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Chang Y, Wu S, Li J, Bao H, Wu C. Identification of Candidate Genes for Red-Eyed (Albinism) Domestic Guppies Using Genomic and Transcriptomic Analyses. Int J Mol Sci 2024; 25:2175. [PMID: 38396851 PMCID: PMC10888696 DOI: 10.3390/ijms25042175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Guppies are small tropical fish with brightly colored bodies and variable tail shapes. There are two phenotypes of domestic guppy eye color: red and black. The wild type is black-eyed. The main object of this study was to identify candidate genes for the red-eyed phenotype in domestic guppies. We hope to provide molecular genetic information for the development of new domestic guppy strains. Additionally, the results also contribute to basic research concerning guppies. In this study, 121 domestic guppies were used for genomic analysis (GWAS), and 44 genes were identified. Furthermore, 21 domestic guppies were used for transcriptomic analysis, and 874 differentially expressed genes (DEGs) were identified, including 357 upregulated and 517 downregulated genes. Through GO and KEGG enrichment, we identified some important terms or pathways mainly related to melanin biosynthesis and ion transport. qRT-PCR was also performed to verify the differential expression levels of four important candidate genes (TYR, OCA2, SLC45A2, and SLC24A5) between red-eyed and black-eyed guppies. Based on the results of genomic and transcriptomic analyses, we propose that OCA2 is the most important candidate gene for the red-eyed phenotype in guppies.
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Affiliation(s)
| | | | | | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.C.); (S.W.); (J.L.); (C.W.)
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Peterson SM, Watowich MM, Renner LM, Martin S, Offenberg E, Lea A, Montague MJ, Higham JP, Snyder-Mackler N, Neuringer M, Ferguson B. Genetic variants in melanogenesis proteins TYRP1 and TYR are associated with the golden rhesus macaque phenotype. G3 (BETHESDA, MD.) 2023; 13:jkad168. [PMID: 37522525 PMCID: PMC10542561 DOI: 10.1093/g3journal/jkad168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/09/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Nonhuman primates (NHPs) are vital translational research models due to their high genetic, physiological, and anatomical homology with humans. The "golden" rhesus macaque (Macaca mulatta) phenotype is a naturally occurring, inherited trait with a visually distinct pigmentation pattern resulting in light blonde colored fur. Retinal imaging also reveals consistent hypopigmentation and occasional foveal hypoplasia. Here, we describe the use of genome-wide association in 2 distinct NHP populations to identify candidate variants in genes linked to the golden phenotype. Two missense variants were identified in the Tyrosinase-related protein 1 gene (Asp343Gly and Leu415Pro) that segregate with the phenotype. An additional and distinct association was also found with a Tyrosinase variant (His256Gln), indicating the light-colored fur phenotype can result from multiple genetic mechanisms. The implicated genes are related through their contribution to the melanogenesis pathway. Variants in these 2 genes are known to cause pigmentation phenotypes in other species and to be associated with oculocutaneous albinism in humans. The novel associations presented in this study will permit further investigations into the role these proteins and variants play in the melanogenesis pathway and model the effects of genetic hypopigmentation and altered melanogenesis in a naturally occurring nonhuman primate model.
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Affiliation(s)
- Samuel M Peterson
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Marina M Watowich
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Lauren M Renner
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Samantha Martin
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Emma Offenberg
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Amanda Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James P Higham
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School for Human Evolution & Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Martha Neuringer
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
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Garcia-Elfring A, Sabin CE, Iouchmanov AL, Roffey HL, Samudra SP, Alcala AJ, Osman RS, Lauderdale JD, Hendry AP, Menke DB, Barrett RDH. Piebaldism and chromatophore development in reptiles are linked to the tfec gene. Curr Biol 2023; 33:755-763.e3. [PMID: 36702128 DOI: 10.1016/j.cub.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/12/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023]
Abstract
Reptiles display great diversity in color and pattern, yet much of what we know about vertebrate coloration comes from classic model species such as the mouse and zebrafish.1,2,3,4 Captive-bred ball pythons (Python regius) exhibit a remarkable degree of color and pattern variation. Despite the wide range of Mendelian color phenotypes available in the pet trade, ball pythons remain an overlooked species in pigmentation research. Here, we investigate the genetic basis of the recessive piebald phenotype, a pattern defect characterized by patches of unpigmented skin (leucoderma). We performed whole-genome sequencing and used a case-control approach to discover a nonsense mutation in the gene encoding the transcription factor tfec, implicating this gene in the leucodermic patches in ball pythons. We functionally validated tfec in a lizard model (Anolis sagrei) using the gene editing CRISPR/Cas9 system and TEM imaging of skin. Our findings show that reading frame mutations in tfec affect coloration and lead to a loss of iridophores in Anolis, indicating that tfec is required for chromatophore development. This study highlights the value of captive-bred ball pythons as a model species for accelerating discoveries on the genetic basis of vertebrate coloration.
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Affiliation(s)
- Alan Garcia-Elfring
- Department of Biology, Redpath Museum, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Christina E Sabin
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Neuroscience Division of the Biomedical and Translational Sciences Institute, University of Georgia, Athens, GA 30602, USA
| | - Anna L Iouchmanov
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Heather L Roffey
- Biology Department, Vanier College, Montreal, QC H4L 3X9, Canada
| | - Sukhada P Samudra
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Aaron J Alcala
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rida S Osman
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - James D Lauderdale
- Neuroscience Division of the Biomedical and Translational Sciences Institute, University of Georgia, Athens, GA 30602, USA; Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrew P Hendry
- Department of Biology, Redpath Museum, McGill University, Montreal, QC H3A 0G4, Canada
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rowan D H Barrett
- Department of Biology, Redpath Museum, McGill University, Montreal, QC H3A 0G4, Canada.
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Plants as Modulators of Melanogenesis: Role of Extracts, Pure Compounds and Patented Compositions in Therapy of Pigmentation Disorders. Int J Mol Sci 2022; 23:ijms232314787. [PMID: 36499134 PMCID: PMC9736547 DOI: 10.3390/ijms232314787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The kingdom of plants as a "green biofabric" of valuable bioactive molecules has long been used in many ailments. Currently, extracts and pure compounds of plant origin are used to aid in pigmentation skin problems by influencing the process of melanogenesis. Melanin is a very important pigment that protects human skin against ultraviolet radiation and oxidative stress. It is produced by a complex process called melanogenesis. However, disturbances in the melanogenesis mechanism may increase or decrease the level of melanin and generate essential skin problems, such as hyperpigmentation and hypopigmentation. Accordingly, inhibitors or activators of pigment formation are desirable for medical and cosmetic industry. Such properties may be exhibited by molecules of plant origin. Therefore, that literature review presents reports on plant extracts, pure compounds and compositions that may modulate melanin production in living organisms. The potential of plants in the therapy of pigmentation disorders has been highlighted.
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Russo I, Sartor E, Fagotto L, Colombo A, Tiso N, Alaibac M. The Zebrafish model in dermatology: an update for clinicians. Discov Oncol 2022; 13:48. [PMID: 35713744 PMCID: PMC9206045 DOI: 10.1007/s12672-022-00511-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/04/2022] Open
Abstract
Recently, the zebrafish has been established as one of the most important model organisms for medical research. Several studies have proved that there is a high level of similarity between human and zebrafish genomes, which encourages the use of zebrafish as a model for understanding human genetic disorders, including cancer. Interestingly, zebrafish skin shows several similarities to human skin, suggesting that this model organism is particularly suitable for the study of neoplastic and inflammatory skin disorders. This paper appraises the specific characteristics of zebrafish skin and describes the major applications of the zebrafish model in dermatological research.
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Affiliation(s)
- Irene Russo
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Emma Sartor
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Laura Fagotto
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Anna Colombo
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Natascia Tiso
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Mauro Alaibac
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy.
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