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Lv FH, Cao YH, Liu GJ, Luo LY, Lu R, Liu MJ, Li WR, Zhou P, Wang XH, Shen M, Gao L, Yang JQ, Yang H, Yang YL, Liu CB, Wan PC, Zhang YS, Pi WH, Ren YL, Shen ZQ, Wang F, Wang YT, Li JQ, Salehian-Dehkordi H, Hehua E, Liu YG, Chen JF, Wang JK, Deng XM, Esmailizadeh A, Dehghani-Qanatqestani M, Charati H, Nosrati M, Štěpánek O, Rushdi HE, Olsaker I, Curik I, Gorkhali NA, Paiva SR, Caetano AR, Ciani E, Amills M, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Periasamy K, Johansson AM, Hallsson JH, Kantanen J, Coltman DW, Bruford MW, Lenstra JA, Li MH. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci. Mol Biol Evol 2021; 39:6459180. [PMID: 34893856 PMCID: PMC8826587 DOI: 10.1093/molbev/msab353] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
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Affiliation(s)
- Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ran Lu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jian-Fei Chen
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Kui Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xue-Mei Deng
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Hadi Charati
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Animal Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
- CTLGH and SRUC, The Roslin Institute Building, Easter Bush Campus, Edinburgh, Scotland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jón H Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, Wales, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Wales, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Corresponding author: E-mail:
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Cao YH, Xu SS, Shen M, Chen ZH, Gao L, Lv FH, Xie XL, Wang XH, Yang H, Liu CB, Zhou P, Wan PC, Zhang YS, Yang JQ, Pi WH, Hehua EE, Berry DP, Barbato M, Esmailizadeh A, Nosrati M, Salehian-Dehkordi H, Dehghani-Qanatqestani M, Dotsev AV, Deniskova TE, Zinovieva NA, Brem G, Štěpánek O, Ciani E, Weimann C, Erhardt G, Mwacharo JM, Ahbara A, Han JL, Hanotte O, Miller JM, Sim Z, Coltman D, Kantanen J, Bruford MW, Lenstra JA, Kijas J, Li MH. Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep. Mol Biol Evol 2021; 38:838-855. [PMID: 32941615 PMCID: PMC7947771 DOI: 10.1093/molbev/msaa236] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.
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Affiliation(s)
- Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - EEr Hehua
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Hui Autonomous Region, Yinchuan, Ningxia, China
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24, Moro, Bari, Italy
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Addis Abeba, Ethiopia
- Center for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Fish and Wildlife Enforcement Branch Forensic Unit, Government of Alberta, Edmonton, AB, Canada
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, QLD, Australia
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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3
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Li X, Yang J, Shen M, Xie XL, Liu GJ, Xu YX, Lv FH, Yang H, Yang YL, Liu CB, Zhou P, Wan PC, Zhang YS, Gao L, Yang JQ, Pi WH, Ren YL, Shen ZQ, Wang F, Deng J, Xu SS, Salehian-Dehkordi H, Hehua E, Esmailizadeh A, Dehghani-Qanatqestani M, Štěpánek O, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Lenstra JA, Kantanen J, Coltman DW, Kijas JW, Bruford MW, Periasamy K, Wang XH, Li MH. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat Commun 2020; 11:2815. [PMID: 32499537 PMCID: PMC7272655 DOI: 10.1038/s41467-020-16485-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/04/2020] [Indexed: 01/15/2023] Open
Abstract
Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.
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Affiliation(s)
- Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Ya-Xi Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Ondřej Štěpánek
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Christina Weimann
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, Germany
| | - Georg Erhardt
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Center for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - James W Kijas
- CSIRO Livestock Industries, St Lucia, Brisbane, QLD, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
- Sustainable Places Research Institute, Cardiff University, CF10 3BA, Cardiff, Wales, UK
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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