1
|
Cai Z, Villumsen TM, Asp T, Guldbrandtsen B, Sahana G, Lund MS. SNP markers associated with body size and pelt length in American mink (Neovison vison). BMC Genet 2018; 19:103. [PMID: 30419805 PMCID: PMC6233529 DOI: 10.1186/s12863-018-0688-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background Identification of genes underlying production traits is a key aim of the mink research community. Recent availability of genomic tools have opened the possibility for faster genetic progress in mink breeding. Availability of mink genome assembly allows genome-wide association studies in mink. Results In this study, we used genotyping-by-sequencing to obtain single nucleotide polymorphism (SNP) genotypes of 2496 mink. After multiple rounds of filtering, we retained 28,336 high quality SNPs and 2352 individuals for a genome-wide association study (GWAS). We performed the first GWAS for body weight, behavior, along with 10 traits related to fur quality in mink. Conclusions Combining association results with existing functional information of genes and mammalian phenotype databases, we proposed WWC3, MAP2K4, SLC7A1 and USP22 as candidate genes for body weight and pelt length in mink. Electronic supplementary material The online version of this article (10.1186/s12863-018-0688-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.
| | - Trine Michelle Villumsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Torben Asp
- Section of Crop Genetics and Biotechnology, Department of Molecular Biology and Genetics, Aarhus University, 4200, Slagelse, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| |
Collapse
|
2
|
Cai Z, Petersen B, Sahana G, Madsen LB, Larsen K, Thomsen B, Bendixen C, Lund MS, Guldbrandtsen B, Panitz F. The first draft reference genome of the American mink (Neovison vison). Sci Rep 2017; 7:14564. [PMID: 29109430 PMCID: PMC5674041 DOI: 10.1038/s41598-017-15169-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/23/2017] [Indexed: 01/28/2023] Open
Abstract
The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It's an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we present the first draft genome of mink. In our study, two mink individuals were sequenced by Illumina sequencing with 797 Gb sequence generated. Assembly yielded 7,175 scaffolds with an N50 of 6.3 Mb and length of 2.4 Gb including gaps. Repeat sequences constitute around 31% of the genome, which is lower than for dog and cat genomes. The alignments of mink, ferret and dog genomes help to illustrate the chromosomes rearrangement. Gene annotation identified 21,053 protein-coding sequences present in mink genome. The reference genome's structure is consistent with the microsatellite-based genetic map. Mapping of well-studied genes known to be involved in coat quality and coat color, and previously located fur quality QTL provide new knowledge about putative candidate genes for fur traits. The draft genome shows great potential to facilitate genomic research towards improved breeding for high fur quality animals and strengthen our understanding on evolution of Carnivora.
Collapse
Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Lone B Madsen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Knud Larsen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Bo Thomsen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Christian Bendixen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Frank Panitz
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| |
Collapse
|
3
|
Cirera S, Markakis MN, Kristiansen T, Vissenberg K, Fredholm M, Christensen K, Anistoroaei R. A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in American mink. Mamm Genome 2016; 27:135-43. [DOI: 10.1007/s00335-016-9620-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/31/2016] [Indexed: 02/03/2023]
|
4
|
Anistoroaei R, Nielsen V, Markakis MN, Karlskov-Mortensen P, Jørgensen CB, Christensen K, Fredholm M. A re-assigned American mink (Neovison vison) map optimal for genome-wide studies. Gene 2012; 511:66-72. [DOI: 10.1016/j.gene.2012.08.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/07/2012] [Accepted: 08/23/2012] [Indexed: 10/27/2022]
|
5
|
The Transferability of Illumina Canine BeadChip Single-Nucleotide Polymorphisms (SNPs) to American Mink (Neovison vison). Biochem Genet 2012; 50:717-21. [DOI: 10.1007/s10528-012-9514-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/27/2011] [Indexed: 10/28/2022]
|
6
|
Benkel BF, Smith A, Christensen K, Anistoroaei R, Zhang Y, Sensen CW, Farid H, Paterson L, Teather RM. A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison). Genes Genomics 2012. [DOI: 10.1007/s13258-011-0160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
7
|
Anistoroaei R, ten Hallers B, Nefedov M, Christensen K, de Jong P. Construction of an American mink bacterial artificial chromosome (BAC) library and sequencing candidate genes important for the fur industry. BMC Genomics 2011; 12:354. [PMID: 21740547 PMCID: PMC3143106 DOI: 10.1186/1471-2164-12-354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 07/08/2011] [Indexed: 12/03/2022] Open
Abstract
Background Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. Results Here, we report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison). The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs), representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library. These included candidate genes for coat coloring, hair growth and length, coarseness, and some receptors potentially involved in viral diseases in mink. The extensive screening yielded positive results for 19 of these genes. Thirty-five clones corresponding to 19 genes were sequenced using 454 Roche, and large contigs (184 kb in average) were assembled. Knowing the complete sequences of these candidate genes will enable confirmation of the association with a phenotype and the finding of causative mutations for the targeted phenotypes. Additionally, 1577 BAC clones were end sequenced; 2505 BAC end sequences (80% of BACs) were obtained. An excess of 2 Mb has been analyzed, thus giving a snapshot of the mink genome. Conclusions The availability of the CHORI-321 American mink BAC library will aid in identification of genes and genomic regions of interest. We have demonstrated how the library can be used to identify specific genes of interest, develop genetic markers, and for BAC end sequencing and deep sequencing of selected clones. To our knowledge, this is the first report of 454 sequencing of selected BAC clones in mammals and re-assures the suitability of this technique for obtaining the sequence information of genes of interest in small genomics projects. The BAC end sequences described in this paper have been deposited in the GenBank data library [HN339419-HN341884, HN604664-HN604702]. The 454 produced contigs derived from selected clones are deposited with reference numbers [GenBank: JF288166-JF288183 &JF310744].
Collapse
Affiliation(s)
- Razvan Anistoroaei
- University of Copenhagen, Department of Basic Animal and Veterinary Sciences, Division of Animal Genetics and Bioinformatics, Groennegaardsvej 3, Frederiksberg C, Denmark.
| | | | | | | | | |
Collapse
|
8
|
Demontis D, Larsen PF, Baekgaard H, Sønderup M, Hansen BK, Nielsen VH, Loeschcke V, Zalewski A, Zalewska H, Pertoldi C. Inbreeding affects fecundity of American mink (Neovison vison) in Danish farm mink. Anim Genet 2011; 42:437-9. [PMID: 21749427 DOI: 10.1111/j.1365-2052.2010.02155.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inbreeding is an increasing problem in farmed mink, because of limited exchange of individuals between farms. In this study, genetic relatedness within seven American mink (Neovison vison) colour strains originating from 13 different mink farms in Denmark was analysed using 21 polymorphic microsatellite loci. We detected large differences in the level of relatedness (range 0.017-0.520) within colour strains. Moreover, a very strong and highly significant negative correlation between the level of relatedness and fecundity was observed (r = 0.536, P < 0.001) [Correction added after online publication on 9 March 2011: r(2) has been changed to r]. To our knowledge, this is the first time that such a correlation has been demonstrated for commercially farmed mink.
Collapse
Affiliation(s)
- D Demontis
- Department of Human Genetics, Aarhus University, Denmark
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Anistoroaei R, Ansari S, Farid A, Benkel B, Karlskov-Mortensen P, Christensen K. An extended anchored linkage map and virtual mapping for the American mink genome based on homology to human and dog. Genomics 2009; 94:204-10. [DOI: 10.1016/j.ygeno.2009.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 05/20/2009] [Accepted: 05/28/2009] [Indexed: 11/30/2022]
|
10
|
Kukekova AV, Vorobieva NV, Beklemisheva VR, Johnson JL, Temnykh SV, Yudkin DV, Trut LN, Andre C, Galibert F, Aguirre GD, Acland GM, Graphodatsky AS. Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes. ACTA ACUST UNITED AC 2009; 100 Suppl 1:S42-53. [PMID: 19546120 DOI: 10.1093/jhered/esp037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.
Collapse
Affiliation(s)
- Anna V Kukekova
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Borodin PM, Basheva EA, Zhelezova AI. Immunocytological analysis of meiotic recombination in the American mink (Mustela vison). Anim Genet 2009; 40:235-8. [DOI: 10.1111/j.1365-2052.2008.01808.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Anistoroaei R, Fredholm M, Christensen K, Leeb T. Albinism in the American mink (Neovison vison) is associated with a tyrosinase nonsense mutation. Anim Genet 2008; 39:645-8. [PMID: 18822100 DOI: 10.1111/j.1365-2052.2008.01788.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Albino phenotypes are documented in various species including the American mink. In other species the albino phenotypes are associated with tyrosinase (TYR) gene mutations; therefore TYR was considered the candidate gene for albinism in mink. Four microsatellite markers were chosen in the predicted region of the TYR gene. Genotypes at the markers Mvi6025 and Mvi6034 were found to be associated with the albino phenotype within an extended half-sib family. A BAC clone containing Mvi6034 was mapped to chromosome 7q1.1-q1.3 by fluorescent in situ hybridization. Subsequent analysis of genomic TYR sequences from wild-type and albino mink samples identified a nonsense mutation in exon 1, which converts a TGT codon encoding cysteine to a TGA stop codon (c.138T>A, p.C46X; EU627590). The mutation truncates more than 90% of the normal gene product including the putative catalytic domains. The results indicate that the nonsense mutation is responsible for the albino phenotype in the American mink.
Collapse
Affiliation(s)
- R Anistoroaei
- Division of Animal Genetics and Bioinformatics, Department of Basic Animal and Veterinary Sciences, The Faculty of Life Sciences, University of Copenhagen, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.
| | | | | | | |
Collapse
|