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Davoudi P, Do DN, Colombo S, Rathgeber B, Sargolzaei M, Plastow G, Wang Z, Hu G, Valipour S, Miar Y. Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 2024; 14:24. [PMID: 38167844 PMCID: PMC10762091 DOI: 10.1038/s41598-023-50497-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Tobin DJ. How to design robust assays for human skin pigmentation: A "Tortoise and Hare challenge". Exp Dermatol 2021; 30:624-627. [PMID: 33899266 DOI: 10.1111/exd.14350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Desmond J Tobin
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin, Ireland.,The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Plikus MV, Chuong CM. Understanding skin morphogenesis across developmental, regenerative and evolutionary levels. Exp Dermatol 2019; 28:327-331. [PMID: 30951234 PMCID: PMC7444456 DOI: 10.1111/exd.13932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
- Integrative Stem Cell Center, China Medical University, Taichung, Taiwan
- International Wound Repair and Regenerative Center, National Cheng Kung University, Tainan, Taiwan
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Bachg AC, Horsthemke M, Skryabin BV, Klasen T, Nagelmann N, Faber C, Woodham E, Machesky LM, Bachg S, Stange R, Jeong HW, Adams RH, Bähler M, Hanley PJ. Phenotypic analysis of Myo10 knockout (Myo10 tm2/tm2) mice lacking full-length (motorized) but not brain-specific headless myosin X. Sci Rep 2019; 9:597. [PMID: 30679680 PMCID: PMC6345916 DOI: 10.1038/s41598-018-37160-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/04/2018] [Indexed: 01/04/2023] Open
Abstract
We investigated the physiological functions of Myo10 (myosin X) using Myo10 reporter knockout (Myo10tm2) mice. Full-length (motorized) Myo10 protein was deleted, but the brain-specific headless (Hdl) isoform (Hdl-Myo10) was still expressed in homozygous mutants. In vitro, we confirmed that Hdl-Myo10 does not induce filopodia, but it strongly localized to the plasma membrane independent of the MyTH4-FERM domain. Filopodia-inducing Myo10 is implicated in axon guidance and mice lacking the Myo10 cargo protein DCC (deleted in colorectal cancer) have severe commissural defects, whereas MRI (magnetic resonance imaging) of isolated brains revealed intact commissures in Myo10tm2/tm2 mice. However, reminiscent of Waardenburg syndrome, a neural crest disorder, Myo10tm2/tm2 mice exhibited pigmentation defects (white belly spots) and simple syndactyly with high penetrance (>95%), and 24% of mutant embryos developed exencephalus, a neural tube closure defect. Furthermore, Myo10tm2/tm2 mice consistently displayed bilateral persistence of the hyaloid vasculature, revealed by MRI and retinal whole-mount preparations. In principle, impaired tissue clearance could contribute to persistence of hyaloid vasculature and syndactyly. However, Myo10-deficient macrophages exhibited no defects in the phagocytosis of apoptotic or IgG-opsonized cells. RNA sequence analysis showed that Myo10 was the most strongly expressed unconventional myosin in retinal vascular endothelial cells and expression levels increased 4-fold between P6 and P15, when vertical sprouting angiogenesis gives rise to deeper layers. Nevertheless, imaging of isolated adult mutant retinas did not reveal vascularization defects. In summary, Myo10 is important for both prenatal (neural tube closure and digit formation) and postnatal development (hyaloid regression, but not retinal vascularization).
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Affiliation(s)
- Anne C Bachg
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Markus Horsthemke
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Boris V Skryabin
- Department of Medicine, Transgenic Animal and Genetic Engineering Models (TRAM), Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Tim Klasen
- Department of Clinical Radiology, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Nina Nagelmann
- Department of Clinical Radiology, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Cornelius Faber
- Department of Clinical Radiology, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Emma Woodham
- Cancer Research UK Beatson Institute, Glasgow University College of Medical, Veterinary and Life Sciences Garscube Estate, Glasgow, G61 1BD, United Kingdom
| | - Laura M Machesky
- Cancer Research UK Beatson Institute, Glasgow University College of Medical, Veterinary and Life Sciences Garscube Estate, Glasgow, G61 1BD, United Kingdom
| | - Sandra Bachg
- Department of Regenerative Musculoskeletal Medicine, Institute of Musculoskeletal Medicine (IMM), University Hospital Münster, 48149, Münster, Germany
| | - Richard Stange
- Department of Regenerative Musculoskeletal Medicine, Institute of Musculoskeletal Medicine (IMM), University Hospital Münster, 48149, Münster, Germany
| | - Hyun-Woo Jeong
- Max Planck Institute for Molecular Biomedicine, Department of Tissue Morphogenesis, and University of Münster, Faculty of Medicine, 48149, Münster, Germany
| | - Ralf H Adams
- Max Planck Institute for Molecular Biomedicine, Department of Tissue Morphogenesis, and University of Münster, Faculty of Medicine, 48149, Münster, Germany
| | - Martin Bähler
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Peter J Hanley
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany.
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Serre C, Busuttil V, Botto JM. Intrinsic and extrinsic regulation of human skin melanogenesis and pigmentation. Int J Cosmet Sci 2018; 40:328-347. [PMID: 29752874 DOI: 10.1111/ics.12466] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/04/2018] [Indexed: 12/11/2022]
Abstract
In human skin, melanogenesis is a tightly regulated process. Indeed, several extracellular signals are transduced via dedicated signalling pathways and mostly converge to MITF, a transcription factor integrating upstream signalling and regulating downstream genes involved in the various inherent mechanisms modulating melanogenesis. The synthesis of melanin pigments occurs in melanocytes inside melanosomes where melanogenic enzymes (tyrosinase and related proteins) are addressed with the help of specific protein complexes. The melanosomes loaded with melanin are then transferred to keratinocytes. A more elaborate level of melanogenesis regulation comes into play via the action of non-coding RNAs (microRNAs, lncRNAs). Besides this canonical regulation, melanogenesis can also be modulated by other non-specific intrinsic pathways (hormonal environment, inflammation) and by extrinsic factors (solar irradiation such as ultraviolet irradiation, environmental pollution). We developed a bioinformatic interaction network gathering the multiple aspects of melanogenesis and skin pigmentation as a resource to better understand and study skin pigmentation biology.
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Affiliation(s)
- C Serre
- Global Skin Research Center, Ashland, 655, route du Pin Montard, Sophia Antipolis, 06904, France
| | - V Busuttil
- Global Skin Research Center, Ashland, 655, route du Pin Montard, Sophia Antipolis, 06904, France
| | - J-M Botto
- Global Skin Research Center, Ashland, 655, route du Pin Montard, Sophia Antipolis, 06904, France
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Liakath-Ali K, Vancollie VE, Sequeira I, Lelliott CJ, Watt FM. Myosin 10 is involved in murine pigmentation. Exp Dermatol 2018; 28:391-394. [PMID: 29509981 PMCID: PMC6519374 DOI: 10.1111/exd.13528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2018] [Indexed: 12/25/2022]
Abstract
Myosins are molecular motors that are well known for their role in cell movement and contractile functions. Although extensively studied in muscle physiology, little is known about the function of myosins in mammalian skin. As part of the Sanger Institute Mouse Genetics Project, we have identified a role for Myo10 in pigmentation, with a phenotype unlike those of Myo5a or Myo7a. Adult mice homozygous for a disrupted Myo10 allele on a C57BL/6N background displayed a high degree of penetrance for white patches on their abdomen and dorsal surface. Forepaw syndactyly and hind paw syndactyly were also observed in these mice. Tail epidermal wholemounts showed a complete lack of melanocytes in the hair follicles and interfollicular epidermis. Myo10 has previously been implicated in human pigmentation. Our current study reveals involvement of Myo10 in murine skin pigmentation.
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Affiliation(s)
| | | | - Inês Sequeira
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, UK
| | | | - Fiona M Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, UK
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