1
|
Guo P, Chen J, Luo L, Zhang X, Li X, Huang Y, Wu Z, Tian Y. Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese. Animals (Basel) 2024; 14:1508. [PMID: 38791725 PMCID: PMC11117251 DOI: 10.3390/ani14101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.
Collapse
Affiliation(s)
- Pengyun Guo
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Junpeng Chen
- Shantou Baisha Research Institute of Original Species of Poultry and Stock, Shantou 515800, China;
| | - Lei Luo
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Xumeng Zhang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Xiujin Li
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Yunmao Huang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Zhongping Wu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Yunbo Tian
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| |
Collapse
|
2
|
Nannan M, Wenjun W, Ran Z, Yongsheng S, Rongyan Z, Hui C, Sumin Z, Hui X. Population genomics reveals that a missense mutation in EDNRB2 contributes to white plumage color in pigeons. Poult Sci 2024; 103:103225. [PMID: 38035860 PMCID: PMC10698677 DOI: 10.1016/j.psj.2023.103225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
Plumage color is an important economic trait for breed feature identification and consumer's requirements in pigeons. The domestic pigeon has multiple types of plumage color, thereby providing a unique opportunity to identify the genetic basis of plumage coloration. White feather color is common for meat and medicinal use. To investigate the genetic variation associated with white plumage color in pigeons, we use genome resequencing and population genomics to identify the genomic regions with strong selective signature between pigeons with brown and white plumage color. Meanwhile, we obtained some candidate genes with melanin or melanosome biosynthesis in selected regions. Finally, we identified a missense mutation p.E256K in the EDNRB2 completely associated with white plumage color. These findings provide a basis for genetic variation in pigeons with plumage color phenotype.
Collapse
Affiliation(s)
- Mao Nannan
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Wang Wenjun
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhang Ran
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Sun Yongsheng
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhou Rongyan
- Hebei Agricultural University, Baoding, Hebei 071001, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China.
| | - Chen Hui
- Hebei Agricultural University, Baoding, Hebei 071001, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China
| | - Zang Sumin
- Hebei Agricultural University, Baoding, Hebei 071001, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China
| | - Xie Hui
- Fuping Xige Industrial Co., Ltd., Fuping, Hebei 073200, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China
| |
Collapse
|
3
|
Lin R, Zhao F, Xiong T, Lai L, Li H, Lin W, Xiao T, Lin W. Genetic mapping identifies SNP mutations in MITF-M promoter associated with melanin formation in Putian black duck. Poult Sci 2024; 103:103191. [PMID: 37980740 PMCID: PMC10679944 DOI: 10.1016/j.psj.2023.103191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/21/2023] Open
Abstract
The coloration of plumage in poultry species has substantial economic significance. Putian black ducks encompass 2 distinct strains characterized by black and white plumage variations resulting from selective breeding. This study aimed to identify the molecular mechanisms responsible for plumage coloration in these 2 distinct strains. A comprehensive genome-wide association study was conducted using DNA data sourced from a F2 segregating population, consisting of 71 individuals with black plumage and 39 individuals with white plumage, derived from these distinct 2 strains. This analysis revealed that 894 nucleotide polymorphisms and identified 58 candidate genes. Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes coenrichment analyses identified MITF as a key candidate gene implicated in melanin biosynthesis. Furthermore, extensive screening of significant polymorphic loci within MITF was carried out via mass spectrometry in 3 distinct populations: 100 individuals with black plumage and 100 individuals with white plumage from the F0 generation; and 50 with black plumage form the F1 generation). Eighteen candidate polymorphic loci were identified demonstrating significant associations with variations in black and white plumage. Notably, 8 of these loci were located within the 2,000 bp region upstream of MITF-M. To validate the critical regulatory role of MITF-M in black and white plumage formation, a dual-fluorescence reporter system was constructed, and dual-fluorescence activity was assessed. The results revealed that the fluorescence activity at wild-type sites (corresponding to black plumage) was significantly higher than that at the mutant-type sites (associated with white plumage) (P < 0.01). To corroborate the pivotal role of MITF-M in black and white plumage formation, qPCR was employed to evaluate the expression levels of various MITF variants in black and white feather bulbs. This analysis demonstrated that only MITF-M exhibited specific expression in black feather bulbs. These results elucidate the central role of polymorphic mutations within the MITF promoter region in the regulation of black and white plumage coloration in Putian black ducks. This study extends our understanding of mechanisms governing duck plumage coloration and provides valuable molecular markers for future research in duck production and breeding based on plumage coloration.
Collapse
Affiliation(s)
- Ruiyi Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Fanglu Zhao
- Department of Animal Science, Jiangxi Biological Vocational College, No. 608 Nanlian Road, Nanchang 330200, China
| | - Taimin Xiong
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lianjie Lai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Huihuang Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Weilong Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tianfang Xiao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Weimin Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| |
Collapse
|
4
|
Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. PLoS Genet 2023; 19:e1010880. [PMID: 37862332 PMCID: PMC10588866 DOI: 10.1371/journal.pgen.1010880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
Collapse
Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550625. [PMID: 37546953 PMCID: PMC10402103 DOI: 10.1101/2023.07.26.550625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
Collapse
Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
7
|
Dao UM, Lederer I, Tabor RL, Shahid B, Graves CW, Seidel HS. Stripes and loss of color in ball pythons (Python regius) are associated with variants affecting endothelin signaling. G3 (BETHESDA, MD.) 2023; 13:jkad063. [PMID: 37191439 PMCID: PMC10320763 DOI: 10.1093/g3journal/jkad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 05/17/2023]
Abstract
Color patterns in nonavian reptiles are beautifully diverse, but little is known about the genetics and development of these patterns. Here, we investigated color patterning in pet ball pythons (Python regius), which have been bred to show color phenotypes that differ dramatically from the wildtype form. We report that several color phenotypes in pet animals are associated with putative loss-of-function variants in the gene encoding endothelin receptor EDNRB1: (1) frameshift variants in EDNRB1 are associated with conversion of the normal mottled color pattern to skin that is almost fully white, (2) missense variants affecting conserved sites of the EDNRB1 protein are associated with dorsal, longitudinal stripes, and (3) substitutions at EDNRB1 splice donors are associated with subtle changes in patterning compared to wildtype. We propose that these phenotypes are caused by loss of specialized color cells (chromatophores), with loss ranging from severe (fully white) to moderate (dorsal striping) to mild (subtle changes in patterning). Our study is the first to describe variants affecting endothelin signaling in a nonavian reptile and suggests that reductions in endothelin signaling in ball pythons can produce a variety of color phenotypes, depending on the degree of color cell loss.
Collapse
Affiliation(s)
- Uyen M Dao
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Izabella Lederer
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Ray L Tabor
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Basmah Shahid
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Chiron W Graves
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| |
Collapse
|
8
|
Using comparative genomics to detect mutations regulating plumage variations in graylag (A. anser) and swan geese (A. cygnoides). Gene 2022; 834:146612. [PMID: 35618220 DOI: 10.1016/j.gene.2022.146612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/30/2023]
Abstract
Although graylag geese (A. anser) showed similar plumages of white, grey, and white with grey patches compared to those in swan geese (A. cygnoides), it was believed the substantial molecular mechanism for plumage variations were different. To date, studies on genes responsible for diverse plumages among graylag geese were limited and causal mutations remain unknown. In this study, genomes from 57 individuals belonging to six breeds showing different plumages were sequenced at ∼10X depth. Firstly, the allele frequency differences (AFD) of variants on the scaffold394 (NW_013185915.1) between grey and white goose breeds (A. anser) was calculated and a genomic region between 768,290-779,889 bp was detected to carry candidate variants associated with plumages, including one SNP (g. 775,151G > T, ∼18.6 kb upstream of EDNRB2) found to be fixed in white geese. This region was overlapped with the one detected by the haplotype-based sweep analysis, in which significant signals defined a candidate region of 736,610-820,622 bp on the same scaffold. Results from the transcriptomic data showed that expression levels of EDNRB2 and many other melanogenesis-related genes were significantly decreased among white geese compared to that in grey geese, especially at late embryonic stages (>E15). Modifications at transcriptional levels might result in abnormal melanocyte developments and thus the white plumages when they grow up. In addition, a frameshift mutation (C > -) in exon4 of MLANA gene on scaffold176 (NW_013185876.1) was suggested as the causal mutation for sex-linked dilution phenotype in graylag geese although this requires more demonstration experiments. Together with observed white plumages caused by EDNRB2 mutations in coding regions among swan geese and chicken, our study provided new examples to study the parallel evolution.
Collapse
|
9
|
Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks. Genes (Basel) 2022; 13:genes13081391. [PMID: 36011302 PMCID: PMC9407491 DOI: 10.3390/genes13081391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023] Open
Abstract
Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F2 population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the MITF, EDNRB2, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of EDNRB2, TYR, TYRP1, and MITF-M were significantly different between the black and yellow tibiae. MITF and EDNRB2 may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds.
Collapse
Affiliation(s)
- Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Correspondence:
| |
Collapse
|
10
|
Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks. Genes (Basel) 2022; 13:genes13071249. [PMID: 35886032 PMCID: PMC9317390 DOI: 10.3390/genes13071249] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.
Collapse
Affiliation(s)
- Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-187-9660-8824 (H.B.); +86-178-5197-5060 (G.C.)
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-187-9660-8824 (H.B.); +86-178-5197-5060 (G.C.)
| |
Collapse
|
11
|
Maclary ET, Phillips B, Wauer R, Boer EF, Bruders R, Gilvarry T, Holt C, Yandell M, Shapiro MD. Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). Mol Biol Evol 2021; 38:5376-5390. [PMID: 34459920 PMCID: PMC8662629 DOI: 10.1093/molbev/msab260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.
Collapse
Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tyler Gilvarry
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
12
|
Hou H, Wang X, Ding W, Xiao C, Cai X, Lv W, Tu Y, Zhao W, Yao J, Yang C. Whole‐genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (
Columba livia
). Evol Appl 2021; 15:603-617. [PMID: 35505885 PMCID: PMC9046921 DOI: 10.1111/eva.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/17/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro‐pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.
Collapse
Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Weixing Ding
- Shanghai Academy of Agricultural Sciences Shanghai China
| | - Changfeng Xiao
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Wenwei Lv
- National Poultry Engineer Research Center Shanghai China
| | - Yingying Tu
- National Poultry Engineer Research Center Shanghai China
| | - Weimin Zhao
- Shanghai Jinhuang Pigeon Company Shanghai China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| |
Collapse
|
13
|
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]
|
14
|
Xi Y, Xu Q, Huang Q, Ma S, Wang Y, Han C, Zhang R, Wang J, Liu H, Li L. Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks. BMC Genomics 2021; 22:381. [PMID: 34034661 PMCID: PMC8146663 DOI: 10.1186/s12864-021-07719-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
Background Birds have various plumage color patterns, and spot is a common phenotype. Herein, we conducted genome-wide association studies (GWAS) in a population of 225 ducks with different sized black spots to reveal the genetic basis of this phenomenon. Results First, we quantified the black spot phenotype within the duck population. The results showed that the uncolored area of the body surface first appeared on the ventral side. With increasing duck age, the area of the black spots was highly conserved across the whole body surface. The GWAS results identified a 198 kb (Chr4: 10,149,651 bp to 10,348,068 bp) genetic region that was significantly associated with the black spot phenotype. The conditional GWAS and linkage disequilibrium (LD) analysis further narrowed the ultimate candidate region to 167 kb (Chr4: 10,180,939 bp to 10,348,068 bp). A key gene regulating melanoblast migration and differentiation, EDNRB2 (Endothelin B receptor-like), was found in the candidate region and having significant mRNA expression level changes in embryonic duck skin tissue with different spot sizes. The significant SNPs (single nucleotide polymorphisms) associated with the EDNRB2 gene were annotated, and two mutations (Chr4: 10,180,939 T > C and Chr4: 10,190,671 A > T) were found to result in the loss of binding sites for two trans-factors, XBP1 and cMYB. The phenotypic effect of these two mutations suggested that they can regulate the size of black spots in a dose-dependent manner, and Chr4: 10,180,939 T > C was the major allele locus. Conclusions Our results revealed that EDNRB2 was the gene responsible for the variation in duck body surface spot size. Chr4: 10,180,939 T > C was the major allele that explained 49.5 % (dorsal side) and 32.9 % (ventral side) of the variation in duck body surface spot size, while 32.1 % (dorsal side) and 19.1 % (ventral side) of the variation could be explained by Chr4: 10,190,671 A > T. The trans-factor prediction also suggested that XBP1 and cMYB have the potential to interact with EDNRB2, providing new insights into the mechanism of action of these genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07719-7.
Collapse
Affiliation(s)
- Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Qian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Qin Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Yushi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Rongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China.
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China.
| |
Collapse
|
15
|
Liu Z, Zhang L, Yan Z, Ren Z, Han F, Tan X, Xiang Z, Dong F, Yang Z, Liu G, Wang Z, Zhang J, Que T, Tang C, Li Y, Wang S, Wu J, Li L, Huang C, Roos C, Li M. Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats. Mol Biol Evol 2021; 37:952-968. [PMID: 31846031 DOI: 10.1093/molbev/msz301] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Knowledge of the physiological and morphological evolution and adaptation of nonhuman primates is critical to understand hominin origins, physiological ecology, morphological evolution, and applications in biomedicine. Particularly, limestone langurs represent a direct example of adaptations to the challenges of exploiting a high calcium and harsh environment. Here, we report a de novo genome assembly (Tfra_2.0) of a male François's langur (Trachypithecus francoisi) with contig N50 of 16.3 Mb and resequencing data of 23 individuals representing five limestone and four forest langur species. Comparative genomics reveals evidence for functional evolution in genes and gene families related to calcium signaling in the limestone langur genome, probably as an adaptation to naturally occurring high calcium levels present in water and plant resources in karst habitats. The genomic and functional analyses suggest that a single point mutation (Lys1905Arg) in the α1c subunit of the L-type voltage-gated calcium channel Cav1.2 (CACNA1C) attenuates the inward calcium current into the cells in vitro. Population genomic analyses and RNA-sequencing indicate that EDNRB is less expressed in white tail hair follicles of the white-headed langur (T. leucocephalus) compared with the black-colored François's langur and hence might be responsible for species-specific differences in body coloration. Our findings contribute to a new understanding of gene-environment interactions and physiomorphological adaptative mechanisms in ecologically specialized primate taxa.
Collapse
Affiliation(s)
- Zhijin Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Liye Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongze Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Zhijie Ren
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fengming Han
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Xiang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Dong
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Zuomin Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,School of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Guangjian Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Ziming Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Tengcheng Que
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-Aid Monitoring Epidemic Diseases Research Center, Nanning 530001, Guangxi Province, China
| | - Chaohui Tang
- Wuzhou Langur Breeding and Research Center, Wuzhou 543002, Guangxi Province, China
| | - Yifeng Li
- Wuzhou Langur Breeding and Research Center, Wuzhou 543002, Guangxi Province, China
| | - Song Wang
- Nanning Zoo, Nanning 530000, Guangxi Province, China
| | - Junyi Wu
- Nanning Zoo, Nanning 530000, Guangxi Province, China
| | - Legong Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chengming Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| |
Collapse
|
16
|
Ullate-Agote A, Tzika AC. Characterization of the Leucistic Texas Rat Snake Pantherophis obsoletus. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.583136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Albinism and leucism are phenotypes resulting from impaired melanin pigmentation in the skin and skin appendages. However, melanin pigmentation of eyes remains unaffected in leucism. Here, using transmission electron microscopy, we show that the leucistic morph of the Texas rat snake (Pantherophis obsoletus lindheimeri) lacks both melanophores and xanthophores in its skin and exhibits a uniform ivory white color generated by iridophores and collagen fibers. In addition, we sequenced the full genome of a leucistic individual and obtained a highly-contiguous near-chromosome quality assembly of 1.69 Gb with an N50 of 14.5 Mb and an L50 of 29 sequences. Using a candidate-gene approach, we then identify in the leucistic genome a single-nucleotide deletion that generates a frameshift and a premature termination codon in the melanocyte inducing transcription factor (MITF) gene. This mutation shortens the translated protein from 574 to 286 amino acids, removing the helix-loop-helix DNA-binding domain that is highly conserved among vertebrates. Genotyping leucistic animals of independent lineages showed that not all leucistic individuals carry this single-nucleotide deletion. Subsequent gene expression analyses reveal that all leucistic individuals that we analyzed exhibit a significantly decreased expression of MITF. We thus suggest that mutations affecting the regulation and, in some cases, the coding sequence of MITF, the former probably predating the latter, could be associated with the leucistic phenotype in Texas rat snakes. MITF is involved in the development and survival of melanophores in vertebrates. In zebrafish, a classical model species for pigmentation that undergoes metamorphosis, larvae and adults of homozygous mitfa mutants lack melanophores, show an excess of iridophores and exhibit reduced yellow pigmentation. On the contrary, in the leucistic Texas rat snake, a non-metamorphic species, only iridophores persist. Our results suggest that fate determination of neural-crest derived melanophores and xanthophores, but not of iridophores, could require the expression of MITF during snake embryonic development.
Collapse
|
17
|
Xi Y, Liu H, Li L, Xu Q, Liu Y, Wang L, Ma S, Wang J, Bai L, Zhang R, Han C. Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body. Front Cell Dev Biol 2020; 8:560766. [PMID: 33117797 PMCID: PMC7559526 DOI: 10.3389/fcell.2020.560766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
Certain animals exhibit a special dorsoventral pattern with a lighter ventral side compared to the dorsal one and this phenomenon was preserved in the long-term evolution process. Birds also retain this trait. Recently, Inaba et al. (2019) found that ASIP (agouti signal protein) regulated interconversion between different melanocyte types leads to dorsal stripe pattern, which may partly explain the birds' dorsoventral plumage color difference. In this study, we used the embryo samples of LBM (light brown mottling) ducks (Anas platyrhynchos) with white ventral and dark dorsal body parts to investigate the mechanism of dorsoventral color variation. Firstly, melanin deposition process of duck embryos was investigated. The result indicated that E13 and E16 were the active stages of melanin synthesis. Moreover, the melanin deposition on the dorsum of LBM ducks was higher than that on the ventral side throughout. Then, RNA-seq was conducted for the dorsal and ventral skin tissues from E7 (early), E13 (middle) and E19 (late) of LBM ducks. Expression pattern analysis showed that the mRNA expression of most melanin synthesis related genes were at the highest level at E13, which was consistent with the section analysis. A correlation was found between melanogenesis pathway and dorsoventral color difference by co-expression analysis. In the DEG (differentially expressed gene) analysis, we added the dorsal skin transcriptome of embryonic white and black duck of same subspecies (Anas platyrhynchos domestica) for horizontal comparison. The results showed that 8 melanogenesis related genes (TYR, TYRP1, MLANA, RAB38, OCA2, TSPAN10, MC1R, and MSLN) were the common DEGs (Differential expressed genes) in the comparisons of body parts and breeds suggesting that the underlying molecular regulatory mechanism of dorsoventral plumage color difference may be similar to that of albino and melanic duck, which were caused by the different expression of multiple genes in melanin synthesis pathway. In addition, the molecular regulation of melanin synthesis pathway in the dorsal and ventral side of LBM ducks was analyzed. In this pathway, ASIP, MC1R, TYR, and TYRP1 have differential mRNA expression. ASIP, as an upstream gene in this pathway, was likely to play a decisive role in determining the dorsoventral plumage pattern.
Collapse
Affiliation(s)
- Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yisi Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianmei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
18
|
Xi Y, Wang L, Liu H, Ma S, Li Y, Li L, Wang J, Chunchun H, Bai L, Mustafa A, He H. A 14-bp insertion in endothelin receptor B-like (EDNRB2) is associated with white plumage in Chinese geese. BMC Genomics 2020; 21:162. [PMID: 32066369 PMCID: PMC7027040 DOI: 10.1186/s12864-020-6562-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 02/07/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Gang goose is a native species with gray plumage in Sichuan, China. As a result of overhunting, the number of gray Gang geese has decreased dramatically. To keep the species from extinction, conservation work for Gang geese was undertaken. In the process of pure breeding of gray Gang geese, approximately 2% of the offspring of each generation were white. This study aims to explain the genetic mechanism of this phenomenon and provide reliable molecular markers for goose-related plumage color breeding. RESULTS We used the method of pooled whole genome sequencing and Fst (fixation statistics) to identify the differentiation degree of alleles between gray Gang geese and white Gang geese from their offspring. In this way, EDNRB2, a key gene that affects the migration of melanoblasts, was identified. Then, the transcriptome was sequenced for the two geese plumage color populations, and the DEGs (differentially expressed genes) were analyzed. The results indicated that EDNRB2, as a possible candidate gene, had a significantly differential mRNA expression. In addition, a 14-bp insertion (NW_013185915.1: g. 750,748-750,735 insertion. CACAGGTGAGCTCT) in exon 3 of EDNRB2 was analyzed and found to have a significant association between gray geese and Chinese white breeds (P = 0.00), while this mutation was not found in European geese. Meanwhile, the insertion was homozygous in all the white geese we detected and heterozygous in gray geese, indicating that this mutation is recessive. Furthermore, this 14-bp insertion leads to a frameshift mutation in the EDNRB2 coding region and nonsense-mediated mRNA decay. CONCLUSION Our study strongly suggests that the 14-bp insertion in exon 3 of the EDNRB2 gene is associated with the white plumage phenotype in Chinese geese. This study is the first to investigate the relationship between EDNRB2 and white plumage in geese.
Collapse
Affiliation(s)
- Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Lei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Han Chunchun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Ahsan Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People’s Republic of China
| |
Collapse
|
19
|
Fogelholm J, Henriksen R, Höglund A, Huq N, Johnsson M, Lenz R, Jensen P, Wright D. CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken. Sci Rep 2020; 10:1161. [PMID: 31980681 PMCID: PMC6981141 DOI: 10.1038/s41598-020-57710-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 12/28/2019] [Indexed: 01/12/2023] Open
Abstract
Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic × wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.
Collapse
Affiliation(s)
- J Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - R Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - A Höglund
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - N Huq
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - M Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, United Kingdom.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - R Lenz
- ITN Dept of Science and Technology, Linköping University, Linköping, 58183, Sweden
| | - P Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - D Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden.
| |
Collapse
|
20
|
Liu H, Luo Q, Zhang J, Mo C, Wang Y, Li J. Endothelins (EDN1, EDN2, EDN3) and their receptors (EDNRA, EDNRB, EDNRB2) in chickens: Functional analysis and tissue distribution. Gen Comp Endocrinol 2019; 283:113231. [PMID: 31351053 DOI: 10.1016/j.ygcen.2019.113231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 11/27/2022]
Abstract
Endothelins (EDNs) and their receptors (EDNRs) are reported to be involved in the regulation of many physiological/pathological processes, such as cardiovascular development and functions, pulmonary hypertension, neural crest cell proliferation, differentiation and migration, pigmentation, and plumage in chickens. However, the functionality, signaling, and tissue expression of avian EDN-EDNRs have not been fully characterized, thus impeding our comprehensive understanding of their roles in this model vertebrate species. Here, we reported the cDNAs of three EDN genes (EDN1, EDN2, EDN3) and examined the functionality and expression of the three EDNs and their receptors (EDNRA, EDNRB and EDNRB2) in chickens. The results showed that: 1) chicken (c-) EDN1, EDN2, and EDN3 cDNAs were predicted to encode bioactive EDN peptides of 21 amino acids, which show remarkable degree of amino acid sequence identities (91-95%) to their respective mammalian orthologs; 2) chicken (c-) EDNRA expressed in HEK293 cells could be preferentially activated by chicken EDN1 and EDN2, monitored by the three cell-based luciferase reporter assays, indicating that cEDNRA is a functional receptor common for both cEDN1 and cEDN2. In contrast, both cEDNRB and cEDNRB2 could be activated by all three EDN peptides with similar potencies, indicating that both receptors can function as common receptors for the three EDNs and share functional similarity. Moreover, activation of three EDNRs could stimulate intracellular calcium, MAPK/ERK, and cAMP/PKA signaling pathways. 3) qPCR assay revealed that cEDNs and cEDNRs are widely, but differentially, expressed in adult chicken tissues. Taken together, our data establishes a clear molecular basis to uncover the physiological/pathological roles of EDN-EDNR system in birds and helps to reveal the conserved actions of EDN-EDNR signaling across vertebrates.
Collapse
Affiliation(s)
- Haikun Liu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Qin Luo
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Jiannan Zhang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Chunheng Mo
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yajun Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Juan Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail. Sci Rep 2018; 8:16732. [PMID: 30425278 PMCID: PMC6233202 DOI: 10.1038/s41598-018-34827-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/12/2018] [Indexed: 11/08/2022] Open
Abstract
The L strain of Japanese quail exhibits a plumage phenotype that is light yellowish in colour. In this study, we identified a nonsense mutation in the premelanosome protein (PMEL) gene showing complete concordance with the yellowish plumage within a pedigree as well as across strains by genetic linkage analysis of an F2 intercross population using approximately 2,000 single nucleotide polymorphisms (SNPs) that were detected by double digest restriction site-associated DNA sequencing (ddRAD-seq). The yellowish plumage was inherited in an autosomal recessive manner, and the causative mutation was located within an 810-kb genomic region of the LGE22C19W28_E50C23 linkage group (LGE22). This region contained the PMEL gene that is required for the normal melanosome morphogenesis and eumelanin deposition. A nonsense mutation that leads to a marked truncation of the deduced protein was found in PMEL of the mutant. The gene expression level of PMEL decreased substantially in the mutant. Genotypes at the site of the nonsense mutation were fully concordant with plumage colour phenotypes in 196 F2 offspring. The nonsense mutation was not found in several quail strains with non-yellowish plumage. Thus, the yellowish plumage may be caused by the reduced eumelanin content in feathers because of the loss of PMEL function.
Collapse
|
23
|
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.
Collapse
|
24
|
Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M. A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. BMC Genet 2017; 18:29. [PMID: 28356074 PMCID: PMC5372274 DOI: 10.1186/s12863-017-0497-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/25/2017] [Indexed: 11/17/2022] Open
Abstract
Background Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. Results To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated. Our target capture method has a unique feature, i.e., it covers not only exonic regions but also conserved non-coding sequences (CNSs) among vertebrates; therefore, it has the potential to detect regulatory mutations. We identified a deletion of approximately 50 kb in length approximately 50 kb upstream of Ednrb. A comparative analysis with the epigenomic data in the corresponding region in humans and mice showed that one of the CNSs might be an enhancer. Further comparison with Hi-C data, which provide information about chromosome conformation, indicated that the putative enhancer is spatially close to the promoter of Ednrb, suggesting that it acts as an enhancer of Ednrb. Conclusions These in silico data analyses strongly suggest that the identified deletion in the intergenic region upstream of Ednrb, which might contain a melanocyte-specific enhancer, is the mutation causative of the head spot phenotype in the KFRS4/Kyo rat strain. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0497-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Minako Yoshihara
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan
| | - Tetsuya Sato
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan
| | - Daisuke Saito
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Takashi Kuramoto
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Mikita Suyama
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. .,AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan.
| |
Collapse
|
25
|
Woodcock MR, Vaughn-Wolfe J, Elias A, Kump DK, Kendall KD, Timoshevskaya N, Timoshevskiy V, Perry DW, Smith JJ, Spiewak JE, Parichy DM, Voss SR. Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum. Sci Rep 2017; 7:6. [PMID: 28127056 PMCID: PMC5428337 DOI: 10.1038/s41598-017-00059-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/19/2016] [Indexed: 01/04/2023] Open
Abstract
The molecular genetic toolkit of the Mexican axolotl, a classic model organism, has matured to the point where it is now possible to identify genes for mutant phenotypes. We used a positional cloning-candidate gene approach to identify molecular bases for two historic axolotl pigment phenotypes: white and albino. White (d/d) mutants have defects in pigment cell morphogenesis and differentiation, whereas albino (a/a) mutants lack melanin. We identified in white mutants a transcriptional defect in endothelin 3 (edn3), encoding a peptide factor that promotes pigment cell migration and differentiation in other vertebrates. Transgenic restoration of Edn3 expression rescued the homozygous white mutant phenotype. We mapped the albino locus to tyrosinase (tyr) and identified polymorphisms shared between the albino allele (tyr a ) and tyr alleles in a Minnesota population of tiger salamanders from which the albino trait was introgressed. tyr a has a 142 bp deletion and similar engineered alleles recapitulated the albino phenotype. Finally, we show that historical introgression of tyr a significantly altered genomic composition of the laboratory axolotl, yielding a distinct, hybrid strain of ambystomatid salamander. Our results demonstrate the feasibility of identifying genes for traits in the laboratory Mexican axolotl.
Collapse
Affiliation(s)
- M. Ryan Woodcock
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
| | | | | | - D. Kevin Kump
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
| | - Katharina Denise Kendall
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
- School of Integrative Biology, University of Illinois, Urbana-Champaign, Urbana IL 61801 USA
| | | | | | - Dustin W. Perry
- Transposagen Biopharmaceuticals, 535 W 2nd Suite l0, Lexington, KY 40508 USA
| | - Jeramiah J. Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
| | | | - David M. Parichy
- Department of Biology, University of Washington, Seattle, WA 98195 USA
- Department of Biology, University of Virginia, Charlottesville, VA 22903 USA
| | - S. Randal Voss
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
| |
Collapse
|
26
|
Nunome M, Nakano M, Tadano R, Kawahara-Miki R, Kono T, Takahashi S, Kawashima T, Fujiwara A, Nirasawa K, Mizutani M, Matsuda Y. Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers. PLoS One 2017; 12:e0169978. [PMID: 28107483 PMCID: PMC5249226 DOI: 10.1371/journal.pone.0169978] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 12/25/2016] [Indexed: 12/25/2022] Open
Abstract
To assess the genetic diversity of domestic Japanese quail (Coturnix japonica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources-the pre-war and post-war populations-which is well supported by their breeding histories.
Collapse
Affiliation(s)
- Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mikiharu Nakano
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ryo Tadano
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Ryoka Kawahara-Miki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Shinji Takahashi
- General Affairs Department, National Institute for Environmental Studies, Tsukuba, Japan
| | - Takaharu Kawashima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba 305–8506, Japan
| | - Akira Fujiwara
- Laboratory Animal Research Station, Nippon Institute for Biological Science, Hokuto, Japan
| | - Keijiro Nirasawa
- Animal Breeding and Reproduction Research Division, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Makoto Mizutani
- 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, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| |
Collapse
|
27
|
Wu N, Qin H, Wang M, Bian Y, Dong B, Sun G, Zhao W, Chang G, Xu Q, Chen G. Variations in endothelin receptor B subtype 2 (EDNRB2) coding sequences and mRNA expression levels in 4 Muscovy duck plumage colour phenotypes. Br Poult Sci 2017; 58:116-121. [DOI: 10.1080/00071668.2016.1259531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- N. Wu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People’s Republic of China
| | - H. Qin
- National Waterfowl Germplasm Resource Pool, Taizhou, People’s Republic of China
| | - M. Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People’s Republic of China
| | - Y. Bian
- National Waterfowl Germplasm Resource Pool, Taizhou, People’s Republic of China
| | - B. Dong
- National Waterfowl Germplasm Resource Pool, Taizhou, People’s Republic of China
| | - G. Sun
- National Waterfowl Germplasm Resource Pool, Taizhou, People’s Republic of China
| | - W. Zhao
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People’s Republic of China
| | - G. Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People’s Republic of China
| | - Q. Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People’s Republic of China
| | - G. Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People’s Republic of China
| |
Collapse
|
28
|
Ahi EP, Sefc KM. A gene expression study of dorso-ventrally restricted pigment pattern in adult fins of Neolamprologus meeli, an African cichlid species. PeerJ 2017; 5:e2843. [PMID: 28097057 PMCID: PMC5228514 DOI: 10.7717/peerj.2843] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/29/2016] [Indexed: 01/04/2023] Open
Abstract
Fish color patterns are among the most diverse phenotypic traits found in the animal kingdom. Understanding the molecular and cellular mechanisms that control in chromatophore distribution and pigmentation underlying this diversity is a major goal in developmental and evolutionary biology, which has predominantly been pursued in the zebrafish model system. Here, we apply results from zebrafish work to study a naturally occurring color pattern phenotype in the fins of an African cichlid species from Lake Tanganyika. The cichlid fish Neolamprologus meeli displays a distinct dorsal color pattern, with black and white stripes along the edges of the dorsal fin and of the dorsal half of the caudal fin, corresponding with differences in melanophore density. To elucidate the molecular mechanisms controlling the differences in dorsal and ventral color patterning in the fins, we quantitatively assessed the expression of 15 candidate target genes involved in adult zebrafish pigmentation and stripe formation. For reference gene validation, we screened the expression stability of seven widely expressed genes across the investigated tissue samples and identified tbp as appropriate reference. Relative expression levels of the candidate target genes were compared between the dorsal, striped fin regions and the corresponding uniform, grey-colored regions in the anal and ventral caudal fin. Dorso-ventral expression differences, with elevated levels in both white and black stripes, were observed in two genes, the melanosome protein coding gene pmel and in igsf11, which affects melanophore adhesion, migration and survival. Next, we predicted potential shared upstream regulators of pmel and igsf11. Testing the expression patterns of six predicted transcriptions factors revealed dorso-ventral expression difference of irf1 and significant, negative expression correlation of irf1 with both pmel and igsf11. Based on these results, we propose pmel, igsf11 and irf1 as likely components of the genetic mechanism controlling distinct dorso-ventral color patterns in N. meeli fins.
Collapse
Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Zoology, Universitätsplatz 2, Universität Graz , Graz , Austria
| | - Kristina M Sefc
- Institute of Zoology, Universitätsplatz 2, Universität Graz , Graz , Austria
| |
Collapse
|
29
|
Menzi F, Keller I, Reber I, Beck J, Brenig B, Schütz E, Leeb T, Drögemüller C. Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation. Sci Rep 2016; 6:28438. [PMID: 27329507 PMCID: PMC4916431 DOI: 10.1038/srep28438] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023] Open
Abstract
The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.
Collapse
Affiliation(s)
- Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Irene Keller
- Department of Clinical Research and Swiss Institute of Bioinformatics, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Julia Beck
- Chronix Biomedical, Goetheallee 8, 37073 Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| |
Collapse
|
30
|
Different Photoperiodic Responses in Four Lines of Japanese Quail. J Poult Sci 2016; 53:63-66. [PMID: 32908366 PMCID: PMC7477246 DOI: 10.2141/jpsa.0150097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Organisms measure day length to better adapt to seasonal changes in the environment; this phenomenon is called photoperiodism. The Japanese quail has a highly sophisticated photoperiodic mechanism and is an excellent model for the study of photoperiodism. Various lines of quail have been established during the domestication process. In the present study, we examined the effect of long day (LD) followed by short day (SD) on testicular weight in four lines of quail (L, AMRP, NIES-Br, and WE). When the quail were raised under SD conditions, testicular development was suppressed in all examined lines. The speed of the LD-induced testicular development of NIES-Br line was faster than that of AMRP line, while the speed of the SD-induced testicular regression of L line was significantly faster than that of WE line. These quail lines provide excellent model to uncover the underlying mechanism of seasonal testicular regression.
Collapse
|
31
|
Abstract
Colour patterns are prominent features of many animals and have important functions in communication, such as camouflage, kin recognition and mate choice. As targets for natural as well as sexual selection, they are of high evolutionary significance. The molecular mechanisms underlying colour pattern formation in vertebrates are not well understood. Progress in transgenic tools, in vivo imaging and the availability of a large collection of mutants make the zebrafish (Danio rerio) an attractive model to study vertebrate colouration. Zebrafish display golden and blue horizontal stripes that form during metamorphosis as mosaics of yellow xanthophores, silvery or blue iridophores and black melanophores in the hypodermis. Lineage tracing revealed the origin of the adult pigment cells and their individual cellular behaviours during the formation of the striped pattern. Mutant analysis indicated that interactions between all three pigment cell types are required for the formation of the pattern, and a number of cell surface molecules and signalling systems have been identified as mediators of these interactions. The understanding of the mechanisms that underlie colour pattern formation is an important step towards deciphering the genetic basis of variation in evolution.
Collapse
|
32
|
Li L, Li D, Liu L, Li S, Feng Y, Peng X, Gong Y. Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas platyrhynchos). PLoS One 2015; 10:e0125883. [PMID: 25955279 PMCID: PMC4425580 DOI: 10.1371/journal.pone.0125883] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/08/2015] [Indexed: 01/24/2023] Open
Abstract
Endothelin receptor B subtype 2 (EDNRB2) is a seven-transmembrane G-protein coupled receptor. In this study, we investigated EDNRB2 gene as a candidate gene for duck spot plumage pattern according to studies of chicken and Japanese quail. The entire coding region was cloned by the reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis showed that duck EDNRB2 cDNA contained a 1311bp open reading frame and encoded a putative protein of 436 amino acids residues. The transcript shared 89%-90% identity with the counterparts in other avian species. A phylogenetic tree based on amino acid sequences showed that duck EDNRB2 was evolutionary conserved in avian clade. The entire coding region of EDNRB2 were sequenced in 20 spot and 20 non-spot ducks, and 13 SNPs were identified. Two of them (c.940G>A and c.995G>A) were non-synonymous substitutions, and were genotyped in 647 ducks representing non-spot and spot phenotypes. The c.995G>A mutation, which results in the amino acid substitution of Arg332His, was completely associated with the spot phenotype: all 152 spot ducks were carriers of the AA genotype and the other 495 individuals with non-spot phenotype were carriers of GA or GG genotype, respectively. Segregation in 17 GA×GG and 22 GA×GA testing combinations confirmed this association since the segregation ratios and genotypes of the offspring were in agreement with the hypothesis. In order to investigate the underlying mechanism of the spot phenotype, MITF gene was used as cell type marker of melanocyte progenitor cells while TYR and TYRP1 gene were used as cell type markers of mature melanocytes. Transcripts of MITF, TYR and TYRP1 gene with expected size were identified in all pigmented skin tissues while PCR products were not obtained from non-pigmented skin tissues. It was inferred that melanocytes are absent in non-pigmented skin tissues of spot ducks.
Collapse
Affiliation(s)
- Ling Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuli Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
| |
Collapse
|
33
|
Braasch I, Schartl M. Evolution of endothelin receptors in vertebrates. Gen Comp Endocrinol 2014; 209:21-34. [PMID: 25010382 DOI: 10.1016/j.ygcen.2014.06.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/07/2014] [Accepted: 06/26/2014] [Indexed: 02/03/2023]
Abstract
Endothelin receptors are G protein coupled receptors (GPCRs) of the β-group of rhodopsin receptors that bind to endothelin ligands, which are 21 amino acid long peptides derived from longer prepro-endothelin precursors. The most basal Ednr-like GPCR is found outside vertebrates in the cephalochordate amphioxus, but endothelin ligands are only present among vertebrates, including the lineages of jawless vertebrates (lampreys and hagfishes), cartilaginous vertebrates (sharks, rays, and chimaeras), and bony vertebrates (ray-finned fishes and lobe-finned vertebrates including tetrapods). A bona fide endothelin system is thus a vertebrate-specific innovation with important roles for regulating the cardiovascular system, renal and pulmonary processes, as well as for the development of the vertebrate-specific neural crest cell population and its derivatives. Expectedly, dysregulation of endothelin receptors and the endothelin system leads to a multitude of human diseases. Despite the importance of different types of endothelin receptors for vertebrate development and physiology, current knowledge on endothelin ligand-receptor interactions, on the expression of endothelin receptors and their ligands, and on the functional roles of the endothelin system for embryonic development and in adult vertebrates is very much biased towards amniote vertebrates. Recent analyses from a variety of vertebrate lineages, however, have shown that the endothelin system in lineages such as teleost fish and lampreys is more diverse and is divergent from the mammalian endothelin system. This diversity is mainly based on differential evolution of numerous endothelin system components among vertebrate lineages generated by two rounds of whole genome duplication (three in teleosts) during vertebrate evolution. Here we review current understanding of the evolutionary history of the endothelin receptor family in vertebrates supplemented with surveys on the endothelin receptor gene complement of newly available genome assemblies from phylogenetically informative taxa. Our assessment further highlights the diversity of the vertebrate endothelin system and calls for detailed functional and pharmacological analyses of the endothelin system beyond tetrapods.
Collapse
Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97080 Würzburg, Germany.
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Nakamura Y, Tasai M, Takeda K, Nirasawa K, Tagami T. Production of functional gametes from cryopreserved primordial germ cells of the Japanese quail. J Reprod Dev 2013; 59:580-7. [PMID: 24077020 PMCID: PMC3934152 DOI: 10.1262/jrd.2013-065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The Japanese quail (Coturnix japonica) is a valuable bird as both
an experimental animal, for a wide range of scientific disciplines, and an
agricultural animal, for the production of eggs and meat. Cryopreservation of PGCs
would be a feasible strategy for the conservation of both male and female fertility
cells in Japanese quail. However, the effects of freeze-thaw treatment on viability,
migration ability and germline transmission ability of quail PGCs still remain
unclear. In the present study, male and female PGCs were isolated from the blood of
2-day-old embryos, which were cooled by slow freezing and then cryopreserved at –196
C for 77–185 days, respectively. The average recovery rate of PGCs after
freeze-thawing was 47.0%. The viability of PGCs in the frozen group was significantly
lower than that of the control group (P<0.05) (85.5% vs. 95.1%).
Both fresh and Frozen-thawed PGCs that were intravascularly transplanted into
recipient embryos migrated toward and were incorporated into recipient gonads,
although the number of PGCs settled in the gonads was 48.5% lower in the frozen group
than in the unfrozen control group (P<0.05). Genetic cross analysis revealed that
one female and two male recipients produced live progeny derived from the
frozen-thawed PGCs. The frequency of donor-derived offspring was slightly lower than
that of unfrozen controls, but the difference was not significant (4.0
vs. 14.0%). These results revealed that freeze-thaw treatment
causes a decrease in viability, migration ability and germline transmission ability
of PGCs in quail.
Collapse
Affiliation(s)
- Yoshiaki Nakamura
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institute of Natural Sciences, Aichi 444-8787, Japan
| | | | | | | | | |
Collapse
|
36
|
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.
Collapse
Affiliation(s)
- Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
| | | |
Collapse
|
37
|
Greenwood AK, Cech JN, Peichel CL. Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks. Evol Dev 2012; 14:351-62. [PMID: 22765206 DOI: 10.1111/j.1525-142x.2012.00553.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pigment pattern variation across species or populations offers a tractable framework in which to investigate the evolution of development. Juvenile threespine sticklebacks (Gasterosteus aculeatus) from marine and freshwater environments exhibit divergent pigment patterns that are associated with ecological differences. Juvenile marine sticklebacks have a silvery appearance, whereas sticklebacks from freshwater environments exhibit a pattern of vertical bars. We investigated both the developmental and molecular basis of this population-level variation in pigment pattern. Time course imaging during the transition from larval to juvenile stages revealed differences between marine and freshwater fish in spatial patterns of chromatophore differentiation as well as in pigment amount and dispersal. In freshwater fish, melanophores appear primarily within dark bars whereas iridophores appear within light bars. By contrast, in marine fish, these chromatophores are interspersed across the flank. In addition to spatially segregated chromatophore differentiation, pigment amount and dispersal within melanophores varies spatially across the flank of freshwater, but not marine fish. To gain insight into the molecular pathways that underlie the differences in pigment pattern development, we evaluated differential gene expression in the flanks of developing fish using high-throughput cDNA sequencing (RNA-seq) and quantitative PCR. We identified several genes that were differentially expressed across dark and light bars of freshwater fish, and between freshwater and marine fish. Together, these experiments begin to shed light on the process of pigment pattern evolution in sticklebacks.
Collapse
Affiliation(s)
- Anna K Greenwood
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | | | | |
Collapse
|
38
|
Dobson AE, Schmidt DJ, Hughes JM. Sequence Variation in the Melanocortin-1 Receptor (MC1R) Does Not Explain Continent-wide Plumage Color Differences in the Australian Magpie (Cracticus tibicen). J Hered 2012; 103:769-80. [DOI: 10.1093/jhered/ess053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
39
|
Gene duplication of endothelin 3 is closely correlated with the hyperpigmentation of the internal organs (Fibromelanosis) in silky chickens. Genetics 2011; 190:627-38. [PMID: 22135351 DOI: 10.1534/genetics.111.136705] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
During early development in vertebrates, pluripotent cells are generated from the neural crest and migrate according to their presumptive fate. In birds and mammals, one of the progeny cells, melanoblasts, generally migrate through a dorsolateral route of the trunk region and differentiate to melanocytes. However, Silky is an exceptional chicken in which numerous melanoblasts travel via a ventral pathway and disperse into internal organs. Finally, these ectopic melanocytes induce heavy dermal and visceral melanization known as Fibromelanosis (Fm). To identify the genetic basis of this phenotype, we confirmed the mode of inheritance of Fm as autosomal dominant and then performed linkage analysis with microsatellite markers and sequence-tagged site markers. Using 85 backcross progeny from crossing Black Minorca chickens (BM-C) with F(1) individuals between White Silky (WS) and BM-C Fm was located on 10.2-11.7 Mb of chicken chromosome 20. In addition, we noticed a DNA marker that all Silky chickens and the F(1) individuals showed heterozygous genotyping patterns, suggesting gene duplication in the Fm region. By quantitative real-time PCR assay, Silky line-specific gene duplication was detected as an ~130-kb interval. It contained five genes including endothelin 3 (EDN3), which encoded a potent mitogen for melanoblasts/melanocytes. EDN3 with another three of these duplicated genes in Silky chickens expressed almost twofold of those in BM-C. Present results strongly suggest that the increase of the expression levels resulting from the gene duplication in the Fm region is the trigger of hypermelanization in internal organs of Silky chickens.
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Michael Cieslak
- Leibniz Institute for Zoo and Wildlife Research, Research Group of Evolutionary Genetics, Berlin, Germany
| | | | | | | |
Collapse
|
41
|
Braasch I, Brunet F, Volff JN, Schartl M. Pigmentation pathway evolution after whole-genome duplication in fish. Genome Biol Evol 2009; 1:479-93. [PMID: 20333216 PMCID: PMC2839281 DOI: 10.1093/gbe/evp050] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2009] [Indexed: 12/29/2022] Open
Abstract
Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate
lineage, but their evolutionary significance for phenotypic evolution remains
elusive. Here, we have investigated the impact of the fish-specific genome
duplication (FSGD) on the evolution of pigmentation pathways in teleost fishes.
Pigmentation and color patterning are among the most diverse traits in teleosts,
and their pigmentary system is the most complex of all vertebrate groups. Using a comparative genomic approach including phylogenetic and synteny analyses,
the evolution of 128 vertebrate pigmentation genes in five teleost genomes
following the FSGD has been reconstructed. We show that pigmentation genes have
been preferentially retained in duplicate after the FSGD, so that teleosts have
30% more pigmentation genes compared with tetrapods. This is significantly
higher than genome-wide estimates of FSGD gene duplicate retention in teleosts.
Large parts of the melanocyte regulatory network have been retained in two
copies after the FSGD. Duplicated pigmentation genes follow general evolutionary
patterns such as the preservation of protein complex stoichiometries and the
overrepresentation of developmental genes among retained duplicates. These
results suggest that the FSGD has made an important contribution to the
evolution of teleost-specific features of pigmentation, which include novel
pigment cell types or the division of existing pigment cell types into distinct
subtypes. Furthermore, we have observed species-specific differences in
duplicate retention and evolution that might contribute to pigmentary diversity
among teleosts. Our study therefore strongly supports the hypothesis that WGDs have promoted the
increase of complexity and diversity during vertebrate phenotypic evolution.
Collapse
Affiliation(s)
- Ingo Braasch
- Physiological Chemistry I, University of Würzburg, Biozentrum, Würzburg, Germany.
| | | | | | | |
Collapse
|
42
|
Phylogeny, taxonomy, and evolution of the endothelin receptor gene family. Mol Phylogenet Evol 2009; 52:677-87. [PMID: 19410007 DOI: 10.1016/j.ympev.2009.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 03/28/2009] [Accepted: 04/23/2009] [Indexed: 01/29/2023]
Abstract
A gene phylogeny provides the natural historical order to classify genes and to understand their functional, structural, and genomic diversity. The gene family of endothelin receptors (EDNR) is responsible for many key physiological and developmental processes of tetrapods and teleosts. This study provides a well-defined gene phylogeny for the EDNR family, which is used to classify its members and to assess their evolution. The EDNR phylogeny supports the recognition of the EDNRA, EDNRB, and EDNRC subfamilies, as well as more lineage-specific duplicates of teleosts and the African clawed frog. The duplications for these nominal genes are related to the various whole-genome amplifications of vertebrates, jawed vertebrates, fishes, and frog. The EDNR phylogeny also identifies several gene losses, including that of EDNRC from placental and marsupial (therian) mammals. When coupled with structural and biochemical information, site-specific analyses of evolutionary rate shifts reveal two distinct patterns of potential functional changes at the sequence level between therian versus non-therian EDNRA and EDNRB (i.e., between groups without and with EDNRC). An analysis of linkage maps and tetrapod synteny further suggests that the loss of therian EDNRC may be related to a chromosomal deletion in its common ancestor.
Collapse
|
43
|
Harris ML, Hall R, Erickson CA. Directing pathfinding along the dorsolateral path - the role of EDNRB2 and EphB2 in overcoming inhibition. Development 2008; 135:4113-22. [PMID: 19004859 DOI: 10.1242/dev.023119] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Neural crest cells that become pigment cells migrate along a dorsolateral route between the ectoderm and the somite, whereas most other neural crest cells are inhibited from entering this space. This pathway choice has been attributed to unique, cell-autonomous migratory properties acquired by neural crest cells when they become specified as melanoblasts. By shRNA knockdown and overexpression experiments, we investigated the roles of three transmembrane receptors in regulating dorsolateral pathfinding in the chick trunk. We show that Endothelin receptor B2 (EDNRB2) and EphB2 are both determinants in this process, and that, unlike in other species, c-KIT is not. We demonstrate that the overexpression of EDNRB2 can maintain normal dorsolateral migration of melanoblasts in the absence of EphB2, and vice versa, suggesting that changes in receptor expression levels regulate the invasion of this pathway. Furthermore, by heterotopic grafting, we show that neural crest cell populations that do not rely on the activation of these receptors can migrate dorsolaterally only if this path is free of inhibitory molecules. We conclude that the requirement for EDNRB2 and EphB2 expression by melanoblasts is to support their migration by helping them to overcome repulsive or non-permissive cues in the dorsolateral environment.
Collapse
Affiliation(s)
- Melissa L Harris
- University of California, Davis, Department of Molecular and Cellular Biology, One Shields Avenue, Davis, CA 95616, USA
| | | | | |
Collapse
|
44
|
Mutations of Japanese Quail ( Coturnix japonica) and Recent Advances of Molecular Genetics for This Species. J Poult Sci 2008. [DOI: 10.2141/jpsa.45.159] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
45
|
Nadeau NJ, Mundy NI, Gourichon D, Minvielle F. Association of a single-nucleotide substitution in TYRP1 with roux in Japanese quail (Coturnix japonica). Anim Genet 2007; 38:609-13. [DOI: 10.1111/j.1365-2052.2007.01667.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|