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Zhang R, Mu C, Chang L, Shen X, Bu Z, Yang M, Fu S, Tang Q, Liu P, Yang X. Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon. Animals (Basel) 2024; 14:1047. [PMID: 38612286 PMCID: PMC11011069 DOI: 10.3390/ani14071047] [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: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.
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Affiliation(s)
- Rui Zhang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Chunyu Mu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Lingling Chang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Xinyue Shen
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Zhu Bu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Mingjun Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Shengyong Fu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Qingping Tang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Peiyao Liu
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Xiaoming Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
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Hou H, Wang X, Li X, Cai X, Tu Y, Yang C, Yao J. Genome-wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons. Anim Genet 2024; 55:110-122. [PMID: 38069460 DOI: 10.1111/age.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/03/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024]
Abstract
Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome-wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight (BW) and body size (BS) of 556 meat pigeons at 52 and 80 weeks of age were collected. In total, 160 434 high-quality single nucleotide polymorphism sites were obtained by restriction site-associated DNA sequencing. The GWAS analysis revealed that MSTN, IGF2BP3 and NCAPG/LCORL were important candidate genes affecting the growth traits of meat pigeons. IGF2BP3 and NCAPG/LCORL were highly correlated to BW and BS, which are related to overall growth and development, while MSTN was associated with pectoral thickness and BW. Phenotypic association validation with the use of two meat pigeon populations found that the MSTN mutation c.C861T determines the MM. These results provide new insights into the genetic mechanisms underlying phenotypic variations of growth traits and MM in commercial meat pigeons. The identified markers and genes provide a theoretical basis for the selective breeding of meat pigeons.
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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
| | - Xin Li
- 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
| | - Yingying Tu
- National Poultry Engineer Research Center, Shanghai, China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- National Poultry Engineer Research Center, Shanghai, China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences, Shanghai, China
- National Poultry Engineer Research Center, Shanghai, China
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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.
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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
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Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. J Evol Biol 2023; 36:1226-1241. [PMID: 37485603 DOI: 10.1111/jeb.14200] [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: 12/14/2022] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Mercè Palacios
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Oscar Frías
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Keith Hobson
- Biology Department, Western University, London, Ontario, Canada
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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Williams D. Eagle eyed or bird brained? Eye (Lond) 2023; 37:2426-2430. [PMID: 37353509 PMCID: PMC10397276 DOI: 10.1038/s41433-023-02568-y] [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: 12/23/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 06/25/2023] Open
Abstract
The importance of the visual system to birds for behaviours from feeding, mate choice, flying, navigation and determination of seasons, together with the presence of photoreceptors in the retina, the pineal and the brain, render the avian visual system a particularly fruitful model for understanding of eye-brain interactions. In this review we will particularly focus on the pigeon, since here we have a brain stereotactically mapped and a genome fully sequenced, together with a particular bird, the homing pigeon, with remarkable ability to navigate over hundreds of miles and return to exactly the same roosting site with exceptional precision. We might denigrate the avian species by the term bird brained, but here are animals with phenomenal abilities to use their exceptional vision, their eagle eyedness, to best advantage.
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Yáñez JM, Xu P, Carvalheiro R, Hayes B. Genomics applied to livestock and aquaculture breeding. Evol Appl 2022; 15:517-522. [PMID: 35505887 PMCID: PMC9046759 DOI: 10.1111/eva.13378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- José M. Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms College of Ocean and Earth Sciences Xiamen University Xiamen China
| | - Roberto Carvalheiro
- Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista Jaboticabal, São Paulo Brazil
- CSIRO Agriculture & Food Hobart Tasmania Australia
| | - Ben Hayes
- Centre for Animal Science Queensland Alliance for Agriculture and Food Innovation The University of Queensland Australia
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