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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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Brown AR, Comai K, Mannino D, McCullough H, Donekal Y, Meyers HC, Graves CW, Seidel HS. A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius). PLoS One 2022; 17:e0276376. [PMID: 36260636 PMCID: PMC9581371 DOI: 10.1371/journal.pone.0276376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Color morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs-Albino, Lavender Albino, and Ultramel-show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.
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Affiliation(s)
- Autumn R. Brown
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Kaylee Comai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Dominic Mannino
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Haily McCullough
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Yamini Donekal
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Hunter C. Meyers
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Chiron W. Graves
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
- * E-mail: (CWG); (HSS)
| | - Hannah S. Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
- * E-mail: (CWG); (HSS)
| | - The BIO306W Consortium
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
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3
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Guo Y, Ou J, Zan Y, Wang Y, Li H, Zhu C, Chen K, Zhou X, Hu X, Carlborg Ö. Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history. Evol Appl 2022; 15:553-564. [PMID: 35505888 PMCID: PMC9046761 DOI: 10.1111/eva.13241] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In-depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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Affiliation(s)
- Ying Guo
- State Key Laboratory for Agro‐BiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthChina Agricultural UniversityBeijingChina
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Jen‐Hsiang Ou
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Yanjun Zan
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Yuzhe Wang
- State Key Laboratory for Agro‐BiotechnologyChina Agricultural UniversityBeijingChina
| | - Huifang Li
- Jiangsu Institute of Poultry ScienceYangzhouChina
| | - Chunhong Zhu
- Jiangsu Institute of Poultry ScienceYangzhouChina
| | - Kuanwei Chen
- Jiangsu Institute of Poultry ScienceYangzhouChina
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthChina Agricultural UniversityBeijingChina
| | - Xiaoxiang Hu
- State Key Laboratory for Agro‐BiotechnologyChina Agricultural UniversityBeijingChina
- National Engineering Laboratory for Animal BreedingChina Agricultural UniversityBeijingChina
| | - Örjan Carlborg
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
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4
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Kulikova IV. Molecular Mechanisms and Gene Regulation of Melanic Plumage Coloration in Birds. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542108007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Behjatian Esfahani M, Moravej H, Ghaffarzadeh M, Nehzati Paghaleh GA. Comparison the Zn-Threonine, Zn-Methionine, and Zn Oxide on Performance, Egg Quality, Zn Bioavailability, and Zn Content in Egg and Excreta of Laying Hens. Biol Trace Elem Res 2021; 199:292-304. [PMID: 32367378 DOI: 10.1007/s12011-020-02141-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 03/31/2020] [Indexed: 11/26/2022]
Abstract
The experiment was conducted to investigate the effect of supplementary zinc-threonine (Zn-Thr), zinc-methionine (Zn-Met), and zinc oxide (ZnO) on the laying performance, egg quality, Zn content in egg and excreta. One hundred and sixty hens (Hy-Line W36) were randomly divided into 10 treatments with 4 replications of 4 hens each. During the first 4 weeks, groups were fed a corn-soy basal diet without extra zinc (30.3 mg Zn/kg diet) to depletion storage zinc from the body and it was used as the control diet. During the ensuing 10 weeks from 36 to 45 weeks of age, 3 levels of 30, 60, and 90 mg Zn/kg were added to the diet by ZnO, Zn-Met, and Zn-Thr sources. Results showed that there were no significant differences between the experimental treatments in terms of egg weight, feed intake, eggshell weight, eggshell percentage, and albumen weight. In total experimental period, the supplementation of Zn-Met and Zn-Thr decreased feed conversion ratio and increased egg mass and egg production compared with ZnO 30 and 60 mg Zn/kg and control treatments (P < 0.05). The results showed that treatment effect on Zn content in egg and excreta was significant (P < 0.05). It is concluded that diets supplied with lower levels of organic Zn can maintain egg production performance, improve egg quality, enrich eggs, increase bioavailability, and reduce the negative effects of age on egg quality characteristics in laying hens compared with their oxide form.
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Affiliation(s)
| | - Hossein Moravej
- College of Agriculture & Natural Resources, Department of Animal Science, University of Tehran, Karaj, Iran.
| | - Mohammad Ghaffarzadeh
- Chemistry and Chemical Engineering Research Center of Iran, Po Box 14335-186, Tehran, Iran
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6
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Adetula AA, Liu X, Yang L, Fang C, Yu H, Li H, Li S. RAI14 in the blood feather regulates chicken pigmentation. Arch Anim Breed 2020; 63:231-239. [PMID: 34084896 PMCID: PMC8161265 DOI: 10.5194/aab-63-231-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 06/12/2020] [Indexed: 01/11/2023] Open
Abstract
A genome-wide association study (GWAS) was performed on a resource
family consisting of white and colored chickens for identification of genes
related to plumage coloration using the Fixed and random model Circulating
Probability Unification (FarmCPU) package. GWAS identified three chromosomal
single-nucleotide polymorphisms (SNPs), demonstrating the polygenic basis of
plumage phenotypes. Herein, retinoic acid-induced protein 14 (RAI14), a developmentally
regulated gene that encodes a protein containing many ankyrin repeats, was
identified as a candidate gene involved in plumage color. In this study,
mRNA expression profiles of chicken RAI14 were determined, indel (insertion–deletion) variants were
identified, and their association was analyzed in white and colored
chickens. RA114 mRNA was expressed in all tissues tested (brain, spleen, liver,
heart, oviduct, kidney, lung, pituitary gland, ovary, muscle, feather bulb,
and skin). A relatively high RAI14 expression in white feather bulb compared to
colored feather bulb (P<0.01) indicated a potential association with plumage
color. Additionally, statistical analysis revealed that a 4 bp indel genetic
variation in RAI14 was associated with plumage phenotypes (P<0.01).
Together, our analysis of the identification of the RAI14 gene will enable us to
understand the genetic mechanisms behind chicken pigmentation.
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Affiliation(s)
- Adeyinka Abiola Adetula
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Shenzhen, China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liubin Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hui Yu
- College of Life Science, Foshan University, Foshan, Guangdong, China
| | - Hua Li
- College of Life Science, Foshan University, Foshan, Guangdong, China
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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7
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Affiliation(s)
- M. Tixier-Boichard
- Institut National de la Recherche Agronomique, Département de Génétique Animale, Laboratoire de Génétique Factorielle, 78352 Jouy-en-Josas Cedex, France,
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8
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Yu S, Wang G, Liao J. Association of a novel SNP in the ASIP gene with skin color in black-bone chicken. Anim Genet 2019; 50:283-286. [PMID: 30883845 DOI: 10.1111/age.12768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2018] [Indexed: 11/28/2022]
Abstract
The agouti signaling protein gene (ASIP) is a widely studied pigmentation gene that plays an important role in melanin synthesis. To determine the variety of ASIP expression in the Muchuan Black-Bone chicken, we examined genetic variation in the ASIP promoter region. A single nucleotide polymorphism (c.-1826A>T) was found to be associated with the skin color (dorsal and subalar) of black-bone chicken. Individuals with TT and AT genotypes had higher ASIP mRNA levels in the skin than did those with the AA genotype (P < 0.01). In addition, individuals with the TT genotype had higher ASIP mRNA levels than did those with the AT genotype (P < 0.05). Expression of melanogenesis-related genes (melanocortin 1 receptor and tyrosinase genes) was higher in the skin of chickens with the TT and AT genotypes than in those with the AA genotype (P < 0.01). A luciferase assay showed that promoter activity was higher in chickens with the TT genotype than in those with the AA genotype. Putative transcription factor prediction suggested that the c.-1826A>T mutation might shift the promoter binding affinity with differential transcription factors. In summary, we identified a novel mutation in the ASIP gene promoter that may affect chicken skin color by altering ASIP transcriptional activity.
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Affiliation(s)
- S 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
| | - G 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
| | - J 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
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9
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Nunome M, Kinoshita K, Ishishita S, Ohmori Y, Murai A, Matsuda Y. Genetic diversity of 21 experimental chicken lines with diverse origins and genetic backgrounds. Exp Anim 2018; 68:177-193. [PMID: 30542001 PMCID: PMC6511517 DOI: 10.1538/expanim.18-0139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The genetic characteristics and diversity of 21 experimental chicken lines registered with the National BioResource Project of Japan were examined using mitochondrial D-loop sequences and 54 microsatellite DNA markers. A total of 12 haplotypes were detected in the 500-bp mitochondrial DNA sequences of the hypervariable segment I for 349 individuals of 21 lines. The 12 haplotypes belonged to three (A, D, and E) haplogroups, out of the eight (A‒H) common haplogroups in domestic chickens and red junglefowls. The haplogroups A and D were widely represented in indigenous chickens in the Asian and Pacific regions, and the haplogroup E was the most prevalent in domestic chickens. Genetic clustering by discriminant analysis of principal components with microsatellite markers divided 681 individuals of 21 lines into three groups that consisted of Fayoumi-, European-, and Asian- derived lines. In each of the cladograms constructed with Nei's genetic distances based on allele frequencies and the membership coefficients provided by STRUCTURE and with the genetic distance based on the proportion of shared alleles, the genetic relationships coincided well with the breeding histories of the lines. Microsatellite markers showed remarkably lower genetic heterozygosities (less than 0.1 observed heterozygosity) for eight lines (GSP, GSN/1, YL, PNP, BM-C, WL-G, BL-E, and #413), which have been maintained as closed colonies for more than 40 years (except for #413), indicating their usefulness as experimental chicken lines in laboratory animal science research.
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Affiliation(s)
- Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Satoshi Ishishita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yasushige Ohmori
- Laboratory of Animal Morphology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Atsushi Murai
- Laboratory of Nutrition Science, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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Feather follicles transcriptome profiles in Bashang long-tailed chickens with different plumage colors. Genes Genomics 2018; 41:1357-1367. [PMID: 30229509 DOI: 10.1007/s13258-018-0740-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/01/2018] [Indexed: 01/05/2023]
Abstract
Despite the rich variety in plumage color found in nature, genetic studies on how feather follicles affect pigmentation are often limited to animals that have black and white pigment. To test how gene expression influences plumage color, transcriptomes of chicken feather follicles with white, black, hemp, reed catkins, silvery grey, and landscape plumage colors were generated using Illumina sequencing. We generated six RNA-Seq libraries with over 25 million paired-end clean reads per library with percentage of paired-end clean reads ranging from 96.73 to 96.98%. 78% of the reads mapped to the chicken genome, and approximately 70% of the reads were mapped to exons and 6% mapped to introns. Transcriptomes of feather follicles producing hemp and land plumage were similar, but these two showed moderate differences compared with gray and reed colored plumage. The black and white follicle transcriptomes were most divergent from the other colors. We identified several candidate genes, including GPNMB, PMEL, TYRP1, GPR143, OCA2, SOX10, SLC45A2, KRT75, and TYR. All of these genes are known to induce pigment formation in mice. White feathers result from the lack of pigment formation, and our results suggest that the white chickens due to the recessive insertion mutation of TYR. The formation of black area size and color depth may be due to the expression levels of GPNMB, PMEL, TYRP1, GPR143, OCA2, SOX10, SLC45A2, KRT75, and TYR. The GO analysis of the differentially expressed genes (DEGs) revealed that DEGs in our transcriptome analysis were enriched in cytoskeleton and cell structure related pathways. The black plumage transcriptome showed significant differences in melanogenesis, tyrosine metabolism, and riboflavin metabolism compared with transcriptomes of other plumage colors. The transcriptome profiles of the different chicken plumage colors provide a valuable resource to understand how gene expression influences plumage color, and will be an important resource for identifying candidate genes in breeding programs.
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11
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Zhang XT, Wei KJ, Chen YY, Shi ZC, Liu LK, Li J, Zhang GR, Ji W. Molecular cloning and expression analysis of tyr and tyrp1 genes in normal and albino yellow catfish Tachysurus fulvidraco. JOURNAL OF FISH BIOLOGY 2018; 92:979-998. [PMID: 29460483 DOI: 10.1111/jfb.13556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/08/2018] [Indexed: 06/08/2023]
Abstract
The full-length complementary DNA of two genes related to vertebrate albinism, the tyrosinase gene tyr and tyrosinase-related protein 1 gene tyrp1, were cloned and analysed from normal and albino yellow catfish Tachysurus fulvidraco. The open reading frames (ORF) of tyr and tyrp1 encode putative peptides of 533 and 526 amino acids (amino-acid), both of which possess two conserved copper binding sites. The homologous identities of deduced amino-acid sequences showed that both Tyr and Tyrp1 of T. fulvidraco share considerable similarity with that of channel catfish Ictalurus punctatus. Both tyr and tyrp1 were expressed in a wide range of adult tissues. Tyr gene had the highest expression level in the brain of both normal and albino T. fulvidraco. Tyrp1 had the highest expression level in the skin of normal groups, and the fin of albino groups. The messenger (m)RNA expressions of tyr and tyrp1 were detectable at different early developmental stages and varied with embryonic and larval growth. Tyr and tyrp1 mRNA have obvious tissue specificity both in normal and albino T. fulvidraco and higher expression levels were detected in the normal group revealing that tyr and tyrp1 may have an important role in pigmentation. These results will provide useful data for understanding the molecular mechanism of melanin formation and the occurrence of albinism in T. fulvidraco.
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Affiliation(s)
- X T Zhang
- Department of Aquatic Animal Medicines, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - K J Wei
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Y Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Z C Shi
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - L K Liu
- Department of Aquatic Animal Medicines, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - J Li
- Department of Aquatic Animal Medicines, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - G R Zhang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - W Ji
- Department of Aquatic Animal Medicines, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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12
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Yu S, Liao J, Tang M, Wang Y, Wei X, Mao L, Zeng C, Wang G. A functional single nucleotide polymorphism in the tyrosinase gene promoter affects skin color and transcription activity in the black-boned chicken. Poult Sci 2017; 96:4061-4067. [DOI: 10.3382/ps/pex217] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/22/2017] [Indexed: 12/14/2022] Open
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13
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Wang Y, Li SM, Huang J, Chen SY, Liu YP. Mutations of TYR and MITF Genes are Associated with Plumage Colour Phenotypes in Geese. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:778-83. [PMID: 25050014 PMCID: PMC4093182 DOI: 10.5713/ajas.2013.13350] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/25/2013] [Accepted: 01/08/2014] [Indexed: 12/29/2022]
Abstract
The polymorphism of microphthalmia-associated transcription factor (MITF) and tyrosinase (TYR) genes have been proposed to play a vital role in coat colour genesis in mammals, but their role remains ambiguous in geese at best. Here, we cloned and sequenced 1,397 bp coding region of MITF gene and a 588 bp fragment of TYR exon 1 for polymorphism analysis among 157 domestic geese showing three types of plumage colour. We detected a total of three SNPs (c.280T>C, c.345G>A, and c.369G>A) in TYR and six haplotypes (H1–H6). Among them, haplotypes H1, H2, H3, and H5 were significantly associated with white plumage trait of Zhedong White Geese. However, only diplotype H1H1 and H3H5 were significantly associated with white plumage trait of Zhedong White Geese (p<0.01). We only detected one SNP (c.1109C>T) for MITF gene and found that genotype CT and TT were significantly associated with white plumage trait of Zhedong White Geese. Briefly, our study suggested an association between polymorphisms of TYR and MITF genes and the plumage colour trait in domestic geese.
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Affiliation(s)
- Ye Wang
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang, Jiangxi 330200, China
| | - Si-Ming Li
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang, Jiangxi 330200, China
| | - Jing Huang
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang, Jiangxi 330200, China
| | - Shi-Yi Chen
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang, Jiangxi 330200, China
| | - Yi-Ping Liu
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang, Jiangxi 330200, China
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Kinoshita K, Akiyama T, Mizutani M, Shinomiya A, Ishikawa A, Younis HH, Tsudzuki M, Namikawa T, Matsuda Y. Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w) ) and mottled (mo) plumage phenotypes in the chicken. PLoS One 2014; 9:e86361. [PMID: 24466053 PMCID: PMC3900529 DOI: 10.1371/journal.pone.0086361] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/08/2013] [Indexed: 12/03/2022] Open
Abstract
A mutation that confers white plumage with black eyes was identified in the Minohiki breed of Japanese native chicken (Gallus gallus domesticus). The white plumage, with a few partially pigmented feathers, was not associated with the tyrosinase gene, and displayed an autosomal recessive mode of inheritance against the pigmented phenotype. All F1 offspring derived from crosses with mottled chickens (mo/mo), which show characteristic pigmented feathers with white tips, had plumage with a mottled-like pattern. This result indicates that the white plumage mutation is a novel allele at the mo locus; we propose the gene symbol mo(w) for this mutant allele. Furthermore, the F1 hybrid between the mo(w) /mo(w) chicken and the panda (s/s) mutant of Japanese quail (Coturnix japonica), whose causative gene is the endothelin receptor B2 (EDNRB2) gene, showed a mo(w)/mo(w) chicken-like plumage, suggesting the possibility that the mutations in parental species are alleles of the same gene, EDNRB2. Nucleotide sequencing of the entire coding region of EDNRB2 revealed a non-synonymous G1008T substitution, which causes Cys244Phe amino acid substitution in exon 5 (which is part of the extracellular loop between the putative fourth and fifth transmembrane domains of EDNRB2) in the mutant chicken. This Cys244Phe mutation was also present in individuals of four Japanese breeds with white plumage. We also identified a non-synonymous substitution leading to Arg332His substitution that was responsible for the mottled (mo/mo) plumage phenotype. These results suggest that the EDN3 (endothelin 3)-EDNRB2 signaling is essential for normal pigmentation in birds, and that the mutations of EDNRB2 may cause defective binding of the protein with endothelins, which interferes with melanocyte differentiation, proliferation, and migration.
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Affiliation(s)
- Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Makoto Mizutani
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ai Shinomiya
- Department of Biology, Keio University, Yokohama, Japan
| | - Akira Ishikawa
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hassan Hassan Younis
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Poultry Production, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takao Namikawa
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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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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Damé MCF, Xavier GM, Oliveira-Filho JP, Borges AS, Oliveira HN, Riet-Correa F, Schild AL. A nonsense mutation in the tyrosinase gene causes albinism in water buffalo. BMC Genet 2012; 13:62. [PMID: 22817390 PMCID: PMC3411452 DOI: 10.1186/1471-2156-13-62] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 07/20/2012] [Indexed: 11/29/2022] Open
Abstract
Background Oculocutaneous albinism (OCA) is an autosomal recessive hereditary pigmentation disorder affecting humans and several other animal species. Oculocutaneous albinism was studied in a herd of Murrah buffalo to determine the clinical presentation and genetic basis of albinism in this species. Results Clinical examinations and pedigree analysis were performed in an affected herd, and wild-type and OCA tyrosinase mRNA sequences were obtained. The main clinical findings were photophobia and a lack of pigmentation of the hair, skin, horns, hooves, mucosa, and iris. The results of segregation analysis suggest that this disease is acquired through recessive inheritance. In the OCA buffalo, a single-base substitution was detected at nucleotide 1,431 (G to A), which leads to the conversion of tryptophan into a stop codon at residue 477. Conclusion This premature stop codon produces an inactive protein, which is responsible for the OCA buffalo phenotype. These findings will be useful for future studies of albinism in buffalo and as a possible model to study diseases caused by a premature stop codon.
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Li S, Wang C, Yu W, Zhao S, Gong Y. Identification of genes related to white and black plumage formation by RNA-Seq from white and black feather bulbs in ducks. PLoS One 2012; 7:e36592. [PMID: 22615785 PMCID: PMC3352928 DOI: 10.1371/journal.pone.0036592] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/03/2012] [Indexed: 01/19/2023] Open
Abstract
To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F(2) population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck.
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Affiliation(s)
- Shijun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Cui Wang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenhua Yu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanzhang Gong
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
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Abstract
During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat-colour-associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat-colour variants. Recent studies demonstrate that this selection for coat-colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat-colour-associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat-colour-associated genes act.
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Affiliation(s)
- Michael Cieslak
- Leibniz Institute for Zoo and Wildlife Research, Research Group of Evolutionary Genetics, Berlin, Germany
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Jorge W, Cunha LM. Inheritance of a new albino mutation in Brazilian free-range black chickens. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2008. [DOI: 10.1590/s1516-635x2008000300003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- W Jorge
- Universidade Federal de Minas Gerais
| | - LM Cunha
- Universidade Federal de Minas Gerais
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Sato S, Otake T, Suzuki C, Saburi J, Kobayashi E. Mapping of the Recessive White Locus and Analysis of the Tyrosinase Gene in Chickens. Poult Sci 2007; 86:2126-33. [PMID: 17878441 DOI: 10.1093/ps/86.10.2126] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
An F(2) chicken population of 265 individuals, obtained from an intercross between the Japanese Game (colored plumage) and the White Plymouth Rock (the recessive white) and genotyped for microsatellite markers, was used for determining the locus of the gene responsible for the recessive white plumage phenotype in chickens. Two hundred twenty-five markers were mapped in 28 linkage groups. Linkage analysis revealed that the recessive white gene was mapped to chromosome 1. Detailed analysis using additional markers uncovered a significant linkage between 2 new markers, mapped to the flanking region of the tyrosinase gene, which is associated with skin and plumage color. The sequence of the tyrosinase gene was investigated in recessive white chickens and colored chickens. There were no obvious differences in the tyrosinase gene exons between the recessive white chicken and the colored chicken. However, sequence analysis of tyrosinase intron 4 in the recessive white chicken revealed a presence of an insertion of an avian retroviral sequence. The White Plymouth Rock and the F(2) generation with white plumage were identified as homozygous carriers of the retroviral sequence. Expression of the normal transcript containing exon 5 was substantially decreased in the recessive white chicken compared with the colored chicken. Some abnormal tyrosinase gene transcripts were expressed in the skin of the White Plymouth Rock: reverse transcription PCR products amplified from exon 3 to intron 4 and from retroviral sequence 3' long terminal repeat to exon 5. Based on these results, it was confirmed that an avian retroviral sequence insertion in the tyrosinase gene was the cause of recessive white phenotype in chickens.
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Affiliation(s)
- S Sato
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan
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Rymer J, Choh V, Bharadwaj S, Padmanabhan V, Modilevsky L, Jovanovich E, Yeh B, Zhang Z, Guan H, Payne W, Wildsoet CF. The albino chick as a model for studying ocular developmental anomalies, including refractive errors, associated with albinism. Exp Eye Res 2007; 85:431-42. [PMID: 17651735 PMCID: PMC2072995 DOI: 10.1016/j.exer.2007.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Revised: 06/06/2007] [Accepted: 06/12/2007] [Indexed: 11/22/2022]
Abstract
Albinism is associated with a variety of ocular anomalies including refractive errors. The purpose of this study was to investigate the ocular development of an albino chick line. The ocular development of both albino and normally pigmented chicks was monitored using retinoscopy to measure refractive errors and high frequency A-scan ultrasonography to measure axial ocular dimensions. Functional tests included an optokinetic nystagmus paradigm to assess visual acuity, and flash ERGs to assess retinal function. The underlying genetic abnormality was characterized using a gene microarray, PCR and a tyrosinase assay. The ultrastructure of the retinal pigment epithelium (RPE) was examined using transmission electron microscopy. PCR confirmed that the genetic abnormality in this line is a deletion in exon 1 of the tyrosinase gene. Tyrosinase gene expression in isolated RPE cells was minimally detectable, and there was minimal enzyme activity in albino feather bulbs. The albino chicks had pink eyes and their eyes transilluminated, reflecting the lack of melanin in all ocular tissues. All three main components, anterior chamber, crystalline lens and vitreous chamber, showed axial expansion over time in both normal and albino animals, but the anterior chambers of albino chicks were consistently shallower than those of normal chicks, while in contrast, their vitreous chambers were longer. Albino chicks remained relatively myopic, with higher astigmatism than the normally pigmented chicks, even though both groups underwent developmental emmetropization. Albino chicks had reduced visual acuity yet the ERG a- and b-wave components had larger amplitudes and shorter than normal implicit times. Developmental emmetropization occurs in the albino chick but is impaired, likely because of functional abnormalities in the RPE and/or retina as well as optical factors. In very young chicks the underlying genetic mutation may also contribute to refractive error and eye shape abnormalities.
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Affiliation(s)
- Jodi Rymer
- Wildsoet Lab, 588 Minor Hall, University of California-Berkeley, Berkeley CA 94720-2020, USA.
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Chang CM, Furet JP, Coville JL, Coquerelle G, Gourichon D, Tixier-Boichard M. Quantitative effects of an intronic retroviral insertion on the transcription of the tyrosinase gene in recessive white chickens. Anim Genet 2007; 38:162-7. [PMID: 17355394 DOI: 10.1111/j.1365-2052.2007.01581.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recently, we reported the complete association of a retroviral insertion in intron 4 of the tyrosinase gene and the recessive white mutation (c) in chickens. The mutant allele carrying the retroviral insertion produced, in skin samples of 10-week-old chickens, aberrant tyrosinase transcripts that did not contain exon 5. In the present study, we performed serial molecular and statistical analyses on embryos and 10-week-old chickens to characterize the quantitative effect of the retroviral insertion on the expression pattern of tyrosinase in different tissues (skin and retina). By using quantitative real-time RT-PCR, we observed that the expression level of tyrosinase was significantly lower in recessive white chickens than in wild-type coloured chickens, but that this pattern was age- and tissue-dependent. The differential expression in skin was not significant in embryos, whereas it was highly significant in 10-week-old chickens. Furthermore, there was no difference in the expression of tyrosinase in the retinal pigment epithelium of animals with different genotypes; this corresponds to phenotypic data, which show pigmented eyes in both genotypes. These findings show that the retroviral insertion disturbs tyrosinase expression in the recessive white mutant chickens, and suggests that the regulation of tyrosinase expression in chickens differs between embryos and growing animals, as well as between skin and retina.
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Affiliation(s)
- C M Chang
- UMR Génétique et Diversité Animales, INRA/INA P-G, Centre de Recherches de Jouy, 78352 Jouy-en-Josas, France.
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25
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Chang CM, Coville JL, Coquerelle G, Gourichon D, Oulmouden A, Tixier-Boichard M. Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens. BMC Genomics 2006; 7:19. [PMID: 16457736 PMCID: PMC1373650 DOI: 10.1186/1471-2164-7-19] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 02/05/2006] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In chickens, three mutant alleles have been reported at the C locus, including the albino mutation, and the recessive white mutation, which is characterized by white plumage and pigmented eyes. The albino mutation was found to be a 6 bp deletion in the tyrosinase (TYR) gene. The present work describes an approach to identify the structural rearrangement in the TYR gene associated with the recessive white mutation. RESULTS Molecular analysis of the chicken TYR gene has revealed a major structural difference (Restriction Fragment Length Polymorphism, RFLP) in the genomic DNA of the recessive white chicken. A major size difference of 7.7 kb was found in intron 4 of the TYR gene by long-range PCR. Molecular cloning and sequencing results showed the insertion of a complete avian retroviral sequence of the Avian Leukosis Virus (ALV) family. Several aberrant transcripts of the tyrosinase gene were found in 10 week old recessive white chickens but not in the homozygous wild type colored chicken. We established a rapid genotyping diagnostic test based on the discovery of this retroviral insertion. It shows that all homozygous carriers of this insertion had a white plumage in various chicken strains. Furthermore, it was possible to distinguish heterozygous carriers from homozygous normal chickens in a segregating line. CONCLUSION In this study, we conclude that the insertion of a complete avian retroviral sequence in intron 4 of the tyrosinase gene is diagnostic of the recessive white mutation in chickens. This insertion causes aberrant transcripts lacking exon 5, and we propose that this insertion is the causal mutation for the recessive white allele in the chicken.
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Affiliation(s)
- Chung-Ming Chang
- UMR Génétique et Diversité Animales, INRA/INA P-G, Centre de Recherches de Jouy, 78352 Jouy-en-Josas, France
| | - Jean-Luc Coville
- UMR Génétique et Diversité Animales, INRA/INA P-G, Centre de Recherches de Jouy, 78352 Jouy-en-Josas, France
| | - Gérard Coquerelle
- UMR Génétique et Diversité Animales, INRA/INA P-G, Centre de Recherches de Jouy, 78352 Jouy-en-Josas, France
| | - David Gourichon
- Unité Expérimentale de Génétique Factorielle Avicole, INRA, Centre de Recherches de Tours, 37380 Nouzilly, France
| | - Ahmad Oulmouden
- UMR Génétique Moléculaire Animale, INRA/Université de Limoges, 87061 Limoges, France
| | - Michèle Tixier-Boichard
- UMR Génétique et Diversité Animales, INRA/INA P-G, Centre de Recherches de Jouy, 78352 Jouy-en-Josas, France
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Andersson L, Georges M. Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet 2004; 5:202-12. [PMID: 14970822 DOI: 10.1038/nrg1294] [Citation(s) in RCA: 350] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden.
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Norman JA, Christidis L, Joseph L, Slikas B, Alpers D. Unravelling a biogeographical knot: origin of the 'leapfrog' distribution pattern of Australo-Papuan sooty owls (Strigiformes) and logrunners (Passeriformes). Proc Biol Sci 2002; 269:2127-33. [PMID: 12396487 PMCID: PMC1691145 DOI: 10.1098/rspb.2002.2136] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular analysis of two Australo-Papuan rainforest birds exhibiting correlated 'leapfrog' patterns were used to elucidate the evolutionary origin of this unusual pattern of geographical differentiation. In both sooty owls (Tyto) and logrunners (Orthonyx), phenotypically similar populations occupy widely disjunct areas (central-eastern Australia and upland New Guinea) with a third, highly distinctive population, occurring between them in northeastern Queensland. Two mechanisms have been proposed to explain the origin of leapfrog patterns in avian distributions: recent shared ancestry of terminal populations and unequal rates or phenotypic change among populations. As the former should generate correlated patterns of phenotypic and genetic differentiation, we tested for a sister relationship between populations from New Guinea and central-eastern Australia using nuclear and mitochondrial DNA sequences. The resulting phylogenies not only refute recent ancestry as an explanation for the leapfrog pattern, but provide evidence of vastly different spatio-temporal histories for sooty owls and logrunners within the Australo-Papuan rainforests. This incongruence indicates that the evolutionary processes responsible for generating leapfrog patterns in these co-distributed taxa are complex, possibly involving a combination of selection and drift in sooty owls and convergence or retention of ancestral characteristics in logrunners.
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Affiliation(s)
- J A Norman
- Sciences Department, Museum Victoria, GPO Box 666E, Melbourne, Victoria 3001, Australia
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Schmidtz BH, Buchanan FC, Plante Y, Schmutz SM. Linkage mapping of the tyrosinase gene to bovine chromosome 29. Anim Genet 2001; 32:119-20. [PMID: 11421957 DOI: 10.1046/j.1365-2052.2001.0700j.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- B H Schmidtz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Canada
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