1
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Lin R, Li J, Zhao F, Zhou M, Wang J, Xiao T. Transcriptome analysis of genes potentially associated with white and black plumage formation in Chinese indigenous ducks ( Anas platyrhynchos). Br Poult Sci 2022; 63:466-474. [PMID: 35094630 DOI: 10.1080/00071668.2022.2035676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1. Plumage colour is an important recognisable characteristic of duck (Anas platyrhynchos), but the coloration mechanisms remain largely unknown. To elucidate the molecular mechanisms underlying the formation of black and white plumage, the following study applied RNA sequencing (RNA-Seq) to catalogue the global gene expression profiles in the duck feather bulbs of black and white colours.2. Black feather bulbs were collected from Putian Black ducks (B-PTB) and black Longsheng Jade-green ducks (B-LS), while white feather bulbs were collected from Putian White ducks (W-PTW), Putian Black ducks (W-PTB) and Longsheng Jade-green ducks (W-LS). Sixteen cDNA libraries were constructed and sequenced for transcriptional analysis. Three comparison groups were employed to analyse differentially expressed genes (DEGs), including W-PTB versus B-PTB, W-PTW versus B-PTB and W-LS versus B-LS.3. The results showed 180 DEGs between W-PTB and B-PTB, 303 DEGs between W-PTW and B-PTB, and 108 DEGs between W-LS and B-LS. Further analysis showed that 18 DEGs were directly involved in the pigmentation process and melanogenesis signalling pathway. Additionally, the distribution of DEGs varied amongst groups whereby ASIP appeared only in the W-LS versus B-LS group, GNAI1 and ZEB2 appeared only in the W-PTW versus B-PTB group, and KITLG, EDN3 and FZD4 appeared only in W-PTB versus B-PTB.4. The findings suggested that the mechanism of feather albinism may differ between duck breeds. This study provided new information for discovering genes that are important for feather pigmentation and helps elucidate molecular mechanisms involved in black and white plumage in ducks.
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Affiliation(s)
- Ruiyi Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaquan Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fanglu Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mai Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junhui Wang
- The Animal Husbandry Station in Fujian Province, Fuzhou, China
| | - Tianfang Xiao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Cho E, Kim M, Manjula P, Cho SH, Seo D, Lee SS, Lee JH. A retroviral insertion in the tyrosinase ( TYR) gene is associated with the recessive white plumage color in the Yeonsan Ogye chicken. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:751-758. [PMID: 34447952 PMCID: PMC8367395 DOI: 10.5187/jast.2021.e71] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 01/16/2023]
Abstract
The recessive white (locus c) phenotype observed in chickens is associated with three alleles (recessive white c, albino ca , and red-eyed white cre ) and causative mutations in the tyrosinase (TYR) gene. The recessive white mutation (c) inhibits the transcription of TYR exon 5 due to a retroviral sequence insertion in intron 4. In this study, we genotyped and sequenced the insertion in TYR intron 4 to identify the mutation causing the unusual white plumage of Yeonsan Ogye chickens, which normally have black plumage. The white chickens had a homozygous recessive white genotype that matched the sequence of the recessive white type, and the inserted sequence exhibited 98% identity with the avian leukosis virus ev-1 sequence. In comparison, brindle and normal chickens had the homozygous color genotype, and their sequences were the same as the wild-type sequence, indicating that this phenotype is derived from other mutation(s). In conclusion, white chickens have a recessive white mutation allele. Since the size of the sample used in this study was limited, further research through securing additional samples to perform validation studies is necessary. Therefore, after validation studies, a selection system for conserving the phenotypic characteristics and genetic diversity of the population could be established if additional studies to elucidate specific phenotype-related genes in Yeonsan Ogye are performed.
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Affiliation(s)
- Eunjin Cho
- Department of Bio-Big Data, Chungnam National University, Daejeon 34134, Korea
| | - Minjun Kim
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea
| | - Prabuddha Manjula
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Sung Hyun Cho
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Dongwon Seo
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea.,Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Seung-Sook Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea.,Jisan Farm, Nonsan 32910, Korea
| | - Jun Heon Lee
- Department of Bio-Big Data, Chungnam National University, Daejeon 34134, Korea.,Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea.,Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
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3
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Zheng X, Zhang B, Zhang Y, Zhong H, Nie R, Li J, Zhang H, Wu C. Transcriptome analysis of feather follicles reveals candidate genes and pathways associated with pheomelanin pigmentation in chickens. Sci Rep 2020; 10:12088. [PMID: 32694523 PMCID: PMC7374586 DOI: 10.1038/s41598-020-68931-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/03/2020] [Indexed: 11/20/2022] Open
Abstract
Yellow plumage is common in chickens, especially in breeds such as the Huiyang Bearded chicken, which is indigenous to China. We evaluated plumage colour distribution in F1, F2, and F3 populations of an Huiyang Bearded chicken × White Leghorn chicken cross, the heredity of the yellow plumage trait was distinguished from that of the gold plumage and other known plumage colours. Microscopic analysis of the feather follicles indicated that pheomelanin particles were formed in yellow but not in white feathers. To screen genes related to formation of the pheomelanin particles, we generated transcriptome data from yellow and white feather follicles from 7- and 11-week-old F3 chickens using RNA-seq. We identified 27 differentially expressed genes (DEGs) when comparing the yellow and white feather follicles. These DEGs were enriched in the Gene Ontology classes ‘melanosome’ and ‘melanosome organization’ related to the pigmentation process. Down-regulation of TYRP1, DCT, PMEL, MLANA, and HPGDS, verified using quantitative reverse transcription PCR, may lead to reduced eumelanin and increased pheomelanin synthesis in yellow plumage. Owing to the presence of the Dominant white locus, both white and yellow plumage lack eumelanin, and white feathers showed no pigments. Our results provide an understanding of yellow plumage formation in chickens.
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Affiliation(s)
- Xiaotong Zheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ruixue Nie
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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4
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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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5
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Sun L, Zhou T, Wan QH, Fang SG. Transcriptome Comparison Reveals Key Components of Nuptial Plumage Coloration in Crested Ibis. Biomolecules 2020; 10:biom10060905. [PMID: 32549189 PMCID: PMC7356354 DOI: 10.3390/biom10060905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/02/2020] [Accepted: 06/13/2020] [Indexed: 11/16/2022] Open
Abstract
Nuptial plumage coloration is critical in the mating choice of the crested ibis. This species has a characteristic nuptial plumage that develops from the application of a black sticky substance, secreted by a patch of skin in the throat and neck region. We aimed to identify the genes regulating its coloring, by comparing skin transcriptomes between ibises during the breeding and nonbreeding seasons. In breeding season skins, key eumelanin synthesis genes, TYR, DCT, and TYRP1 were upregulated. Tyrosine metabolism, which is closely related to melanin synthesis, was also upregulated, as were transporter proteins belonging to multiple SLC families, which might act during melanosome transportation to keratinocytes. These results indicate that eumelanin is likely an important component of the black substance. In addition, we observed upregulation in lipid metabolism in breeding season skins. We suggest that the lipids contribute to an oil base, which imbues the black substance with water insolubility and enhances its adhesion to feather surfaces. In nonbreeding season skins, we observed upregulation in cell adhesion molecules, which play critical roles in cell interactions. A number of molecules involved in innervation and angiogenesis were upregulated, indicating an ongoing expansion of nerves and blood vessels in sampled skins. Feather β keratin, a basic component of avian feather filament, was also upregulated. These results are consistent with feather regeneration in the black skin of nonbreeding season ibises. Our results provide the first molecular evidence indicating that eumelanin is the key component of ibis coloration.
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Affiliation(s)
| | | | | | - Sheng-Guo Fang
- Correspondence: ; Tel.: +86-571-8820-6472; Fax: +86-571-8820-6473
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6
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Kabir MH, Takenouchi A, Haqani MI, Nakamura Y, Takeuchi S, Tsudzuki M. Discovery of a new nucleotide substitution in the MC1R gene and haplotype distribution in native and non-Japanese chicken breeds. Anim Genet 2020; 51:235-248. [PMID: 31977074 DOI: 10.1111/age.12906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 01/07/2023]
Abstract
Melanocortin 1-receptor (MC1R) is one of the major genes that controls chicken plumage colour. In this study, we investigated the sequence and haplotype distribution of the MC1R gene in native Japanese chickens, along with non-Japanese chicken breeds. In total, 732 and 155 chickens from 30 Japanese and eight non-Japanese breeds respectively were used. Three synonymous and 11 non-synonymous nucleotide substitutions were detected, resulting in 15 haplotypes (H0-H14). Of these, three were newly found haplotypes (H9, H13 and H14), of which one (H9) was composed of known substitutions C69T, T212C, G274A and G636A. The second one (H13) possessed newly found non-synonymous substitution C919G, apart from the known substitutions C69T, G178A, G274A, G636A and T637C. The third one (H14) comprised a newly discovered substitution C919G in addition to the known C69T, G274A and G409A substitutions. The homozygote for this new haplotype exhibited wt like plumage despite the presence of G274A. In addition to discovering a new nucleotide substitution (C919G) and three new haplotypes, we defined the plumage colour of the bird that was homozygous for the A644C substitution (H5 haplotype) as wheaten-like for the first time; although the substitution has been already reported, its effect was not revealed. Besides detecting the new plumage colour, we also confirmed that the A427G and G274A substitutions contribute in expressing brownish and black plumage colour respectively, as reported by the previous studies. Moreover, we confirmed that the buttercup allele does not express black plumage despite possessing a G274A substitution, under the suppression effect of A644C. In contrast, the birds homozygous for the birchen allele presented solid black plumage, which was contradictory to the previous reports. In conclusion, we revealed a large diversity in the MC1R gene of native Japanese chicken breeds, along with the discovery of a new non-synonymous nucleotide substitution (C919G) and three novel haplotypes (H9, H13 and H14).
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Affiliation(s)
- M H Kabir
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - A Takenouchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - M I Haqani
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Y Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - S Takeuchi
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan.,Graduate School of Natural Science and Technology, Okayama University, Okayama, Okayama, 700-8530, Japan
| | - M Tsudzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
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7
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Wang X, Li D, Song S, Zhang Y, Li Y, Wang X, Liu D, Zhang C, Cao Y, Fu Y, Han R, Li W, Liu X, Sun G, Li G, Tian Y, Li Z, Kang X. Combined transcriptomics and proteomics forecast analysis for potential genes regulating the Columbian plumage color in chickens. PLoS One 2019; 14:e0210850. [PMID: 31693656 PMCID: PMC6834273 DOI: 10.1371/journal.pone.0210850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 10/18/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Coloration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. "Yufen I" is a commercial egg-laying chicken breed in China that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the "Yufen I" H line. To elucidate the molecular mechanism underlying the pigmentation of Columbian plumage, this study utilizes high-throughput sequencing technology to compare the transcriptome and proteome differences in the follicular tissue of different feathers, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the "Yufen I" H line. RESULTS In this study, we identified a total of 21,306 genes and 5,203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Additionally, a specifically expressed MED23 gene and a differentially expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomyocyte adrenergic, calcium and cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that produced results similar to those from RNA-seq. In addition, we found that the expression of the MED23, FZD10, WNT7B and WNT11 genes peaked at approximately 8 weeks in the "Yufen I" H line, which is consistent with the molting cycle. As both groups showed significant differences in terms of the expression of the studied genes, this work opens up avenues for research in the future to assess their exact function in determining plumage color. CONCLUSION Common DEGs and DEPs were enriched in the melanogenesis pathway. MED23 and GNAQ were also reported to play a crucial role in melanin synthesis. In addition, this study is the first to reveal gene and protein variations in in the "Yufen I" H line during Columbian feather color development and to discover principal genes and proteins that will aid in functional genomics studies in the future. The results of the present study provide a significant conceptual basis for the future breeding schemes with the "Yufen I" H line and provide a basis for research on the mechanisms of feather pigmentation.
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Affiliation(s)
- Xinlei Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
- * E-mail: (XK); (ZJL); (XK)
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Sufang Song
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Yanhua Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuanfang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Danli Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- * E-mail: (XK); (ZJL); (XK)
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- * E-mail: (XK); (ZJL); (XK)
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8
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Li D, Wang X, Fu Y, Zhang C, Cao Y, Wang J, Zhang Y, Li Y, Chen Y, Li Z, Li W, Jiang R, Sun G, Tian Y, Li G, Kang X. Transcriptome Analysis of the Breast Muscle of Xichuan Black-Bone Chickens Under Tyrosine Supplementation Revealed the Mechanism of Tyrosine-Induced Melanin Deposition. Front Genet 2019; 10:457. [PMID: 31156710 PMCID: PMC6529781 DOI: 10.3389/fgene.2019.00457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/30/2019] [Indexed: 01/18/2023] Open
Abstract
The Xichuan black-bone chicken, which is a rare local chicken species in China, is an important genetic resource of black-bone chickens. Tyrosine can affect melanin production, but the molecular mechanism underlying tyrosine-induced melanin deposition in Xichuan black-bone chickens is poorly understood. Here, the blackness degree and melanin content of the breast muscle of Xichuan black-bone chickens fed a basic diet with five levels of added tyrosine (i.e., 0.2, 0.4, 0.6, 0.8, and 1.0%; these groups were denoted test groups I-V, respectively) were assessed, and the results showed that 0.8% tyrosine was the optimal level of added tyrosine. Moreover, the effects of tyrosine supplementation on the proliferation and tyrosinase content of melanocytes in Xichuan black-bone chickens were evaluated. The results revealed a dose-dependent relationship between tyrosine supplementation and melanocyte proliferation. In addition, 417 differentially expressed genes (DEGs), including 160 upregulated genes and 257 downregulated genes, were identified in a comparative analysis of the transcriptome profiles constructed using the pooled total RNA from breast muscle tissues of the control group and test group IV, respectively (fold change ≥2.0, P < 0.05). These DEGs were mainly involved in melanogenesis, the calcium signaling pathway, the Wnt signaling pathway, the mTOR signaling pathway, and vascular smooth muscle contraction. The pathway analysis of the DEGs identified some key genes associated with pigmentation, such as DCT and EDNRB2. In summary, the melanin content of breast muscle could be markedly enhanced by adding an appropriate amount of tyrosine to the diet of Xichuan black-bone chickens, and the EDNRB2-mediated molecular regulatory network could play a key role in the biological process of tyrosine-induced melanin deposition. These results have deepened the understanding of the molecular regulatory mechanism of melanin deposition in black-bone chickens and provide a basis for the regulation of nutrition and genetic breeding associated with melanin deposition in Xichuan black-bone chickens.
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Affiliation(s)
- Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xinlei Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jie Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yanhua Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yuanfang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yi Chen
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
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9
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Yu S, Wang G, Liao J, Tang M. Five alternative splicing variants of the TYR gene and their different roles in melanogenesis in the Muchuan black-boned chicken. Br Poult Sci 2018; 60:8-14. [PMID: 30293452 DOI: 10.1080/00071668.2018.1533633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
1. The TYR gene encodes tyrosinase, a multifunctional enzyme that is essential for melanin biosynthesis in melanocytes. This experiment involved the cloning and characterisation of the TYR gene in chicken. Five alternative splice variants were identified in the black feather bulb and designated as TYR-AS1, TYR-AS2, TYR-AS3, TYR-AS4 and TYR-AS5. 2. Among the 11 chicken tissues examined, the feather bulb, comb and skin showed higher levels of all TYR variants. All TYR variants were expressed at significantly different levels in black and white feather bulbs (P < 0.05) and may be involved in melanin formation in plumage. Only TYR-AS1, which plays an important role in muscle melanogenesis, was significantly differentially expressed between black and white muscle (P < 0.01). All TYR variants were expressed at significantly different levels in black and white skin (P < 0.01). 3. The mRNA expression levels of the 5 variants were closely associated with skin melanogenesis in the chicken. These findings provide new clues to the molecular mechanism of melanin formation in the Muchuan black-boned chicken.
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Affiliation(s)
- S Yu
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - G Wang
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - J Liao
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - M Tang
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
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10
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Ng CS, Li WH. Genetic and Molecular Basis of Feather Diversity in Birds. Genome Biol Evol 2018; 10:2572-2586. [PMID: 30169786 PMCID: PMC6171735 DOI: 10.1093/gbe/evy180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 12/16/2022] Open
Abstract
Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago
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11
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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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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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Bourgeois YXC, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Milá B, Thébaud C. Candidate Gene Analysis Suggests Untapped Genetic Complexity in Melanin-Based Pigmentation in Birds. J Hered 2016; 107:327-35. [PMID: 26995742 DOI: 10.1093/jhered/esw017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022] Open
Abstract
Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits 5 plumage color variants that can be grouped into 3 color forms which occupy discrete geographic regions in the lowlands of Réunion, and a fourth high-elevation form which comprises 2 color morphs (grey and brown) and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of 7 candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin, and SLC24A5 Of these 7 genes, 2 (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied are involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other nonmodel species.
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Affiliation(s)
- Yann X C Bourgeois
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá).
| | - Joris A M Bertrand
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Boris Delahaie
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Josselin Cornuault
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Thomas Duval
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Borja Milá
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Christophe Thébaud
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
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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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15
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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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Sohn SH, Park DB, Song HR, Cho EJ, Kang BS, Suh OS. Genotype Frequencies of the Sex-Linked Feathering and Their Phenotypes in Domestic Chicken Breeds for the Establishment of Auto-Sexing Strains. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.4.267] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Ekblom R, Farrell LL, Lank DB, Burke T. Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff. Ecol Evol 2012; 2:2485-505. [PMID: 23145334 PMCID: PMC3492775 DOI: 10.1002/ece3.370] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/01/2012] [Accepted: 08/08/2012] [Indexed: 12/16/2022] Open
Abstract
By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black- and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation.
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Affiliation(s)
- Robert Ekblom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University Norbyvägen 18 D, SE-75236, Uppsala, Sweden ; Department of Animal and Plant Sciences, University of Sheffield Sheffield, S10 2TN, UK
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18
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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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Sato S, Sato S, Otake T, Suzuki C, Uemoto Y, Saburi J, Hashimoto H, Kobayashi E. Sequence analysis of a pea comb locus on chicken chromosome 1. Anim Genet 2011; 41:659-61. [PMID: 20412124 DOI: 10.1111/j.1365-2052.2010.02048.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To facilitate gene identification, this study aimed to narrow the scope of the genome region affecting chicken comb type by using two bird populations. First, an F2 resource population was generated by crossing Japanese game fowl (Shamo; pea comb, P/p and P/P) with White Plymouth Rock (single comb, p/p). Comb types of the 240 F2 offspring produced by an F1 intercross between eight males and 57 females were segregated at a ratio of 3:1 (pea:single). The pea comb locus was mapped to a chromosomal region on Gallus gallus chromosome 1 that was flanked by microsatellite markers MCW0112, MCW0019 and ABR521. The second population (five-generation, n=1300 animals) was derived from a cross between Shamo and Rhode Island Red (single comb, p/p) that had been genotyped for additional polymorphic single nucleotide polymorphisms and microsatellite markers within this region through development of chicken draft sequences. To close some gaps in these draft sequences, we constructed a bacterial artificial chromosome contig and sequenced it using the shotgun sequencing technique. Chickens selected from pedigrees in these populations were grouped by inheritance of a P or p haplotype at the locus constructed by the additional markers. Finally, this locus was fine-mapped to roughly 60 kb based on the association of haplotypes and comb types. Chicken genome sequences suggest that the most likely polymorphism responsible for the pea comb locus is a duplicated sequence and that the sex determining region Y-box 5 gene, one predicted gene and one expressed sequence tag in a critical region may be associated with the duplicated sequence.
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Affiliation(s)
- S Sato
- National Livestock Breeding Center, Nishigo, Fukushima, Japan.
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20
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Zhang JQ, Chen H, Sun ZJ, Liu XL, Qiang-Ba YZ, Gu YL. Flesh color association with polymorphism of the tyrosinase gene in different Chinese chicken breeds. Mol Biol Rep 2009; 37:165-9. [PMID: 19437131 DOI: 10.1007/s11033-009-9567-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Accepted: 05/01/2009] [Indexed: 01/10/2023]
Abstract
In order to study genetic variation of tyrosinase gene in four different flesh color chicken breeds selected from special districts including Guyuan, Wenchang, Tibetan and Hisex chicken, five loci of the TYR gene exon-1 and one locus of 5' flanking region were analyzed in PCR-SSCP and DNA sequencing. The results indicated that there were polymorphisms only at TYR1 and TYR3 locus. At TYR1 locus located in exon-1, there were three genotypes (TT, CC, TC), respectively, in three Chinese chicken breeds, and Genotype CC had not been detected in Hisex chicken. At TYR3 locus located in 5' flanking region, there were three genotypes (GG, AA and GA) in Chinese local chicken breeds and genotype AA had not been detected in Hisex chicken breed. It was concluded that there were many variations of TYR gene in Chinese local chicken breeds. DNA sequencing of PCR products for different genotypes showed that there were two mutation sites, respectively, C to T at TYR1 locus and G to A at TYR3 locus. Mutation at TYR1 locus did not cause any amino acid variation. The chi-square analysis revealed that there were significant statistical differences generally between flesh color and the two loci among four chicken populations (P < 0.01). Our results suggested that the flesh color was related to genotype of TYR gene in Chinese chicken breeds. This study provided original information for elucidating the possible roles of exon-1 of TYR gene and 5' flanking region in chickens with different flesh color chicken.
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Affiliation(s)
- J Q Zhang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Shaanxi, China.
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