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Bendesky A, Brew J, Francis KX, Tello Corbetto EF, González Ariza A, Nogales Baena S, Shimmura T. The main genetic locus associated with the evolution of gamecocks is centered on ISPD. G3 (BETHESDA, MD.) 2024; 14:jkad267. [PMID: 37991999 PMCID: PMC10849328 DOI: 10.1093/g3journal/jkad267] [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: 08/15/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, with 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with nongame chickens. Particularly noteworthy is a variant in an intron of the isoprenoid synthase domain containing gene (ISPD), an extreme outlier present at a frequency of 89% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.
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Affiliation(s)
- Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | - Joseph Brew
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | - Kerel X Francis
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | | | - Antonio González Ariza
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain
- Diputación Provincial de Córdoba, Agropecuary Provincial Centre, 14014 Córdoba, Spain
| | - Sergio Nogales Baena
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain
| | - Tsuyoshi Shimmura
- Department of Biological Production, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
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Yin ZT, Li XQ, Sun YX, Smith J, Hincke M, Yang N, Hou ZC. Selection on the promoter regions plays an important role in complex traits during duck domestication. BMC Biol 2023; 21:303. [PMID: 38129834 PMCID: PMC10740227 DOI: 10.1186/s12915-023-01801-0] [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: 02/01/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the noncoding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood. RESULTS We constructed a genomics, transcriptomics, and epigenomics map of the duck genome and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the overexpression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment. CONCLUSIONS This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.
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Affiliation(s)
- Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiao-Qin Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Maxwell Hincke
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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Bendesky A, Brew J, Francis KX, Tello Corbetto EF, González Ariza A, Nogales Baena S, Shimmura T. Noncoding genetic variation in ISPD distinguishes gamecocks from nongame chickens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553562. [PMID: 37662209 PMCID: PMC10473654 DOI: 10.1101/2023.08.16.553562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and of 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, at 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with, nongame chickens. Particularly noteworthy is a variant in an intron of ISPD, an extreme outlier present at a frequency of 90% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.
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Affiliation(s)
- Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Joseph Brew
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kerel X. Francis
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Antonio González Ariza
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
- Agropecuary Provincial Centre, Diputación Provincial de Córdoba, Córdoba, Spain
| | - Sergio Nogales Baena
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | - Tsuyoshi Shimmura
- Department of Agriculture, Tokyo University of Agriculture and Technology, Japan
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Zhi Y, Wang D, Zhang K, Wang Y, Geng W, Chen B, Li H, Li Z, Tian Y, Kang X, Liu X. Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds. Animals (Basel) 2023; 13:753. [PMID: 36830540 PMCID: PMC9952073 DOI: 10.3390/ani13040753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
There are five indigenous chicken breeds in Henan Province, China. These breeds have their own unique phenotypic characteristics in terms of morphology, behavior, skin and feather color, and productive performance, but their genetic basis is not well understood. Therefore, we analyzed the genetic structure, genomic diversity, and migration history of Henan indigenous chicken populations and the selection signals and genes responsible for Henan gamecock unique phenotypes using whole genome resequencing. The results indicate that Henan native chickens clustered most closely with the chicken populations in neighboring provinces. Compared to other breeds, Henan gamecock's inbreeding and selection intensity were more stringent. TreeMix analysis revealed the gene flow from southern chicken breeds into the Zhengyang sanhuang chicken and from the Xichuan black-bone chicken into the Gushi chicken. Selective sweep analysis identified several genes and biological processes/pathways that were related to body size, head control, muscle development, reproduction, and aggression control. Additionally, we confirmed the association between genotypes of SNPs in the strong selective gene LCORL and body size and muscle development in the Gushi-Anka F2 resource population. These findings made it easier to understand the traits of the germplasm and the potential for using the Henan indigenous chicken.
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Affiliation(s)
- Yihao Zhi
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
| | - Dandan Wang
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
| | - Ke Zhang
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
| | - Yangyang Wang
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
| | - Wanzhuo Geng
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
| | - Botong Chen
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
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