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

Cai, Zexi; Villumsen, Trine Michelle; Asp, Torben; Guldbrandtsen, Bernt; Sahana, Goutam; Lund, Mogens Sandø

doi:10.1186/s12863-018-0688-6

Cited by 14 publications

(19 citation statements)

References 27 publications

(40 reference statements)

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“…High percentage of reads mapped to the reference genome (on average, 98.24%) confirming the high efficiency of the whole genome sequence data in this study. The number of SNPs obtained in this study (8,150,569) was much higher than 52,714 and 34,816 SNPs that were extracted by GBS technique to study the LD pattern [ 35 ] and the genes associated with body size [ 57 ] in American mink, respectively. This is due to the fact that GBS is a restriction enzyme-based technique that can only sequence a reduced subset of genome [ 58 ].…”

Section: Discussionmentioning

confidence: 99%

Population Genomics of American Mink Using Whole Genome Sequencing Data

Karimi

Ngoc

Sargolzaei

et al. 2021

Genes

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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.

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Section: Discussionmentioning

confidence: 99%

Population Genomics of American Mink Using Whole Genome Sequencing Data

Karimi

Ngoc

Sargolzaei

et al. 2021

Genes

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“…Nevertheless, further heritability estimation of growth curve parameters and their genetic correlations with other economically important traits could be useful for future implementation of genetic/genomic selection for improvement of body shape (weight and/or length) based on growth curve parameters. Moreover, the genetic mapping in mink is necessary to better understand the biology underlying growth traits to increase the accuracy of genomic prediction if applied [39][40][41]. In this study, Richards model was suggested for modelling growth in mink but it might be required to be validated in other farms with more records before implementing in the future genetic or genomic selection programs.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Growth Curve Models for Body Weight in American Mink

Ngoc

Miar

2019

Animals

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Simple Summary: Understanding the animal growth is important for optimized management and feeding practices as well as genetic improvement of animals; however, little is known about the growth of mink raised in Canada. This study evaluated the performances of ten models to find the best models describing the growth curves in mink. The results showed that Logistic and Richards were the best model for males and females, respectively. Growth curves were different between males and females. These results suggested that Richards model can be used for modelling the mink growth and modelling might be performed separately for male and female individuals.Abstract: 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 for 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.

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“…A large proportion of sequencing reads (on average, 97.12%) were mapped to the mink genome reference, which revealed the efficiency of methodology applied in this study. The GBS approach was previously used to identify markers associated with body size and pelt length in American mink 44 . The number of detected SNP markers in the current study (62,404) is higher than that (34,816) reported by Cai et al 44 , that might mainly be attributed to different restriction enzymes applied to digest DNA sequences in these studies.…”

Section: Discussionmentioning

confidence: 99%

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

Karimi

Farid

Myles

et al. 2021

Sci Rep

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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.

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

Cited by 14 publications

References 27 publications

Population Genomics of American Mink Using Whole Genome Sequencing Data

Population Genomics of American Mink Using Whole Genome Sequencing Data

Evaluation of Growth Curve Models for Body Weight in American Mink

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

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