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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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Yuan Z, Zhang X, Pang Y, Qi Y, Wang Q, Hu Y, Zhao Y, Ren S, Huo L. Association analysis of melanophilin ( MLPH) gene expression and polymorphism with plumage color in quail. Arch Anim Breed 2023; 66:131-139. [PMID: 37124941 PMCID: PMC10134764 DOI: 10.5194/aab-66-131-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/02/2023] [Indexed: 05/02/2023] Open
Abstract
We explore the relationship between the melanophilin (MLPH) gene and quail plumage color and provide a reference for subsequent quail plumage color breeding. In this experiment, real-time quantitative PCR (RT-qPCR) technology was used to analyze the relative mRNA expression levels of Korean quail (maroon) and Beijing white quail embryos at different developmental stages. Two single-nucleotide polymorphisms (SNPs) in the MLPH gene were screened based on the RNA-sequencing (RNA-Seq) data of skin tissues of Korean quail and Beijing white quail during the embryonic stage. Kompetitive allele-specific PCR (KASP) technology was used for genotyping in the resource population, and correlation analysis was carried out with the plumage color traits of quail. Finally, bioinformatics was used to predict the effects of these two SNPs on the structure and function of the encoded protein. The results showed that the expression level of the MLPH gene during embryonic development of Beijing white quail was significantly higher than that of Korean quail ( P < 0.01 ). The frequency distribution of the three genotypes (CC, CA and AA) of the Beijing white quail at the c.1807C > A mutation site was significantly different from that of the Korean quail ( P < 0.01 ). The frequency distribution of the three genotypes (GG, GA and AA) of the Beijing white quail at the c.2129G > A mutation site was significantly different from that of the Korean quail ( P < 0.01 ). And there was a significant correlation between the c.1807C > A mutation site and the white plumage phenotype. Bioinformatics showed that SNP1 (c.1807C > A) was a neutral mutation and that SNP2 (c.2129G > A) was a deleterious mutation. The prediction of protein conservation showed that the mutation sites of coding proteins R603S and G710D caused by SNP1 (c.1807C > A) and SNP2 (c.2129G > A) were highly conserved.
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Affiliation(s)
- Zhiwen Yuan
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
| | - Xiaohui Zhang
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
- Luoyang Key Laboratory of Animal Genetics and Breeding, Luoyang
471003, China
| | - Youzhi Pang
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
- Luoyang Key Laboratory of Animal Genetics and Breeding, Luoyang
471003, China
| | - Yanxia Qi
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
- Luoyang Key Laboratory of Animal Genetics and Breeding, Luoyang
471003, China
| | - Qiankun Wang
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
| | - Yunqi Hu
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
| | - Yiwei Zhao
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
| | - Shiwei Ren
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
| | - Linke Huo
- College of Animal Science and Technology, Henan University of Science and Technology,
Luoyang 471003, China
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3
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Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks. Genes (Basel) 2022; 13:genes13071249. [PMID: 35886032 PMCID: PMC9317390 DOI: 10.3390/genes13071249] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.
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Affiliation(s)
- Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-187-9660-8824 (H.B.); +86-178-5197-5060 (G.C.)
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-187-9660-8824 (H.B.); +86-178-5197-5060 (G.C.)
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4
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Chen Y, Hu S, Liu M, Zhao B, Yang N, Li J, Chen Q, Zhou J, Bao G, Wu X. Analysis of Genome DNA Methylation at Inherited Coat Color Dilutions of Rex Rabbits. Front Genet 2021; 11:603528. [PMID: 33552123 PMCID: PMC7859435 DOI: 10.3389/fgene.2020.603528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/15/2020] [Indexed: 12/02/2022] Open
Abstract
Background: The dilution of color in rabbits is associated with many different genetic mechanisms that form different color groups. A number of previous studies have revealed potential regulatory mechanisms by which epigenetics regulate pigmentation. However, the genome-wide DNA methylation involved in animal coat color dilution remains unknown. Results: We compared genome-wide DNA methylation profiles in Rex rabbit hair follicles in a Chinchilla group (Ch) and a diluted Chinchilla group (DCh) through whole-genome bisulfite sequencing (WGBS). Approximately 3.5% of the cytosine sites were methylated in both groups, of which the CG methylation type was in greatest abundance. In total, we identified 126,405 differentially methylated regions (DMRs) between the two groups, corresponding to 11,459 DMR-associated genes (DMGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these DMGs were principally involved in developmental pigmentation and Wnt signaling pathways. In addition, two DMRs were randomly selected to verify that the WGBS data were reliable using bisulfite sequencing PCR, and seven DMGs were analyzed to establish the relationship between the level of DNA methylation and mRNA expression using qRT-PCR. Due to the limitation of small sample size, replication of the results with a larger sample size would be important in future studies. Conclusion: These findings provide evidence that there is an association between inherited color dilution and DNA methylation alterations in hair follicles, greatly contributing to our understanding of the epigenetic regulation of rabbit pigmentation.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qiuran Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guolian Bao
- Animal Husbandry and Veterinary Research Institute Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
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5
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Le L, Escobar IE, Ho T, Lefkovith AJ, Latteri E, Haltaufderhyde KD, Dennis MK, Plowright L, Sviderskaya EV, Bennett DC, Oancea E, Marks MS. SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation. Mol Biol Cell 2020; 31:2687-2702. [PMID: 32966160 PMCID: PMC7927184 DOI: 10.1091/mbc.e20-03-0200] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
SLC45A2 encodes a putative transporter expressed primarily in pigment cells. SLC45A2 mutations cause oculocutaneous albinism type 4 (OCA4) and polymorphisms are associated with pigmentation variation, but the localization, function, and regulation of SLC45A2 and its variants remain unknown. We show that SLC45A2 localizes to a cohort of mature melanosomes that only partially overlaps with the cohort expressing the chloride channel OCA2. SLC45A2 expressed ectopically in HeLa cells localizes to lysosomes and raises lysosomal pH, suggesting that in melanocytes SLC45A2 expression, like OCA2 expression, results in the deacidification of maturing melanosomes to support melanin synthesis. Interestingly, OCA2 overexpression compensates for loss of SLC45A2 expression in pigmentation. Analyses of SLC45A2- and OCA2-deficient mouse melanocytes show that SLC45A2 likely functions later during melanosome maturation than OCA2. Moreover, the light skin-associated SLC45A2 allelic F374 variant restores only moderate pigmentation to SLC45A2-deficient melanocytes due to rapid proteasome-dependent degradation resulting in lower protein expression levels in melanosomes than the dark skin-associated allelic L374 variant. Our data suggest that SLC45A2 maintains melanosome neutralization that is initially orchestrated by transient OCA2 activity to support melanization at late stages of melanosome maturation, and that a common allelic variant imparts reduced activity due to protein instability.
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Affiliation(s)
- Linh Le
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Iliana E Escobar
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Tina Ho
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ariel J Lefkovith
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily Latteri
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
| | - Kirk D Haltaufderhyde
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Megan K Dennis
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Biology Department, Marist College, Poughkeepsie, NY 12601
| | - Lynn Plowright
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena V Sviderskaya
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Dorothy C Bennett
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Michael S Marks
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
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6
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Walsh J, Clucas GV, MacManes MD, Thomas WK, Kovach AI. Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone. Ecol Evol 2019; 9:13477-13494. [PMID: 31871659 PMCID: PMC6912898 DOI: 10.1002/ece3.5804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
The role of species divergence due to ecologically based divergent selection-or ecological speciation-in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline-freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes-the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)-to evaluate the influence of selective and demographic processes in shaping genome-wide patterns of divergence. Genome-wide divergence between these two recently diverged sister species was notably high (genome-wide F ST = 0.32). Against a background of high genome-wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism-all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyCornell UniversityIthacaNYUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Gemma V. Clucas
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
- Present address:
Cornell Lab of OrnithologyIthacaNYUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Hubbard Center for Genome StudiesDurhamNHUSA
| | - W. Kelley Thomas
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Hubbard Center for Genome StudiesDurhamNHUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
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7
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Wu Y, Zhang Y, Hou Z, Fan G, Pi J, Sun S, Chen J, Liu H, Du X, Shen J, Hu G, Chen W, Pan A, Yin P, Chen X, Pu Y, Zhang H, Liang Z, Jian J, Zhang H, Wu B, Sun J, Chen J, Tao H, Yang T, Xiao H, Yang H, Zheng C, Bai M, Fang X, Burt DW, Wang W, Li Q, Xu X, Li C, Yang H, Wang J, Yang N, Liu X, Du J. Population genomic data reveal genes related to important traits of quail. Gigascience 2018; 7:4995262. [PMID: 29762663 PMCID: PMC5961004 DOI: 10.1093/gigascience/giy049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/27/2018] [Indexed: 12/18/2022] Open
Abstract
Background Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies. Results Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. Conclusions This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.
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Affiliation(s)
- Yan Wu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China.,Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province,Wuhan 430064, China.,Hubei Innovation Center of Agricultural Science and Technology, Wuhan, Hubei, 430064, China
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jiang Chen
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Huaqiao Liu
- Hubei Shendan Healthy Food Co., Ltd., Wuhan 430206, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Gang Hu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Pingping Yin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Yuejin Pu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | - Hao Zhang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jing Sun
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | - Hu Tao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Ting Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongwei Xiao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Huan Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chuanwei Zheng
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | | | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Wen Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Qingyi Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Chengfeng Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
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8
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Yu S, Wang G, Liao J, Tang M. Transcriptome profile analysis identifies candidate genes for the melanin pigmentation of breast muscle in Muchuan black-boned chicken. Poult Sci 2018; 97:3446-3455. [PMID: 29982752 DOI: 10.3382/ps/pey238] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
Melanin-based coloration in the meat of black-boned chicken is a major economic issue in China. Variation in the pigmentation (hypopigmentation) of chicken muscle causes direct economic losses every year. To determine the molecular mechanisms involved in the melanogenesis of muscle tissue, this study used high-throughput sequencing to compare differences in the transcriptome between black (BM) and white (WM) chicken breast muscles. We constructed 6 cDNA libraries from BM and WM groups in Muchuan black-boned chickens. A comparison between the BM and WM groups revealed 264 differentially expressed genes, of which 152 were upregulated, whereas 112 were downregulated in black muscle. Gene ontology and a Kyoto Encyclopedia of Genes and Genomes pathway analysis identified several differentially enriched biological functions and processes of the 2 muscles. Seven promising candidate genes [PMEL, Ras-related protein RAB29, and 5 solute carrier superfamily genes: SLC6A9, SLC38A4, SLC22A5, SLC35F3, and SLC16A3] may play an important role in the melanogenesis of chicken muscle. Our data provide a valuable resource for identifying genes whose functions are critical for muscle melanogenesis, and will assist studies of the molecular mechanisms of melanogenesis regulation in chicken muscle.
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Affiliation(s)
- Shigang Yu
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Gang Wang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Juan Liao
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Mei Tang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
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Two-exon skipping within MLPH is associated with coat color dilution in rabbits. PLoS One 2013; 8:e84525. [PMID: 24376820 PMCID: PMC3869861 DOI: 10.1371/journal.pone.0084525] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022] Open
Abstract
Coat color dilution turns black coat color to blue and red color to cream and is a characteristic in many mammalian species. Matings among Netherland Dwarf, Loh, and Lionhead Dwarf rabbits over two generations gave evidence for a monogenic autosomal recessive inheritance of coat colour dilution. Histological analyses showed non-uniformly distributed, large, agglomerating melanin granules in the hair bulbs of coat color diluted rabbits. We sequenced the cDNA of MLPH in two dilute and one black rabbit for polymorphism detection. In both color diluted rabbits, skipping of exons 3 and 4 was present resulting in altered amino acids at p.QGL[37-39]QWA and a premature stop codon at p.K40*. Sequencing of genomic DNA revealed a c.111-5C>A splice acceptor mutation within the polypyrimidine tract of intron 2 within MLPH. This mutation presumably causes skipping of exons 3 and 4. In 14/15 dilute rabbits, the c.111-5C>A mutation was homozygous and in a further dilute rabbit, heterozygous and in combination with a homozygous frame shift mutation within exon 6 (c.585delG). In conclusion, our results demonstrated a colour dilution associated MLPH splice variant causing a strongly truncated protein (p.Q37QfsX4). An involvement of further MLPH-associated mutations needs further investigations.
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Bed'hom B, Vaez M, Coville JL, Gourichon D, Chastel O, Follett S, Burke T, Minvielle F. The lavender plumage colour in Japanese quail is associated with a complex mutation in the region of MLPH that is related to differences in growth, feed consumption and body temperature. BMC Genomics 2012; 13:442. [PMID: 22937744 PMCID: PMC3484014 DOI: 10.1186/1471-2164-13-442] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 08/25/2012] [Indexed: 01/08/2023] Open
Abstract
Background The lavender phenotype in quail is a dilution of both eumelanin and phaeomelanin in feathers that produces a blue-grey colour on a wild-type feather pattern background. It has been previously demonstrated by intergeneric hybridization that the lavender mutation in quail is homologous to the same phenotype in chicken, which is caused by a single base-pair change in exon 1 of MLPH. Results In this study, we have shown that a mutation of MLPH is also associated with feather colour dilution in quail, but that the mutational event is extremely different. In this species, the lavender phenotype is associated with a non-lethal complex mutation involving three consecutive overlapping chromosomal changes (two inversions and one deletion) that have consequences on the genomic organization of four genes (MLPH and the neighbouring PRLH, RAB17 and LRRFIP1). The deletion of PRLH has no effect on the level of circulating prolactin. Lavender birds have lighter body weight, lower body temperature and increased feed consumption and residual feed intake than wild-type plumage quail, indicating that this complex mutation is affecting the metabolism and the regulation of homeothermy. Conclusions An extensive overlapping chromosome rearrangement was associated with a non-pathological Mendelian trait and minor, non deleterious effects in the lavender Japanese quail which is a natural knockout for PRLH.
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Affiliation(s)
- Bertrand Bed'hom
- UMR 1313 INRA/AgroParisTech, Génétique Animale et Biologie Intégrative GABI, 78352 Jouy-en-Josas, France
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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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