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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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2
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Large scale phenotypic characterisation of Hierophis viridiflavus (Squamata: Serpentes): climatic and environmental drivers suggest the role of evolutionary processes in a polymorphic species. Evol Ecol 2023. [DOI: 10.1007/s10682-023-10234-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
AbstractColour variability is largely widespread in the animal world as it is tightly associated with fitness and survivorship. Therefore, the drivers and implications of such variability have been of great interest for zoologists in the past decades. Reptiles are excellent models to investigate colour variations and expression under different conditions. Here, we focused on melanism occurrence in the two main lineages of Hierophis viridiflavus at the scale of the species distribution, by extracting available data from iNaturalist, a citizen science network, with the aim of detecting any pure effect of climate or local habitat on colour expression. Our analyses highlighted that habitat does not explain differences in phenotypes, whereas marked effects of geographic and climatic variables were detected. However, the observed climatic effects could be a proxy of the geographical distribution of the two groups, and thus the high occurrence of bright colourations in western populations of the eastern lineage could be addressed to an ongoing event of asymmetric gene flow in contact zones. The current distribution of phenotypes could be the outcome of the evolutionary history of the species combined with the geological history of the Mediterranean region. This investigation, though, is only preliminary and molecular analyses on highly variable regions of the genome are mandatory to address this issue.
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Portillo-Salgado R, Herrera Haro J, Bautista-Ortega J, Chay-Canul A, Cigarroa Vázquez F. Guajolote – A poultry genetic resource native to Mexico. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2028217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- R. Portillo-Salgado
- Programa de Ganadería, Colegio de Postgraduados, Campus Montecillo, Texcoco, México
| | - J.G. Herrera Haro
- Programa de Ganadería, Colegio de Postgraduados, Campus Montecillo, Texcoco, México
| | - J. Bautista-Ortega
- Departamento de Ciencias Agrícolas, Colegio de Postgraduados, Campus Campeche, Champotón, México
| | - A.J. Chay-Canul
- División Acad Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - F.A. Cigarroa Vázquez
- Escuela de Estudios Agropecuarios Mezcalapa, Universidad Autónoma de Chiapas, Copainalá, Chiapas, México
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4
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Kokita T, Ueno K, Yamasaki YY, Matsuda M, Tabata R, Nagano AJ, Mishina T, Watanabe K. Gudgeon fish with and without genetically determined countershading coexist in heterogeneous littoral environments of an ancient lake. Ecol Evol 2021; 11:13283-13294. [PMID: 34646469 PMCID: PMC8495823 DOI: 10.1002/ece3.8050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Countershading, characterized by a darker dorsal surface and lighter ventral surface, is common among many animals. This dorsoventral pigment polarity is often thought to be adaptive coloration for camouflage. By contrast, noncountershaded (melanistic) morphs often occur within a species due to genetic color polymorphism in terrestrial animals. However, the polymorphism with either countershaded or melanistic morphs is poorly known in wild aquatic animals. This study explored the genetic nature of diverged color morphs of a lineage of gudgeon fish (genus Sarcocheilichthys) in the ancient Lake Biwa and propose this system as a novel model for testing hypotheses of functional aspects of countershading and its loss in aquatic environments. This system harbors two color morphs that have been treated taxonomically as separate species; Sarcocheilichthys variegatus microoculus which occurs throughout the littoral zone and Sarcocheilichthys biwaensis which occurs in and around rocky areas. First, we confirmed that the divergence of dorsoventral color patterns between the two morphs is under strict genetic control at the levels of chromatophore distribution and melanin-related gene expression under common garden rearing. The former morph displayed sharp countershading coloration, whereas the latter morph exhibited a strong tendency toward its loss. The crossing results indicated that this divergence was likely controlled by a single locus in a two-allele Mendelian inheritance pattern. Furthermore, our population genomic and genome-wide association study analyses detected no genome-wide divergence between the two morphs, except for one region near a locus that may be associated with the color divergence. Thus, these morphs are either in a state of intraspecific color polymorphism or two incipient species. Evolutionary forces underlying this polymorphism appear to be associated with heterogeneous littoral environments in this lake. Future ecological genomic research will provide insight into adaptive functions of this widespread coloration, including the eco-evolutionary drivers of its loss, in the aquatic world.
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Affiliation(s)
- Tomoyuki Kokita
- Faculty of Marine Science and TechnologyFukui Prefectural UniversityObamaJapan
| | - Kohtaro Ueno
- Faculty of Marine Science and TechnologyFukui Prefectural UniversityObamaJapan
| | | | | | | | - Atsushi J. Nagano
- Faculty of AgricultureRyukoku UniversityOtsuJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaJapan
| | - Tappei Mishina
- Laboratory for Chromosome SegregationRIKEN Center for Biosystems Dynamics ResearchKobeJapan
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5
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Shoyombo AJ, Yakubu A, Adebambo AO, Popoola MA, Olafadehan OA, Wheto M, Alabi OO, Osaiyuwu HO, Ukim CI, Olayanju A, Adebambo OA. Characterisation of indigenous helmeted guinea fowls in Nigeria for meat and egg production. WORLD POULTRY SCI J 2021. [DOI: 10.1080/00439339.2021.1974287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- A. J. Shoyombo
- Department of Animal Science, Landmark University, Omu-Aran, Nigeria
| | - A. Yakubu
- Department of Animal Science, Faculty of Agriculture, Nasarawa State University, Lafia, Nigeria
| | - A. O. Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - M. A. Popoola
- National Biotechnology Development Agency, Tertiary Education Trust Fund, Abuja, Nigeria
| | - O. A. Olafadehan
- Department of Animal Science, Faculty of Agriculture, University of Abuja, Abuja, Nigeria
| | - M. Wheto
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - O. O. Alabi
- Department of Animal Science, Landmark University, Omu-Aran, Nigeria
| | - H. O. Osaiyuwu
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria
| | - C. I. Ukim
- Tertiary Education Trust Fund, Abuja, Nigeria
| | - A. Olayanju
- Department of Animal Science, Landmark University, Omu-Aran, Nigeria
| | - O. A. Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
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6
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Suzuki H, Kinoshita G, Tsunoi T, Noju K, Araki K. Mouse Hair Significantly Lightened Through Replacement of the Cysteine Residue in the N-Terminal Domain of Mc1r Using the CRISPR/Cas9 System. J Hered 2020; 111:640-645. [PMID: 33252683 DOI: 10.1093/jhered/esaa054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
A loss-of-function mutation in the melanocortin 1 receptor gene (MC1R), which switches off the eumelanin production, causes yellowish coat color variants in mammals. In a wild population of sables (Martes zibellina) in Hokkaido, Japan, the mutation responsible for a bright yellow coat color variant was inferred to be a cysteine replacement at codon 35 of the N-terminal extracellular domain of the Mc1r receptor. In the present study, we validated these findings by applying genome editing on Mc1r in mouse strains C3H/HeJ and C57BL/6N, altering the codon for cysteine (Cys33Phe). The resulting single amino acid substitution (Cys33Phe) and unintentionally generated frameshift mutations yielded a color variant exhibiting substantially brighter body color, indicating that the Cys35 replacement produced sufficient MC1R loss of function to confirm that this mutation is responsible for producing the Hokkaido sable yellow color variant. Notably, the yellowish mutant mouse phenotype exhibited brown coloration in subapical hair on the dorsal side in both the C3H/HeJ and C57BL/6N strains, despite the inability of the latter to produce the agouti signaling protein (Asip). This darker hair and body coloration was not apparent in the Hokkaido sable variant, implying the presence of an additional genetic system shaping yellowish hair variability.
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Affiliation(s)
- Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Gohta Kinoshita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takeru Tsunoi
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Koki Noju
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Kimi Araki
- and Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Honjo, Kumamoto, Japan
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7
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Araguas RM, Sanz N, Viñas J, Vidal O. MC1R polymorphism associated with plumage color variations in Coturnix chinensis. Anim Genet 2018; 49:475-477. [PMID: 29974967 DOI: 10.1111/age.12679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2018] [Indexed: 11/26/2022]
Abstract
The melanocortin 1 receptor (MC1R) gene was investigated as a candidate for plumage variations in Chinese painted quail, Coturnix chinensis. Four silent and two missense nucleotide polymorphisms were identified. The correspondent amino acid changes, p.Glu92Lys and p.Pro292Leu, were found in Blue Face and Red Breasted animals respectively. Blue Face is a melanic phenotype similar to the co-dominant Extended Brown of Japanese quail, and both share the p.Glu92Lys mutation. The association of p.Pro292Leu with the recessive Red Breasted was confirmed in 23 animals from an experimental F2 cross.
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Affiliation(s)
- R M Araguas
- Departament de Biologia, Universitat de Girona, E-17071, Girona, Catalonia, Spain
| | - N Sanz
- Departament de Biologia, Universitat de Girona, E-17071, Girona, Catalonia, Spain
| | - J Viñas
- Departament de Biologia, Universitat de Girona, E-17071, Girona, Catalonia, Spain
| | - O Vidal
- Departament de Biologia, Universitat de Girona, E-17071, Girona, Catalonia, Spain
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8
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Corso J, Hepp D, Ledur MC, Peixoto JO, Fagundes NJR, Freitas TRO. Genetic variation of the bronze locus (MC1R) in turkeys from Southern Brazil. Genet Mol Biol 2017; 40:104-108. [PMID: 28323301 PMCID: PMC5409775 DOI: 10.1590/1678-4685-gmb-2016-0136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 11/15/2016] [Indexed: 11/21/2022] Open
Abstract
Domestic turkeys present several color phenotypes controlled by at least five genetic
loci, but only one of these has been identified precisely: the bronze locus, which
turned out to be the melanocortin-1 receptor (MC1R)
gene. MC1R variation is important for breeders interested in
maintaining or developing different color varieties. In this study, we sequenced most
of the MC1R gene from 16 White Holland (the main commercial turkey
variety) and 19 pigmented turkeys from southern Brazil with two purposes. The first
was to describe the MC1R diversity in White Holland turkeys, which
may serve as reservoirs of genetic diversity at this locus. The second was to test
whether the traditional color classification used by Brazilian breeders is related to
previously known MC1R alleles. White Holland turkeys had four
different haplotypes corresponding to the bronze (b+) and black-winged bronze (b1) alleles. Pigmented turkeys also had four haplotypes corresponding to
the b+ and b1 alleles, but different haplotypes represent the most common
b+ allele in these two groups. The black (B) allele was absent
from our samples. Overall, our results suggest that white and pigmented individuals
form two different populations, and that the traditional color classification used by
Brazilian breeders cannot accurately predict the genotypes at the bronze locus.
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Affiliation(s)
- Josmael Corso
- Departmento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Diego Hepp
- Departmento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul (IFRS), Porto Alegre, RS, Brazil
| | | | | | - Nelson J R Fagundes
- Departmento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Thales R O Freitas
- Departmento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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9
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The Relationship between MC1R Mutation and Plumage Color Variation in Pigeons. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3059756. [PMID: 27957493 PMCID: PMC5124481 DOI: 10.1155/2016/3059756] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/20/2016] [Accepted: 10/23/2016] [Indexed: 11/26/2022]
Abstract
The polymorphisms of MC1R gene play a crucial role in coat color variation in mammals; however, the relationship is still unclear in pigeons. In this study, we sequenced 741 bp fragment of the MC1R for 39 individuals with five plumage color patterns (gray plumage, n = 12; black plumage, n = 9; white plumage, n = 3; spotted plumage, n = 12; red plumage, n = 3). A total of three single nucleotide polymorphisms (SNPs) were detected, including G199A, G225A, and A466G, which subsequently determined four haplotypes (H1–H4). Among them, H1 is the predominant haplotype. Association analysis revealed that H1 and H3 were significantly associated with the black plumage trait (P < 0.05), while the H4 was significantly associated with gray plumage trait (P < 0.05). Furthermore, only diplotype H1H1 was significantly associated with black and gray traits of pigeons. Collectively, our study suggested an association between genetic variation of MC1R and plumage color in pigeon.
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10
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Corso J, Mundy NI, Fagundes NJR, de Freitas TRO. Evolution of dark colour in toucans (Ramphastidae): a case of molecular adaptation? J Evol Biol 2016; 29:2530-2538. [PMID: 27654325 DOI: 10.1111/jeb.12982] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/08/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022]
Abstract
In the last decades, researchers have been able to determine the molecular basis of some phenotypes, to test for evidence of natural selection upon them, and to demonstrate that the same genes or genetic pathways can be associated with convergent traits. Colour traits are often subject to natural selection because even small changes in these traits can have a large effect on fitness via camouflage, sexual selection or other mechanisms. The melanocortin-1 receptor locus (MC1R) is frequently associated with intraspecific coat colour variation in vertebrates, but it has been far harder to demonstrate that this locus is involved in adaptive interspecific colour differences. Here, we investigate the contribution of the MC1R gene to the colour diversity found in toucans (Ramphastidae). We found divergent selection on MC1R in the clade represented by the genus Ramphastos and that this coincided with the evolution of darker plumage in members of this genus. Using phylogenetically corrected correlations, we show significant and specific relationships between the rate of nonsynonymous change in MC1R (dN) and plumage darkness across Ramphastidae, and also between the rate of functionally significant amino acid changes in MC1R and plumage darkness. Furthermore, three of the seven amino acid changes in MC1R that occurred in the ancestral Ramphastos branch are associated with melanism in other birds. Taken together, our results suggest that the dark colour of Ramphastos toucans was related to nonsynonymous substitutions in MC1R that may have been subject to positive selection or to a relaxation of selective pressure. These results also demonstrate a quantitative relationship between gene and phenotype evolution, representing an example of how MC1R molecular evolution may affect macroevolution of plumage phenotypes.
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Affiliation(s)
- J Corso
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - N I Mundy
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - N J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - T R O de Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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11
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Darris CE, Tyus JE, Kelley G, Ropelewski AJ, Nicholas HB, Wang X, Nahashon S. Molecular tools to support metabolic and immune function research in the Guinea Fowl (Numida meleagris). BMC Genomics 2015; 16:358. [PMID: 25948401 PMCID: PMC4432510 DOI: 10.1186/s12864-015-1520-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/10/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Guinea fowl (Numidia meleagris) production as an alternative source of meat and poultry has shown potential for economic viability. However, there has been little progress in characterizing the transcriptome of the guinea fowl. In this study RNA-sequencing and de novo transcriptome assembly of several Guinea fowl tissues (pancreas, hypothalamus, liver, bone marrow and bursa) which play key roles in regulating feed intake, satiety, and immune function was performed using Illumina's Hi-Seq 2000. RESULTS 74 million sequences were generated and assembled into 96,492 contigs using the Trinity software suite. Over 39,000 of these transcripts were found to have in silico translated protein sequences that are homologous to chicken protein sequences. Gene ontology analysis uncovered 416 transcripts with metabolic functions and 703 with immune function. CONCLUSION The transcriptome information presented here will support the development of molecular approaches to improve production efficiency of the guinea fowl and other avian species.
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Affiliation(s)
- Carl E Darris
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - James E Tyus
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - Gary Kelley
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - Alexander J Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
| | - Hugh B Nicholas
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
| | - Xiaofei Wang
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - Samuel Nahashon
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
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12
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Parks M, Lambert D. Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study. BMC Genomics 2015; 16:19. [PMID: 25613391 PMCID: PMC4312461 DOI: 10.1186/s12864-015-1219-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/02/2015] [Indexed: 01/01/2023] Open
Abstract
Background Massively parallel sequencing platforms, featuring high throughput and relatively short read lengths, are well suited to ancient DNA (aDNA) studies. Variant identification from short-read alignment could be hindered, however, by low DNA concentrations common to historic samples, which constrain sequencing depths, and post-mortem DNA damage patterns. Results We simulated pairs of sequences to act as reference and sample genomes at varied GC contents and divergence levels. Short-read sequence pools were generated from sample sequences, and subjected to varying levels of “post-mortem” damage by adjusting levels of fragmentation and fragmentation biases, transition rates at sequence ends, and sequencing depths. Mapping of sample read pools to reference sequences revealed several trends, including decreased alignment success with increased read length and decreased variant recovery with increased divergence. Variants were generally called with high accuracy, however identification of SNPs (single-nucleotide polymorphisms) was less accurate for high damage/low divergence samples. Modest increases in sequencing depth resulted in rapid gains in total variant recovery, and limited improvements to recovery of heterozygous variants. Conclusions This in silico study suggests aDNA-associated damage patterns minimally impact variant call accuracy and recovery from short-read alignment, while modest increases in sequencing depth can greatly improve variant recovery. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1219-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew Parks
- Environmental Futures Research Institute, Griffith University, Nathan, 4111, Queensland, Australia.
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, 4111, Queensland, Australia.
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13
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Hoque MR, Jin S, Heo KN, Kang BS, Jo C, Lee JH. Investigation of MC1R SNPs and Their Relationships with Plumage Colors in Korean Native Chicken. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:625-9. [PMID: 25049831 PMCID: PMC4093329 DOI: 10.5713/ajas.2012.12581] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 02/07/2013] [Accepted: 01/11/2013] [Indexed: 11/27/2022]
Abstract
The melanocortin 1 receptor (MC1R) gene is related to the plumage color variations in chicken. Initially, the MC1R gene from 30 individuals was sequenced and nine polymorphisms were obtained. Of these, three and six single nucleotide polymorphisms (SNPs) were confirmed as synonymous and nonsynonymous mutations, respectively. Among these, three selected SNPs were genotyped using the restriction fragment length polymorphism (RFLP) method in 150 individuals from five chicken breeds, which identified the plumage color responding alleles. The neighbor-joining phylogenetic tree using MC1R gene sequences indicated three well-differentiated different plumage pigmentations (eumelanin, pheomelanin and albino). Also, the genotype analyses indicated that the TT, AA and GG genotypes corresponded to the eumelanin, pheomelanin and albino plumage pigmentations at nucleotide positions 69, 376 and 427, respectively. In contrast, high allele frequencies with T, A and G alleles corresponded to black, red/yellow and white plumage color in 69, 376 and 427 nucleotide positions, respectively. Also, amino acids changes at position Asn23Asn, Val126Ile and Thr143Ala were observed in melanin synthesis with identified possible alleles, respectively. In addition, high haplotype frequencies in TGA, CGG and CAA haplotypes were well discriminated based on the plumage pigmentation in chicken breeds. The results obtained in this study can be used for designing proper breeding and conservation strategies for the Korean native chicken breeds, as well as for the developing breed identification markers in chicken.
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Affiliation(s)
- M R Hoque
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - S Jin
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - K N Heo
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - B S Kang
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - C Jo
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - J H Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
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14
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Kerr KCR, Dove CJ. Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis. Ecol Evol 2013; 3:1915-30. [PMID: 23919139 PMCID: PMC3728934 DOI: 10.1002/ece3.597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 11/17/2022] Open
Abstract
The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin-1 receptor gene (MC1R) are associated with dark plumage in the Northern Fulmar. We confirmed that mitochondrial lineages in the Atlantic and Pacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species of Procellariiformes and we recommend elevating these two forms to separate species. We also find that MC1R variation is not associated with color morph but rather is better explained by geographical divergence.
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Affiliation(s)
- Kevin C R Kerr
- Division of Birds, National Museum of Natural History, Smithsonian Institution Washington, DC, 20560
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Roulin A, Ducrest AL. Genetics of colouration in birds. Semin Cell Dev Biol 2013; 24:594-608. [PMID: 23665152 DOI: 10.1016/j.semcdb.2013.05.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 04/19/2013] [Accepted: 05/01/2013] [Indexed: 01/01/2023]
Abstract
Establishing the links between phenotype and genotype is of great importance for resolving key questions about the evolution, maintenance and adaptive function of phenotypic variation. Bird colouration is one of the most studied systems to investigate the role of natural and sexual selection in the evolution of phenotypic diversity. Given the recent advances in molecular tools that allow discovering genetic polymorphisms and measuring gene and protein expression levels, it is timely to review the literature on the genetics of bird colouration. The present study shows that melanin-based colour phenotypes are often associated with mutations at melanogenic genes. Differences in melanin-based colouration are caused by switches of eumelanin to pheomelanin production or by changes in feather keratin structure, melanoblast migration and differentiation, as well as melanosome structure. Similar associations with other types of colourations are difficult to establish, because our knowledge about the molecular genetics of carotenoid-based and structural colouration is quasi inexistent. This discrepancy stems from the fact that only melanin-based colouration shows pronounced heritability estimates, i.e. the resemblance between related individuals is usually mainly explained by genetic factors. In contrast, the expression of carotenoid-based colouration is phenotypically plastic with a high sensitivity to variation in environmental conditions. It therefore appears that melanin-based colour traits are prime systems to understand the genetic basis of phenotypic variation. In this context, birds have a great potential to bring us to new frontiers where many exciting discoveries will be made on the genetics of phenotypic traits, such as colouration. In this context, a major goal of our review is to suggest a number of exciting future avenues.
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Affiliation(s)
- Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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16
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Suzuki H. Evolutionary and phylogeographic views on Mc1r and Asip variation in mammals. Genes Genet Syst 2013; 88:155-64. [DOI: 10.1266/ggs.88.155] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University
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17
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Bourgeois YXC, Bertrand JAM, Thébaud C, Milá B. Investigating the role of the melanocortin-1 receptor gene in an extreme case of microgeographical variation in the pattern of melanin-based plumage pigmentation. PLoS One 2012; 7:e50906. [PMID: 23227219 PMCID: PMC3515493 DOI: 10.1371/journal.pone.0050906] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/26/2012] [Indexed: 11/19/2022] Open
Abstract
UNLABELLED The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic polymorphism in birds, was associated with the observed plumage variation. Although we found three non-synonymous mutations, we detected no association between MC1R variants and color morphs, and the main amino-acid variant found in the Réunion grey white-eye was also present at high frequency in the Mauritius grey white-eye (Zosterops mauritianus), its sister species which shows no melanic polymorphism. In addition, neutrality tests and analysis of population structure did not reveal any obvious pattern of positive or balancing selection acting on MC1R. Altogether these results indicate that MC1R does not play a role in explaining the melanic variation observed in the Réunion grey white-eye. We propose that other genes such as POMC, Agouti or any other genes involved in pigment synthesis will need to be investigated in future studies if we are to understand how selection shapes complex patterns of melanin-based plumage pigmentation. TRIAL REGISTRATION All sequences submitted to Genbank. Accession number: JX914505 to JX914564.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS - Université Paul Sabatier – ENFA, Toulouse, France
- * E-mail:
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS - Université Paul Sabatier – ENFA, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS - Université Paul Sabatier – ENFA, Toulouse, France
| | - Borja Milá
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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18
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Johnson JA, Ambers AD, Burnham KK. Genetics of plumage color in the Gyrfalcon (Falco rusticolus): analysis of the melanocortin-1 receptor gene. ACTA ACUST UNITED AC 2012; 103:315-21. [PMID: 22504110 DOI: 10.1093/jhered/ess023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in a few reported vertebrates. In Gyrfalcon (Falco rusticolus), plumage color variation exists throughout their arctic and subarctic circumpolar distribution, from white to gray and almost black. Multiple color variants do exist within the majority of populations; however, a few areas (e.g., northern Greenland and Iceland) possess a single color variant. Here, we show that the white/melanic color pattern observed in Gyrfalcons is explained by allelic variation at MC1R. Six nucleotide substitutions in MC1R resulted in 9 alleles that differed in geographic frequency with at least 2 MC1R alleles observed in almost all sampled populations in Greenland, Iceland, Canada, and Alaska. In north Greenland, where white Gyrfalcons predominate, a single MC1R allele was observed at high frequency (>98%), whereas in Iceland, where only gray Gyrfalcons are known to breed, 7 alleles were observed. Of the 6 nucleotide substitutions, 3 resulted in amino acid substitutions, one of which (Val(128)Ile) was perfectly associated with the white/melanic polymorphism. Furthermore, the degree of melanism was correlated with number of MC1R variant alleles, with silver Gyrfalcons all heterozygous and the majority of dark gray individuals homozygous (Ile(128)). These results provide strong support that MC1R is associated with plumage color in this species.
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Affiliation(s)
- Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX 76203, USA.
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Corso J, Gonçalves GL, de Freitas TRO. Sequence variation in the melanocortin-1 receptor (MC1R) pigmentation gene and its role in the cryptic coloration of two South American sand lizards. Genet Mol Biol 2012; 35:81-7. [PMID: 22481878 PMCID: PMC3313520 DOI: 10.1590/s1415-47572012005000015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/02/2011] [Indexed: 11/21/2022] Open
Abstract
In reptiles, dorsal body darkness often varies with substrate color or temperature environment, and is generally presumed to be an adaptation for crypsis or thermoregulation. However, the genetic basis of pigmentation is poorly known in this group. In this study we analyzed the coding region of the melanocortin-1-receptor (MC1R) gene, and therefore its role underlying the dorsal color variation in two sympatric species of sand lizards (Liolaemus) that inhabit the southeastern coast of South America: L. occipitalis and L. arambarensis. The first is light-colored and occupies aeolic pale sand dunes, while the second is brownish and lives in a darker sandy habitat. We sequenced 630 base pairs of MC1R in both species. In total, 12 nucleotide polymorphisms were observed, and four amino acid replacement sites, but none of them could be associated with a color pattern. Comparative analysis indicated that these taxa are monomorphic for amino acid sites that were previously identified as functionally important in other reptiles. Thus, our results indicate that MC1R is not involved in the pigmentation pattern observed in Liolaemus lizards. Therefore, structural differences in other genes, such as ASIP, or variation in regulatory regions of MC1R may be responsible for this variation. Alternatively, the phenotypic differences observed might be a consequence of non-genetic factors, such as thermoregulatory mechanisms.
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Affiliation(s)
- Josmael Corso
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Zhan XJ, Dixon A, Fox NC, Bruford MW. Missense SNP of the MC1R gene is associated with plumage variation in the Gyrfalcon (Falco rusticolus). Anim Genet 2011; 43:460-2. [PMID: 22497627 DOI: 10.1111/j.1365-2052.2011.02263.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A single nucleotide polymorphism (MC1R: c.376A>G) in the MC1R gene was found to be highly correlated with pigment phenotype in the Gyrfalcon. Homozygous genotypes c.376GG and c.376AA were found to dominate the extreme white and dark plumage types respectively, and heterozygotes occurred mainly in intermediate phenotypes. However, some heterozygotes were associated with extreme phenotypes, indicating that melanism/albinism might also involve other loci.
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Affiliation(s)
- X J Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, UK
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Vidal O, Viñas J, Pla C. Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus in turkey (Meleagris gallopavo). Poult Sci 2010; 89:1599-602. [PMID: 20634512 DOI: 10.3382/ps.2010-00726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By sequencing the full coding region of the turkey melanocortin 1 receptor (MC1R) gene, we have found 4 mutations (c.96G > A, c.364A > T, c.450C > T, and c.887C > T) that are organized in 5 different haplotypes (MC1R*1 to MC1R*5). These haplotypes correlate perfectly with the 3 alleles of the bronze locus (i.e., B, b(+), and b(1)). We suggest that the dominant black phenotype, associated with the B allele, results from the constitutive activation of the receptor, an effect that might be mediated by the missense mutation c.364A > T (p.Ile122Phe). Moreover, we propose that the recessive black-winged bronze phenotype (linked to b(1)) might be produced by 2 deleterious mutations of MC1R (c.96G > A and c.887C > T). This is an unexpected finding because in mammals, MC1R deleterious polymorphisms are usually related with either red or lighter fur colors.
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Affiliation(s)
- O Vidal
- Departament de Biologia, Universitat de Girona, E-17071 Girona, Catalonia, Spain.
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A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with the Japanese brindling coat colour in rabbits (Oryctolagus cuniculus). BMC Genet 2010; 11:59. [PMID: 20594318 PMCID: PMC3236303 DOI: 10.1186/1471-2156-11-59] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 07/01/2010] [Indexed: 11/18/2022] Open
Abstract
Background In the domestic rabbit (Oryctolagus cuniculus), classical genetic studies have identified five alleles at the Extension locus: ED (dominant black), ES (steel, weaker version of ED), E (wild type, normal extension of black), eJ(Japanese brindling, mosaic distribution of black and yellow) and e (non-extension of black, yellow/red with white belly). Sequencing almost the complete coding sequence (CDS) of the rabbit MC1R gene, we recently identified two in-frame deletions associated with dominant black (c.280_285del6; alleles ED or ES) and recessive red (c.304_333del30; allele e) coat colours. It remained to characterize the eJallele whose phenotypic effect is similar to the Orange and Sex-linked yellow loci of cat and Syrian hamster. Results We sequenced the whole CDS in 25 rabbits of different coat colours including 10 Japanese and 10 Rhinelander (tricolour) rabbits and identified another 6 bp-in frame deletion flanked by a G > A transition in 5' (c.[124G>A;125_130del6]) that was present in all animals with Japanese brindling coat colour and pattern. These mutations eliminate two amino acids in the first transmembrane domain and, in addition, cause an amino acid substitution at position 44 of the wild type sequence. Genotyping 371 rabbits of 31 breeds with different coat colour this allele (eJ) was present in homozygous state in Japanese, Rhinelander and Dutch tricolour rabbits only (except one albino rabbit). Rabbits with eJ/eJ genotype were non fixed at the non-agouti mutation we previously identified in the ASIP gene. Segregation in F1 and F2 families confirmed the order of dominance already determined by classical genetic experiments with a possible dose effect evident comparing eJ/eJ and eJ/e animals. MC1R mRNA was expressed in black hair skin regions only. Conclusions The c.[124A;125_130del6] allele may be responsible for a MC1R variant determining eumelanin production in the black areas. However, the mechanism determining the presence of both red and black hairs in the same animal seems more complex. Expression analyses of the c.[124A;125_130del6] allele suggest that MC1R transcription may be regulated epigenetically in rabbits with the Japanese brindling phenotype. Further studies are needed to clarify this issue.
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