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Budi T, Luu AH, Singchat W, Wongloet W, Rey J, Kumnan N, Chalermwong P, Nguyen CPT, Panthum T, Tanglertpaibul N, Thong T, Ali H, Vangnai K, Chaiyes A, Yokthongwattana C, Sinthuvanich C, Han K, Antunes A, Muangmai N, Duengkae P, Srikulnath K. Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds. Genes Genomics 2024:10.1007/s13258-024-01561-3. [PMID: 39215948 DOI: 10.1007/s13258-024-01561-3] [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: 07/12/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear. OBJECTIVE To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption. METHODS Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from "The Siam Chicken Bioresource Project" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals. RESULT The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks. CONCLUSION Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds.
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Affiliation(s)
- Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Anh Huynh Luu
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, 10900, Thailand.
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Juniman Rey
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Chien Phuoc Tran Nguyen
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Nivit Tanglertpaibul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Hina Ali
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Kanithaporn Vangnai
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi, 11120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Chomdao Sinthuvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Department of Microbiology, College of Bio-Convergence, Dankook University, Cheonan, 31116, Republic of Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Republic of Korea
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea
| | - Agostinho Antunes
- CIIMAR/CIMAR, Terminal de Cruzeiros do Porto de Leixões, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand.
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Gu LH, Wu RR, Zheng XL, Fu A, Xing ZY, Chen YY, He ZC, Lu LZ, Qi YT, Chen AH, Zhang YP, Xu TS, Peng MS, Ma C. Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens. Poult Sci 2024; 103:103376. [PMID: 38228059 PMCID: PMC10823079 DOI: 10.1016/j.psj.2023.103376] [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: 09/27/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.
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Affiliation(s)
- Li-Hong Gu
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Ran-Ran Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li Zheng
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - An Fu
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China
| | - Zeng-Yang Xing
- Wenchang Long-quan Wenchang Chicken Industrial Co., Ltd., Wenchang 571346, China
| | - Yi-Yong Chen
- Hainan Chuang Wen Wenchang Chicken Industry Co., Ltd., Wenchang 571321, China
| | - Zhong-Chun He
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Li-Zhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yan-Tao Qi
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - An-Hong Chen
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tie-Shan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min-Sheng Peng
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Ma
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China.
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Tan X, Zhang J, Dong J, Huang M, Li Q, Wang H, Bai L, Cui M, Zhou Z, Yang S, Wang D. Whole-genome variants dataset of 209 local chickens from China. Sci Data 2024; 11:169. [PMID: 38316816 PMCID: PMC10844214 DOI: 10.1038/s41597-024-02995-w] [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: 03/24/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024] Open
Abstract
Compared to commercial chickens, local breeds exhibit better in meat quality and flavour, but the productivity (e.g., growth rate, body weight) of local chicken breeds is rather low. Genetic analysis based on whole-genome sequencing contributes to elucidating the genetic markers or putative candidate genes related to some economic traits, facilitating the improvement of production performance, the acceleration of breeding progress, and the conservation of genetic resources. Here, a total of 209 local chickens from 13 breeds were investigated, and the observation of approximately 91.4% high-quality sequences (Q30 > 90%) and a mapping rate over 99% for each individual indicated good results of this study, as confirmed by a genome coverage of 97.6%. Over 19 million single nucleotide polymorphisms (SNPs) and 1.98 million insertion-deletions (InDels) were identified using the reference genome (GRCg7b), further contributing to the public database. This dataset provides valuable resources for studying genetic diversity and adaptation and for the cultivation of new chicken breeds/lines.
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Affiliation(s)
- Xiaodong Tan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiawen Zhang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghai Li
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Huanhuan Wang
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Lijuan Bai
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Ming Cui
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Zhenzhen Zhou
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shuyuan Yang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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4
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Ren X, Guan Z, Li H, Zhang L, Wen J, Zhao X, Wang G, Zhang X, Wang H, Yu F, Chen Z, Qu L. Phylogenetic analysis reveals multiple origins of Chinese gamecocks. Poult Sci 2023; 102:103068. [PMID: 37778296 PMCID: PMC10550403 DOI: 10.1016/j.psj.2023.103068] [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: 06/08/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023] Open
Abstract
Cockfighting is popular worldwide, dating back to 2,800 BC. Primarily, 5 modern Chinese gamecock breeds exist, located in the northeast (Luxi and Henan), west (Turpan), south (Xishuangbanna), and southeast (Zhangzhou) of China. However, whether Chinese gamecocks were derived from a single origin or multiple origins remains controversial. Therefore, this study used next-generation resequencing data to elucidate the origin of Chinese gamecocks by constructing genome-wide and SRY-box transcription factor 5 (SOX5) gene phylogenetic trees. Data from 161 chickens from 27 breeds, including 9 gamecock breeds, were included. Before constructing the SOX5 gene tree, we validated that the pea-comb phenotype mutation in all gamecock breeds was attributed to copy number variation in intron 1 of the SOX5 gene, as previously reported. The specific region was chr1: 65,838,000 to 65,846,000. The phylogenetic tree results suggested that Zhangzhou and Xishuangbanna gamecocks have a monophyletic origin, while Luxi, Henan, and Turpan gamecocks have a common ancestor. Our study provides genome-wide evidence that Chinese gamecocks have multiple origins and advances the understanding of the genetic mechanisms of the pea-comb characteristic.
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Affiliation(s)
- Xufang Ren
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zi Guan
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China
| | - Li Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Junhui Wen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huie Wang
- Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Fuqing Yu
- National Animal Husbandry Station, Beijing 100125, China
| | - Zhihua Chen
- Beijing Lanbo Manor Technology Co., Ltd., Beijing 100085, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China.
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