations and sexes over a period of several decades highlights the intensity of selective breeding in shaping the morphology of these animals.

Genomic selection in American mink (Neovison vison) using a single-step genomic best linear unbiased prediction model for size and quality traits graded on live mink

Genomic selection relies on single-nucleotide polymorphisms (SNPs), which are often collected using medium-density SNP arrays. In mink, no such array is available; instead, genotyping by sequencing (GBS) can be used to generate marker information. Here, we evaluated the effect of genomic selection for mink using GBS. We compared the estimated breeding values (EBVs) from single-step genomic best linear unbiased prediction (SSGBLUP) models to the EBV from ordinary pedigree-based BLUP models. We analyzed seven size and quality traits from the live grading of brown mink. The phenotype data consisted of ~20,600 records for the seven traits from the mink born between 2013 and 2016. Genotype data included 2,103 mink born between 2010 and 2014, mostly breeding animals. In total, 28,336 SNP markers from 391 scaffolds were available for genomic prediction. The pedigree file included 29,212 mink. The predictive ability was assessed by the correlation (r) between progeny trait deviation (PTD) and EBV, and the regression of PTD on EBV, using 5-fold cross-validation. For each fold, one-fifth of animals born in 2014 formed the validation set. For all traits, the SSGBLUP model resulted in higher accuracies than the BLUP model. The average increase in accuracy was 15% (between 3% for fur clarity and 28% for body weight). For three traits (body weight, silky appearance of the under wool, and guard hair thickness), the difference in r between the two models was significant (P < 0.05). For all traits, the regression slopes of PTD on EBV from SSGBLUP models were closer to 1 than regression slopes from BLUP models, indicating SSGBLUP models resulted in less bias of EBV for selection candidates than the BLUP models. However, the regression coefficients did not differ significantly. In conclusion, the SSGBLUP model is superior to conventional BLUP model in the accurate selection of superior animals, and, thus, it would increase genetic gain in a selective breeding program. In addition, this study shows that GBS data work well in genomic prediction in mink, demonstrating the potential of GBS for genomic selection in livestock species.

Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data

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-by-sequencing (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 (r² ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r² < 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.

Evaluation of Growth Curve Models for Body Weight in American Mink

Modelling the growth curves of animals is important for optimizing the management and efficiency of animal production; however, little is known about the growth curves in American mink (Neovison vison). The study evaluated the performances of four three-parameter (Logistic, Gompertz, von Bertalanffy, and Brody), four four-parameter (Richards, Weibull, Bridges, and Janoscheck) and two polynomial models for describing the growth curves in mink. Body weights were collected from the third week of life to the week 31 in 738 black mink (373 males and 365 females). Models were fitted using the nls and nlsLM functions in stats and minpack.lm packages in R software, respectively. The Akaike's information criterion (AIC) and Bayesian information criterion (BIC) were used for model comparison. Based on these criteria, Logistic and Richards were the best models for males and females, respectively. Four-parameter models had better performance compared to the other models, except Logistic model. The estimated maximum weight and mature growth rate varied among the models and differed between males and females. The results indicated that males and females had different growth curves as males grew faster and reached to the maximum body weight later compared to females. Further studies on genetic parameters and selection response for growth curve parameters are required for development of selection programs based on the shape of growth curves in mink.