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Melo Rojas C, Bravo Matheus PW, Zapata Coacalla C, Lopez Durand V, Melo Anccasi M. MC1R Gene Variants and Their Relationship with Coat Color in South American Camelids. ScientificWorldJournal 2023; 2023:4871135. [PMID: 37786645 PMCID: PMC10541998 DOI: 10.1155/2023/4871135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/12/2023] [Accepted: 08/21/2023] [Indexed: 10/04/2023] Open
Abstract
In domestic camelids, fleece color is an essential characteristic because it defines the direction of production. Variants were determined in the MC1R gene that showed a relationship with coat color in alpacas and llamas at the level of the coding region. This report sequenced the MC1R gene from 290 alpacas (142 white, 84 black, 50 brown, and 14 light fawn), five brown llamas, nine vicuñas, and three guanacos to analyze the association between coat color and the MC1R gene among South American camelids. A total of nineteen polymorphisms were identified. Seven polymorphisms were significant; three of them were of nonsynonymous type (c.82A > G, c.376G > A, and c.901C > T), two were of synonymous type (c.126 T > C and c.933G > A), one was in the promoter region (-42C > G), and one was in the 3' UTR (+5T > C). More polymorphisms were found in domestic camelids than in wild camelids. Besides polymorphism, the association of polymorphisms might cause white and dark pigmentation in the fleece of South American camelids. In addition, the MC1R protein would answer the pigmentation in alpacas.
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Affiliation(s)
- Carola Melo Rojas
- Laboratorio de Genetica, Escuela Profesional de Medicina Veterinaria Canchis, National University of Saint Anthony the Abbot in Cuzco, Cusco, Peru
| | - P. Walter Bravo Matheus
- Laboratorio de Genetica, Escuela Profesional de Medicina Veterinaria Canchis, National University of Saint Anthony the Abbot in Cuzco, Cusco, Peru
| | - Celso Zapata Coacalla
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Puno, Peru
| | - Victor Lopez Durand
- Laboratorio de Genetica, Escuela Profesional de Medicina Veterinaria Canchis, National University of Saint Anthony the Abbot in Cuzco, Cusco, Peru
| | - Maximo Melo Anccasi
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Puno, Peru
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Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks. Genes (Basel) 2022; 13:genes13071249. [PMID: 35886032 PMCID: PMC9317390 DOI: 10.3390/genes13071249] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.
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Affiliation(s)
- Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-187-9660-8824 (H.B.); +86-178-5197-5060 (G.C.)
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-187-9660-8824 (H.B.); +86-178-5197-5060 (G.C.)
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Zhu T, Liu M, Peng S, Zhang X, Chen Y, Lv X, Yang W, Li K, Zhang J, Wang H, Li H, Ning Z, Wang L, Qu L. A Deletion Upstream of SOX10 Causes Light Yellow Plumage Colour in Chicken. Genes (Basel) 2022; 13:genes13020327. [PMID: 35205371 PMCID: PMC8872211 DOI: 10.3390/genes13020327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Chicken plumage colour is a complex trait controlled by many genes. Herein, through Rhode Island Red (RIR) and White Leghorn (WL) F1 cross populations, the segregation of plumage color was observed in females, showing white in males, and dark red (DR) and light yellow (LY) in females. The white has been found to be caused by dominant white alleles (I) and the DR phenotype is attributed to a sex-linked recessive silver allele (S∗S). LY is a derived feather colour phenotype and the genetic mechanism of this is unclear. In order to explore the genetic basis for LY, we randomly selected 40 DR and 39 LY chickens for paired-end sequencing. Through the use of association analysis, we found the LY phenotype is caused by a 7.6 kb non-coding deletion near the SOX10 gene. This mutation has been reported to be responsible for dark brown plumage in chicken, and subsequent diagnostic PCR tests showed that the length of the long-range non-coding deletion is 7.6 kb instead of 8.3 kb as previously reported.
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Affiliation(s)
- Tao Zhu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
| | - Mengchao Liu
- Beijing Municipal Bureau of Agriculture and Rural Affairs, Beijing 100005, China;
| | - Shan Peng
- Guiyang Municipal General Station of Animal Science, Guizhou 550081, China; (S.P.); (L.W.)
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Kaiyang Li
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Jianwei Zhang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Huie Wang
- College of Animal Science, Tarim University, Alar 843300, China;
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumchi 830000, China;
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
| | - Liang Wang
- Guiyang Municipal General Station of Animal Science, Guizhou 550081, China; (S.P.); (L.W.)
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
- Correspondence:
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Nakamura Y, Nakane Y, Tsudzuki M. Skeletal development in blue-breasted quail embryos. Anim Sci J 2019; 90:353-365. [PMID: 30654411 PMCID: PMC6590581 DOI: 10.1111/asj.13159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 11/30/2022]
Abstract
The blue-breasted quail (Coturnix chinensis), the smallest species of quail with short generation interval and excellent reproductive performance, is a potential avian research model. A normal series of skeletal development of avian embryos could be served as a reference standard in the fields of developmental biology and teratological testing as well as in the investigation of mutation with skeletal abnormalities and in the study of the molecular mechanisms of skeletal development through genome manipulation. Furthermore, ossification sequence shows a species-specific pattern and has potential utility in phylogeny. However, data on the skeletal development of blue-breasted quail embryos are scarce. Here, we established a series of normal stages for the skeletal development of blue-breasted quail embryos. Cartilage and ossified bones of blue-breasted quail embryos were stained blue and red with Alcian blue 8GX and Alizarin red S, respectively. The time and order of chondrification and calcification of their skeletons were documented every 24 hr from 3 to 17 days of incubation, and a 15-stage series of skeletal development was created. Moreover, a comparative study with the Japanese quail (Coturnix japonica) demonstrated that ossification sequence differed significantly between these two species.
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Affiliation(s)
- Yoshiaki Nakamura
- Laboratory of Animal Breeding and GeneticsGraduate School of Biosphere ScienceHiroshima UniversityHigashi‐HiroshimaHiroshimaJapan
- Japanese Avian Bioresource Project Research CenterHiroshima UniversityHigashi‐HiroshimaHiroshimaJapan
| | - Yoshifumi Nakane
- Institute of Laboratory AnimalsGraduate School of MedicineKyoto UniversitySakyou‐kuKyotoJapan
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and GeneticsGraduate School of Biosphere ScienceHiroshima UniversityHigashi‐HiroshimaHiroshimaJapan
- Japanese Avian Bioresource Project Research CenterHiroshima UniversityHigashi‐HiroshimaHiroshimaJapan
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