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Wang MS, Zhang JJ, Guo X, Li M, Meyer R, Ashari H, Zheng ZQ, Wang S, Peng MS, Jiang Y, Thakur M, Suwannapoom C, Esmailizadeh A, Hirimuthugoda NY, Zein MSA, Kusza S, Kharrati-Koopaee H, Zeng L, Wang YM, Yin TT, Yang MM, Li ML, Lu XM, Lasagna E, Ceccobelli S, Gunwardana HGTN, Senasig TM, Feng SH, Zhang H, Bhuiyan AKFH, Khan MS, Silva GLLP, Thuy LT, Mwai OA, Ibrahim MNM, Zhang G, Qu KX, Hanotte O, Shapiro B, Bosse M, Wu DD, Han JL, Zhang YP. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biol 2021; 19:118. [PMID: 34130700 PMCID: PMC8207802 DOI: 10.1186/s12915-021-01052-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/19/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.
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Affiliation(s)
- Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Rachel Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hidayat Ashari
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Bogor, 16911, Indonesia.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Zhu-Qing Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Mukesh Thakur
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Phayao, 56000, Thailand.,Unit of Excellence on Biodiversity and Natural Resources Management, University of Phayao, Phayao, 56000, Thailand
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Department of Animal Science, Shahid Bahonar University of Kerman, P.O. Box 76169133, Kerman, Iran
| | - Nalini Yasoda Hirimuthugoda
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Moch Syamsul Arifin Zein
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Bogor, 16911, Indonesia
| | - Szilvia Kusza
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, H-4032, Hungary
| | - Hamed Kharrati-Koopaee
- Department of Animal Science, Shahid Bahonar University of Kerman, P.O. Box 76169133, Kerman, Iran.,Institute of Biotechnology, School of Agriculture, Shiraz University, P.O. Box 1585, Shiraz, Iran
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yun-Mei Wang
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xue-Mei Lu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, 06123, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, 06123, Perugia, Italy
| | | | | | - Shao-Hong Feng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Hao Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Ministry of Agriculture of China, Beijing, 100193, China
| | | | | | | | - Le Thi Thuy
- National Institute of Animal Husbandry, Hanoi, Vietnam
| | - Okeyo A Mwai
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | | | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-1870, Copenhagen, Denmark
| | - Kai-Xing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Livestock Genetics Program, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mirte Bosse
- Wageningen University & Research - Animal Breeding and Genomics, 6708 PB, Wageningen, The Netherlands.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. .,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China. .,State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, China.
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