1
|
Colombi D, Perini F, Bettini S, Mastrangelo S, Abeni F, Conte G, Marletta D, Cassandro M, Bernabucci U, Ciampolini R, Lasagna E. Genomic responses to climatic challenges in beef cattle: A review. Anim Genet 2024. [PMID: 39219301 DOI: 10.1111/age.13474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/31/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Climate change is a major concern for the near future and for livestock breeding. Cattle breeding, due to its greenhouse gas emissions, is one of the most implicated industries. Consequently, the main future goals are to breed animals resilient to climate change, with the aim of lowering the livestock impact on the environment and selecting animals that will be able to resist different, unsuitable, and changing climates. The aim of this literature review is to compare the most recent studies on the response and adaptation of beef cattle breeds to extreme environments, in terms of genes and pathways involved. Beef breeding is just starting to implement genomics in its selection plans, and shedding light on the genomic responses to extreme climates could speed up and simplify the adaptation of these breeds to climate change. This review discusses the genes involved in climatic stress responses, including those related to extremely cold climates, in beef and dual-purpose cattle breeds. Genes were associated with productive traits, coat and skin structure and development, thermotolerance, cellular physiology and DNA repair mechanisms, immune system, and fertility traits. The knowledge of genes and pathways involved in climate resilience should be taken into consideration for further selection in beef cattle breeding and could promote the valorization of local breeds adapted to extreme environmental conditions. The use of local or resilient breeds could enhance the environmental and social sustainability, animal welfare, and production, compared with the introduction of cosmopolitan breeds with uncertain adaptation in uncontrolled environmental areas.
Collapse
Affiliation(s)
- Daniele Colombi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Francesco Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Stefano Bettini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Fabio Abeni
- Centro di Ricerca Zootecnia e Acquacoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Lodi, Italy
| | - Giuseppe Conte
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| | - Donata Marletta
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| | - Umberto Bernabucci
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Agriculture and Forest Sciences, Università Della Tuscia, Viterbo, Italy
| | - Roberta Ciampolini
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| |
Collapse
|
2
|
Cuellar CJ, Amaral TF, Rodriguez‐Villamil P, Ongaratto F, Martinez DO, Labrecque R, Losano JDDA, Estrada‐Cortés E, Bostrom JR, Martins K, Rae DO, Block J, Hoorn QA, Daigneault BW, Merriam J, Lohuis M, Dikmen S, Bittar JHJ, Maia TS, Carlson DF, Larson S, Sonstegard TS, Hansen PJ. Consequences of gene editing of PRLR on thermotolerance, growth, and male reproduction in cattle. FASEB Bioadv 2024; 6:223-234. [PMID: 39114445 PMCID: PMC11301273 DOI: 10.1096/fba.2024-00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 08/10/2024] Open
Abstract
Global warming is a major challenge to the sustainable and humane production of food because of the increased risk of livestock to heat stress. Here, the example of the prolactin receptor (PRLR) gene is used to demonstrate how gene editing can increase the resistance of cattle to heat stress by the introduction of mutations conferring thermotolerance. Several cattle populations in South and Central America possess natural mutations in PRLR that result in affected animals having short hair and being thermotolerant. CRISPR/Cas9 technology was used to introduce variants of PRLR in two thermosensitive breeds of cattle - Angus and Jersey. Gene-edited animals exhibited superior ability to regulate vaginal temperature (heifers) and rectal temperature (bulls) compared to animals that were not gene-edited. Moreover, gene-edited animals exhibited superior growth characteristics and had larger scrotal circumference. There was no evidence for deleterious effects of the mutation on carcass characteristics or male reproductive function. These results indicate the potential for reducing heat stress in relevant environments to enhance cattle productivity.
Collapse
Affiliation(s)
- Camila J. Cuellar
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Thiago F. Amaral
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
- Present address:
Genus PLC/ABSSão PauloBrazil
| | | | - F. Ongaratto
- AcceligenEaganMinnesotaUSA
- Present address:
University of Wisconsin Biotechnology CenterMadisonWisconsinUSA
| | - D. Onan Martinez
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
- Department of Large Animal Clinical Sciences, College of Veterinary MedicineUniversity of FloridaGainesvilleFloridaUSA
| | | | | | - Eliab Estrada‐Cortés
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
- Campo Experimental Centro Altos de JaliscoInstituto Nacional de Investigaciones Forestales, Agrícola y PecuariasTepatitlán de MorelosMexico
| | | | | | - D. Owen Rae
- Department of Large Animal Clinical Sciences, College of Veterinary MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Jeremy Block
- Department of Animal ScienceUniversity of WyomingLaramieWyomingUSA
| | - Quinn A. Hoorn
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
| | | | | | | | - Serdal Dikmen
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
- Faculty of Veterinary Medicine, Department of Animal ScienceBursa Uludag UniversityBursaTurkey
| | - João H. J. Bittar
- Department of Large Animal Clinical Sciences, College of Veterinary MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Tatiane S. Maia
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
| | | | | | | | - Peter J. Hansen
- Department of Animal SciencesUniversity of FloridaGainesvilleFloridaUSA
| |
Collapse
|
3
|
Ostridge HJ, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM. Local genetic adaptation to habitat in wild chimpanzees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.601734. [PMID: 39026872 PMCID: PMC11257515 DOI: 10.1101/2024.07.09.601734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.
Collapse
Affiliation(s)
- Harrison J Ostridge
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Daniela C Soto
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Joshua M Schmidt
- Flinders Health and Medical Research Institute (FHMRI), Department of Ophthalmology, Flinders University Sturt Rd, Bedford Park South Australia 5042 Australia
| | - Vrishti Saxena
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Marina Alvarez-Estape
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Christopher D Barratt
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Paolo Gratton
- University of Rome "Tor Vergata" Department of Biology Via Cracovia, 1, Roma, Italia
| | - Gaëlle Bocksberger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage, 60325 Frankfurt am Main, Germany
| | - Jack D Lester
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Alfred Kwabena Assumang
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emma Bailey
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Donatienne Barubiyo
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- University of Konstanz, Centre for the Advanced Study of Collective Behaviour, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Rebecca Chancellor
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, 19382 USA
| | - Heather Cohen
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Charlotte Coupland
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tobias Deschner
- Institute of Cognitive Science, University of Osnabrück, Artilleriestrasse 34, 49076 Osnabrück, Germany
| | - Laia Dotras
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Jef Dupain
- Antwerp Zoo Foundation, RZSA, Kon.Astridplein 26, 2018 Antwerp, Belgium
| | - Villard Ebot Egbe
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Anne-Céline Granjon
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Josephine Head
- The Biodiversity Consultancy, 3E Kings Parade, Cambridge, CB2 1SJ, UK
| | - Daniela Hedwig
- Elephant Listening Project, K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Veerle Hermans
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
| | - R Adriana Hernandez-Aguilar
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Kathryn J Jeffery
- School of Natural Sciences, University of Stirling, UK
- Agence National des Parcs Nationaux (ANPN) Batterie 4, BP20379, Libreville, Gabon
| | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Jessica Junker
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Parag Kadam
- Greater Mahale Ecosystem Research and Conservation Project
| | - Michael Kaiser
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Ammie K Kalan
- Department of Anthropology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada
| | - Mbangi Kambere
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Ivonne Kienast
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY 14850, USA
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Deo Kujirakwinja
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard. Bronx, New York 10460, USA
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Institute of Human Origins, Arizona State University, 777 East University Drive, Tempe, AZ 85287 Arizona State University, PO Box 872402, Tempe, AZ 85287-2402 USA
- Institute of Human Origins, Arizona State University, 900 Cady Mall, Tempe, AZ 85287 Arizona State University, PO Box 872402, Tempe, AZ 85287-2402 USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | | | | | - Kevin C Lee
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Manuel Llana
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Rumen Martín
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Amelia Meier
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- Hawai'i Insititute of Marine Biology, University of Hawai'i at Manoa, 46-007 Lilipuna Place, Kaneohe, HI, 96744, USA
| | - David Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark Street, Chicago, Illinois 60614 USA
| | - Emily Neil
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Sonia Nicholl
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Stuart Nixon
- North of England Zoological Society, Chester Zoo, Upton by Chester, CH2 1LH, United Kingdom
| | | | - Christopher Orbell
- Panthera, 8 W 40TH ST, New York, NY 10018, USA
- School of Natural Sciences, University of Stirling, UK
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Robinson Orume
- Korup Rainforest Conservation Society, c/o Korup National Park, P.O. Box 36 Mundemba, South West Region, Cameroon
| | - Liliana Pacheco
- Save the Dogs and Other Animals, DJ 223 Km 3, 905200 Cernavoda CT, Romania
| | - Jodie Preece
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Department of Primate Behavior and Evolution, Deutscher Platz 6, 04103 Leipzig
| | - Aaron Rundus
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, 19382 USA
| | - Crickette Sanz
- Washington University in Saint Louis, Department of Anthropology, One Brookings Drive, St. Louis, MO 63130, USA
- Congo Program, Wildlife Conservation Society, 151 Avenue Charles de Gaulle, Brazzaville, Republic of Congo
| | - Lilah Sciaky
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Volker Sommer
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
| | - Fiona A Stewart
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Nikki Tagg
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Born Free Foundation, Floor 2 Frazer House, 14 Carfax, Horsham, RH12 1ER, UK
| | - Luc Roscelin Tédonzong
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
| | - Joost van Schijndel
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Elleni Vendras
- Frankfurt Zoological Society, Bernhard-Grzimek-Allee 1, 60316 Frankfurt, Germany
| | - Erin G Wessling
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen,Göttingen, Germany
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jacob Willie
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University (UGent), K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Roman M Wittig
- Ape Social Mind Lab, Institute for Cognitive Sciences Marc Jeannerod, CNRS UMR 5229 CNRS, 67 bd Pinel, 69675 Bron CEDEX, France
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, BP 1301, Abidjan 01, CI
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Kyle Yurkiw
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Alex Piel
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
| | | | - Hjalmar S Kühl
- Senckenberg Museum for Natural History Görlitz, Senckenberg - Member of the Leibniz Association Am Museum 1, 02826 Görlitz, Germany
- International Institute Zittau, Technische Universität Dresden, Markt 23, 02763 Zittau, Germany
| | - Megan Y Dennis
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Department of Primate Behavior and Evolution, Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103
| | - Aida M Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| |
Collapse
|
4
|
Sjodin BMF, Schmidt DA, Galbreath KE, Russello MA. Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients. Sci Rep 2024; 14:8568. [PMID: 38609461 PMCID: PMC11014952 DOI: 10.1038/s41598-024-59157-6] [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: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.
Collapse
Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Danielle A Schmidt
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, 1401 Presque Isle Ave, Marquette, MI, 49855, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
| |
Collapse
|
5
|
Laodim T, Koonawootrittriron S, Elzo MA, Suwanasopee T, Jattawa D, Sarakul M. Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations. Anim Biosci 2024; 37:576-590. [PMID: 37946425 PMCID: PMC10915225 DOI: 10.5713/ab.23.0246] [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: 07/04/2023] [Revised: 08/27/2023] [Accepted: 10/01/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. METHODS A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-yearseason, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. RESULTS A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. CONCLUSION Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.
Collapse
Affiliation(s)
- Thawee Laodim
- Department of Animal Science, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140,
Thailand
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, 10900,
Thailand
| | - Mauricio A. Elzo
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Sciences, University of Florida, Gainesville, 32611-0910, FL,
USA
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, 10900,
Thailand
| | - Danai Jattawa
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, 10900,
Thailand
| | - Mattaneeya Sarakul
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture and Technology, Nakhon Phanom University, Nakhon Phanom, 48000,
Thailand
| |
Collapse
|
6
|
Su X, Lu R, Qu Y, Mu D. Methyltransferase-like 3 mediated RNA m 6 A modifications in the reproductive system: Potentials for diagnosis and therapy. J Cell Mol Med 2024; 28:e18128. [PMID: 38332508 PMCID: PMC10853593 DOI: 10.1111/jcmm.18128] [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: 10/24/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Several studies have highlighted the functional indispensability of methyltransferase-like 3 (METTL3) in the reproductive system. However, a review that comprehensively interprets these studies and elucidates their relationships is lacking. Therefore, the present work aimed to review studies that have investigated the functions of METTL3 in the reproductive system (including spermatogenesis, follicle development, gametogenesis, reproductive cancer, asthenozoospermia and assisted reproduction failure). This review suggests that METTL3 functions not only essential for normal development, but also detrimental in the occurrence of disorders. In addition, promising applications of METTL3 as a diagnostic or prognostic biomarker and therapeutic target for reproductive disorders have been proposed. Collectively, this review provides comprehensive interpretations, novel insights, potential applications and future perspectives on the role of METTL3 in regulating the reproductive system, which may be a valuable reference for researchers and clinicians.
Collapse
Affiliation(s)
- Xiaojuan Su
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education)West China Second University Hospital, Sichuan UniversityChengduChina
- NHC Key Laboratory of Chronobiology (Sichuan University)ChengduChina
| | - Ruifeng Lu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education)West China Second University Hospital, Sichuan UniversityChengduChina
- NHC Key Laboratory of Chronobiology (Sichuan University)ChengduChina
| | - Yi Qu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education)West China Second University Hospital, Sichuan UniversityChengduChina
- NHC Key Laboratory of Chronobiology (Sichuan University)ChengduChina
| | - Dezhi Mu
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education)West China Second University Hospital, Sichuan UniversityChengduChina
- NHC Key Laboratory of Chronobiology (Sichuan University)ChengduChina
| |
Collapse
|
7
|
Lyu Y, Guan X, Xu X, Wang P, Li Q, Panigrahi M, Zhang J, Chen N, Huang B, Lei C. A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province. Anim Genet 2023; 54:731-742. [PMID: 37796667 DOI: 10.1111/age.13363] [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: 03/20/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 10/07/2023]
Abstract
Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome-wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.
Collapse
Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinglong Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiaoxian Li
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| |
Collapse
|
8
|
Pallotti S, Picciolini M, Antonini M, Renieri C, Napolioni V. Genome-wide scan for runs of homozygosity in South American Camelids. BMC Genomics 2023; 24:470. [PMID: 37605116 PMCID: PMC10440933 DOI: 10.1186/s12864-023-09547-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. RESULTS A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. CONCLUSIONS The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
Collapse
Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
| | | | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| |
Collapse
|
9
|
Zegeye T, Belay G, Vallejo-Trujillo A, Han J, Hanotte O. Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Front Genet 2023; 14:1050365. [PMID: 37600659 PMCID: PMC10432725 DOI: 10.3389/fgene.2023.1050365] [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: 09/21/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The Tigray region, where we found around eight per cent of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations of the Fertile Crescent and the Indian subcontinent. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million SNPs and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel. Functional annotation of the variants showed around 0.01% SNPs and 0.22%-0.27% indels in coding regions. Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds. They included important genes associated with morphology (SCN4A, TAS1R2 and KCNG4), milk yield (GABRG1), meat quality (MMRN2, VWC2), feed efficiency (PCDH8 and SLC26A3), immune response (LAMC1, PCDH18, CELSR1, TLR6 and ITGA5), heat resistance (NPFFR1 and HTR7) and genes belonging to the olfactory gene family, which may be related to adaptation to harsh environments. Tigray indigenous cattle are very diverse. Their genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036. The number of heterozygous SNPs was about 0.6-0.7 times higher than homozygous ones. The within-breed average number of ROHs ranged from 777.82 to 1000.45, with the average sum of the length of ROHs ranging from 122.01 Mbp to 163.88 Mbp. The genomic inbreeding coefficients differed among animals and breeds, reaching up to 10% in some Begait and Raya animals. Tigray indigenous cattle shared a common ancestry with Asian indicine (85.6%-88.7%) and African taurine (11.3%-14.1%) cattle, with very small, if any, European taurine introgression. This study identified high within-breed genetic diversity representing an opportunity for breeding improvement programs and, also, significant novel variants that could increase the number of known cattle variants, an important contribution to the knowledge of domestic cattle genetic diversity.
Collapse
Affiliation(s)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adriana Vallejo-Trujillo
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jianlin Han
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
10
|
Salehian-Dehkordi H, Huang JH, Pirany N, Mehrban H, Lv XY, Sun W, Esmailizadeh A, Lv FH. Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep. Genes (Basel) 2023; 14:1256. [PMID: 37372436 PMCID: PMC10298528 DOI: 10.3390/genes14061256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.
Collapse
Affiliation(s)
- Hosein Salehian-Dehkordi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Jia-Hui Huang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
| | - Nasrollah Pirany
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Hossein Mehrban
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Xiao-Yang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
| |
Collapse
|
11
|
Álvarez-Rodríguez M, Roca J, Martínez EA, Rodríguez-Martínez H. Mating modifies the expression of crucial oxidative-reductive transcripts in the pig oviductal sperm reservoir: is the female ensuring sperm survival? Front Endocrinol (Lausanne) 2023; 14:1042176. [PMID: 37351104 PMCID: PMC10282951 DOI: 10.3389/fendo.2023.1042176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/17/2023] [Indexed: 06/24/2023] Open
Abstract
Background Mating induces large changes in the female genital tract, warranting female homeostasis and immune preparation for pregnancy, including the preservation of crucial oxidative status among its pathways. Being highly susceptible to oxidative stress, sperm survival and preserved function depend on the seminal plasma, a protection that is removed during sperm handling but also after mating when spermatozoa enter the oviduct. Therefore, it is pertinent to consider that the female sperm reservoir takes up this protection, providing a suitable environment for sperm viability. These aspects have not been explored despite the increasing strategies in modulating the female status through diet control and nutritional supplementation. Aims To test the hypothesis that mating modifies the expression of crucial oxidative-reductive transcripts across the entire pig female genital tract (cervix to infundibulum) and, particularly in the sperm reservoir at the utero-tubal junction, before ovulation, a period dominated by estrogen stimulation of ovarian as well as of seminal origin. Methods The differential expression of estrogen (ER) and progesterone (PR) receptors and of 59 oxidative-reductive transcripts were studied using a species-specific microarray platform, in specific segments of the peri-ovulatory sow reproductive tract in response to mating. Results Mating induced changes along the entire tract, with a conspicuous downregulation of both ER and PR and an upregulation of superoxide dismutase 1 (SOD1), glutaredoxin (GLRX3), and peroxiredoxin 1 and 3 (PRDX1, PRDX3), among other NADH Dehydrogenase Ubiquinone Flavoproteins, in the distal uterus segment. These changes perhaps helped prevent oxidative stress in the area adjacent to the sperm reservoir at the utero-tubal junction. Concomitantly, there were a downregulation of catalase (CAT) and NADH dehydrogenase (ubiquinone) oxidoreductases 1 beta subcomplex, subunit 1 (NDUFB1) in the utero-tubal junction alongside an overall downregulation of CAT, SOD1, and PRDX3 in the ampullar and infundibulum segments. Conclusions Natural mating is an inducer of changes in the expression of female genes commanding antioxidant enzymes relevant for sperm survival during sperm transport, under predominant estrogen influence through the bloodstream and semen. The findings could contribute to the design of new therapeutics for the female to improve oxidative-reductive balance.
Collapse
Affiliation(s)
- Manuel Álvarez-Rodríguez
- Department of Biomedical and Clinical Sciences (BKV), BKH/Obstetrics and Gynecology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Department of Animal Reproduction, Instituto Nacional de Investigación Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
| | - Jordi Roca
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, University of Murcia, Murcia, Spain
| | - Emilio A. Martínez
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, University of Murcia, Murcia, Spain
| | - Heriberto Rodríguez-Martínez
- Department of Biomedical and Clinical Sciences (BKV), BKH/Obstetrics and Gynecology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| |
Collapse
|
12
|
Terefe E, Belay G, Han J, Hanotte O, Tijjani A. Genomic adaptation of Ethiopian indigenous cattle to high altitude. Front Genet 2022; 13:960234. [PMID: 36568400 PMCID: PMC9780680 DOI: 10.3389/fgene.2022.960234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.
Collapse
Affiliation(s)
- Endashaw Terefe
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia,International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella, Ethiopia,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
| |
Collapse
|
13
|
Jones HE, Wilson PB. Progress and opportunities through use of genomics in animal production. Trends Genet 2022; 38:1228-1252. [PMID: 35945076 DOI: 10.1016/j.tig.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
Abstract
The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.
Collapse
Affiliation(s)
- Huw E Jones
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK.
| | - Philippe B Wilson
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK
| |
Collapse
|
14
|
Zhao X, Zhang J, Wang H, Li H, Qu C, Wen J, Zhang X, Zhu T, Nie C, Li X, Muhatai G, Wang L, Lv X, Yang W, Zhao C, Bao H, Li J, Zhu B, Cao G, Xiong W, Ning Z, Qu L. Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens. Genomics 2022; 114:110485. [PMID: 36126832 DOI: 10.1016/j.ygeno.2022.110485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/27/2022] [Accepted: 09/16/2022] [Indexed: 01/14/2023]
Abstract
Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.
Collapse
Affiliation(s)
- Xiurong Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jinxin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Huie Wang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China.
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui 236037, China.
| | - Junhui Wen
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinye Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinghua Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Gemingguli Muhatai
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - XueZe Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Chunjiang Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haigang Bao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Junying Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Bo Zhu
- Animal Health Supervision Institute of Zhuozhou, Hebei Province 072750, China.
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Guangxi Province 538001, China.
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Guangxi Province 538001, China.
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
15
|
Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
Collapse
|
16
|
Zhang S, Yao Z, Li X, Zhang Z, Liu X, Yang P, Chen N, Xia X, Lyu S, Shi Q, Wang E, Ru B, Jiang Y, Lei C, Chen H, Huang Y. Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data. BMC Genomics 2022; 23:460. [PMID: 35729510 PMCID: PMC9215082 DOI: 10.1186/s12864-022-08645-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide. RESULTS: Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, FST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2). CONCLUSION In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.
Collapse
Affiliation(s)
- Shunjin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Zhi Yao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Xinmiao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou Henan, 450008, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou Henan, 450008, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China.
| |
Collapse
|
17
|
Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
Collapse
Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
| |
Collapse
|
18
|
Hou H, Wang X, Ding W, Xiao C, Cai X, Lv W, Tu Y, Zhao W, Yao J, Yang C. Whole-genome sequencing reveals the artificial selection and local environmental adaptability of pigeons ( Columba livia). Evol Appl 2022; 15:603-617. [PMID: 35505885 PMCID: PMC9046921 DOI: 10.1111/eva.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/17/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro-pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.
Collapse
Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural SciencesShanghaiChina
- National Poultry Engineer Research CenterShanghaiChina
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural SciencesShanghaiChina
- National Poultry Engineer Research CenterShanghaiChina
| | - Weixing Ding
- Shanghai Academy of Agricultural SciencesShanghaiChina
| | - Changfeng Xiao
- Shanghai Academy of Agricultural SciencesShanghaiChina
- National Poultry Engineer Research CenterShanghaiChina
| | - Xia Cai
- Shanghai Academy of Agricultural SciencesShanghaiChina
- National Poultry Engineer Research CenterShanghaiChina
| | - Wenwei Lv
- National Poultry Engineer Research CenterShanghaiChina
| | - Yingying Tu
- National Poultry Engineer Research CenterShanghaiChina
| | - Weimin Zhao
- Shanghai Jinhuang Pigeon CompanyShanghaiChina
| | - Junfeng Yao
- Shanghai Academy of Agricultural SciencesShanghaiChina
- National Poultry Engineer Research CenterShanghaiChina
| | - Changsuo Yang
- Shanghai Academy of Agricultural SciencesShanghaiChina
- National Poultry Engineer Research CenterShanghaiChina
| |
Collapse
|
19
|
Cavedon M, vonHoldt B, Hebblewhite M, Hegel T, Heppenheimer E, Hervieux D, Mariani S, Schwantje H, Steenweg R, Watters M, Musiani M. Selection of both habitat and genes in specialized and endangered caribou. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36. [PMID: 35146809 DOI: 10.1111/cobi.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Genetic mechanisms determining habitat selection and specialization of individuals within species have been hypothesized, but not tested at the appropriate individual level in nature. In this work, we analyzed habitat selection for 139 GPS-collared caribou belonging to three declining ecotypes sampled throughout Northwestern Canada. We used Resource Selection Functions (RSFs) comparing resources at used and available locations. We found that the three caribou ecotypes differed in their use of habitat suggesting specialization. On expected grounds, we also found differences in habitat selection between summer and winter, but also, originally, among the individuals within an ecotype. We next obtained Single Nucleotide Polymorphisms (SNPs) for the same caribou individuals, we detected those associated to habitat selection, and then identified genes linked to these SNPs. These genes had functions related in other organisms to habitat and dietary specializations, and climatic adaptations. We therefore suggest that individual variation in habitat selection was based on genotypic variation in the SNPs of individual caribou, indicating that genetic forces underlie habitat and diet selection in the species. We also suggest that the associations between habitat and genes that we detected may lead to lack of resilience in the species, thus contributing to caribou endangerment. Our work emphasizes that similar mechanisms may exist for other specialized, endangered species. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Montana, MT, 59812, USA
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Y1A 2C6, Canada
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, 4999 98 Ave., Edmonton, AB, T6B 2×3, Canada
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, AB, T8V 6J4, Canada
| | - Stefano Mariani
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC, V9T 6J 9, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - Megan Watters
- Land and Resource Specialist, 300 - 10003 110th Avenue Fort, St. John, BC, V1J 6M7, Canada
| | - Marco Musiani
- Dept. of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, AB, T2N 1N4, Canada
| |
Collapse
|
20
|
Genomics Confirm an Alarming Status of the Genetic Diversity of Belgian Red and Belgian White Red Cattle. Animals (Basel) 2021; 11:ani11123574. [PMID: 34944349 PMCID: PMC8697887 DOI: 10.3390/ani11123574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Genetic diversity of livestock is vitally important as it enables the adaptation of future populations to changing environments. Therefore, preserving a sufficiently large genetic diversity is key. However, for many local cattle populations, little is known about their genetic diversity such as inbreeding level, effective size etc. We studied the genetic diversity of two local Belgian red cattle populations (Belgian Red and Belgian White Red cattle) using state-of-the-art genomic techniques. These tools assessed diversity at the population and individual level, and allowed the positioning of these two breeds in an international context of 52 other (European) cattle breeds. Accordingly, we contribute to the general knowledge of European red cattle, and more specifically we help the breeders, breed organization and the government to manage the genetic diversity of both breeds. Abstract Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and Fst analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, Fst and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, Fst analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.
Collapse
|
21
|
Antonopoulos D, Vougiouklaki D, Laliotis GP, Tsironi T, Valasi I, Chatzilazarou A, Halvatsiotis P, Houhoula D. Identification of Polymorphisms of the CSN2 Gene Encoding β-Casein in Greek Local Breeds of Cattle. Vet Sci 2021; 8:vetsci8110257. [PMID: 34822630 PMCID: PMC8625921 DOI: 10.3390/vetsci8110257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
This e research focused on the detection and identification of genetic polymorphisms in exon 7 of the β-casein CSN2 gene in blood samples from Greek Holstein cows and from local breeds of cattle, such as Vrachykeratiki, Katerinis, and Sykias. For this purpose, DNA was isolated from 780 blood samples obtained from Greek Holstein cows, 86 from three local breeds of cattle, namely Brachyceros, Katerinis, and Sykias, and 14 from Greek buffalo. The desired region of exon 7 was amplified by PCR, resulting in 121 and 251 bp products in bovine and buffalo samples. The PCR product was digested with restriction fragment length polymorphism (RFLP) on agarose gels. The restriction enzymes DdeI and TaqI were used. All of the blood samples had the amplified size. The results showed that 74.4% of the Greek Holstein cows had the A2A2 β-casein genotype, the three native breads Vrachykeratiki had 57.7%, and the other two had 100% of the A2A2 β-casein. From the 14 Greek buffalo, 100% had the A2A2 β-casein.
Collapse
Affiliation(s)
- Dionysios Antonopoulos
- Department of Food Science and Technology, Faculty of Food Sciences, University of West Attica, 12243 Athens, Greece; (D.A.); (D.V.)
| | - Despina Vougiouklaki
- Department of Food Science and Technology, Faculty of Food Sciences, University of West Attica, 12243 Athens, Greece; (D.A.); (D.V.)
| | - George P. Laliotis
- Department of Animal Science, Agricultural University of Athens, 11855 Athens, Greece;
| | - Theofania Tsironi
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece;
| | - Irene Valasi
- Department of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
| | - Archodoula Chatzilazarou
- Department of Wine, Vine and Beverage Sciences, Faculty of Food Sciences, University of West Attica, 12243 Athens, Greece;
| | - Panagiotis Halvatsiotis
- 2nd Propaedeutic Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “ATTIKON” University Hospital, 12462 Chaidari, Greece;
| | - Dimitra Houhoula
- Department of Food Science and Technology, Faculty of Food Sciences, University of West Attica, 12243 Athens, Greece; (D.A.); (D.V.)
- Correspondence:
| |
Collapse
|
22
|
Molina Flores B, Camacho Vallejo ME, Delgado Bermejo JV, Navas González FJ, Martínez MDA. Do Pharaohs' cattle still graze the Nile Valley? Genetic characterization of the Egyptian Baladi cattle breed. Anim Biotechnol 2021:1-13. [PMID: 34694188 DOI: 10.1080/10495398.2021.1991938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Egyptian Baladi cattle is one of the few native taurine breeds which remain in the original domestication area of Bos taurus, the Nile Valley (Upper Egypt). Apart from its evolutive relevance, the breed is well-adapted and integrated into the traditional family farming systems, with great potentialities for local sustainable rural development. The diversity and structure of the Baladi population were assessed using 28 genetic microsatellite markers. Within and between-breeds diversity, its relations with other cattle breeds, and an inference on its origin and evolution, were analyzed. Results reported high levels of diversity, with an average number of alleles (Na) of 11.39, observed heterozygosity (Ho) of 0.68, and expected heterozygosity (He) of 0.75. The studied population was in Hardy-Weinberg disequilibrium, which could be ascribed to its internal structure. The comparison between breeds using factorial correspondence analysis, Reynolds genetic distance evaluation, and genetic structure analysis suggested slight influences of Bos indicus. Upper Egypt's rural communities have preserved the Baladi cattle breed, protecting this historical and biological heritage against the constant and indiscriminate introduction of exotic genetic resources along the history of development of the breed. Developing and implementing conservation and breeding programs is crucial for the preservation and improvement of the breed.HIGHLIGHTSBaladi cattle breed is a well-defined and highly diverse breed.Higher diversity levels are found in northern and central governorates.A clear geographical cluster is formed around the Nile Delta.Baladi cattle may be reminiscent of the ancient 'pharaoh' cattle.Assiut's population acted as the most ancestral population nucleus.
Collapse
Affiliation(s)
| | | | | | - Francisco Javier Navas González
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, Córdoba, Spain
| | | |
Collapse
|
23
|
Liu D, Chen Z, Zhao W, Guo L, Sun H, Zhu K, Liu G, Shen X, Zhao X, Wang Q, Ma P, Pan Y. Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits. BMC Genomics 2021; 22:747. [PMID: 34654366 PMCID: PMC8520274 DOI: 10.1186/s12864-021-08042-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08042-x.
Collapse
Affiliation(s)
- Dengying Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Zhenliang Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Wei Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Longyu Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Kai Zhu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Guanglei Liu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Xiuping Shen
- Shanghai Agricultural Development Promotion Center, 200335, Shanghai, PR China
| | - Xiaoduo Zhao
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China.
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China.
| |
Collapse
|
24
|
Gao Y, Yin S, Chu H, Zhang Y, Wang H, Chen H, Liu C, Dai D, Tang L. Genome-Wide SNPs Provide Insights on the Cryptic Genetic Structure and Signatures of Climate Adaption in Amorphophallus albus Germplasms. FRONTIERS IN PLANT SCIENCE 2021; 12:683422. [PMID: 34367210 PMCID: PMC8343094 DOI: 10.3389/fpls.2021.683422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Domesticated species represent unique systems in which the evolutionary genomic consequences of intensive selective breeding and adaptation can be thoroughly investigated. Amorphophallus albus occurs naturally and is in cultivation throughout the downstream region of the Jinshajiang River in Southwest China. This species is characterised by high konjac glucomannan content, and has been cultivated in China for nearly 2,000 years. To study genetic differentiation and local adaption of A. albus, we sampled 13 distinct local cultivated populations of this species. Restriction site-associated DNA sequencing was conducted with 87 samples, resulting in 24,225 SNPs. The population structure analyses suggest two main genetic groups: one in the relatively upstream region, and one downstream. We found evidence of additional sub-structure within the upstream group, demonstrating the statistical power of genomic SNPs in discovering subtle genetic structure. The environmental and geographic factors were all identified as significant in shaping the genetic differentiation of this species. Notably, the proportion of environmental factors was larger than geographic factors in influencing the population genetic patterns of A. albus. We also discovered loci that were associated with local adaptation. These findings will help us understand the genetic differentiation of this newly domesticated species, thereby informing future breeding programs of A. albus.
Collapse
|
25
|
Senczuk G, Mastrangelo S, Ajmone-Marsan P, Becskei Z, Colangelo P, Colli L, Ferretti L, Karsli T, Lancioni H, Lasagna E, Marletta D, Persichilli C, Portolano B, Sarti FM, Ciani E, Pilla F. On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data. Genet Sel Evol 2021; 53:48. [PMID: 34078254 PMCID: PMC8173809 DOI: 10.1186/s12711-021-00639-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00639-w.
Collapse
Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Zsolt Becskei
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, Bulevar Oslobodjenja street 18, 11000, Belgrade, Serbia
| | - Paolo Colangelo
- National Council of Research (CNR), Research Institute On Terrestrial Ecosystems (IRET), Via Salaria km 29.300, Montelibretti, 00015, Rome, Italy
| | - Licia Colli
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Italy, Pavia
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di sotto, 06123, Perugia, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donata Marletta
- Department of Agriculture, Food and Environment, University of Catania, 95125, Catania, Italy
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Baldassare Portolano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceuticals, University of Bari, 70124, Bari, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| |
Collapse
|
26
|
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: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
27
|
Wiener P, Robert C, Ahbara A, Salavati M, Abebe A, Kebede A, Wragg D, Friedrich J, Vasoya D, Hume DA, Djikeng A, Watson M, Prendergast JGD, Hanotte O, Mwacharo JM, Clark EL. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biol Evol 2021; 13:evab014. [PMID: 33501931 PMCID: PMC7955157 DOI: 10.1093/gbe/evab014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
Collapse
Affiliation(s)
- Pamela Wiener
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Christelle Robert
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, United Kingdom
- Department of Zoology, Misurata University, Misurata, Libya
| | - Mazdak Salavati
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - David Wragg
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Juliane Friedrich
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Deepali Vasoya
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Appolinaire Djikeng
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - James G D Prendergast
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- School of Life Sciences, University of Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- Animal and Veterinary Sciences Group, Scotland’s Rural College (SRUC), Midlothian, United Kingdom
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Emily L Clark
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| |
Collapse
|
28
|
Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
Collapse
Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
29
|
Gorssen W, Meyermans R, Janssens S, Buys N. A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species. Genet Sel Evol 2021; 53:2. [PMID: 33397285 PMCID: PMC7784028 DOI: 10.1186/s12711-020-00599-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/11/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. RESULTS The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). CONCLUSIONS We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.
Collapse
Affiliation(s)
- Wim Gorssen
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Roel Meyermans
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium.
| |
Collapse
|
30
|
Gebrehiwot NZ, Strucken EM, Aliloo H, Marshall K, Gibson JP. The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data. BMC Genomics 2020; 21:869. [PMID: 33287702 PMCID: PMC7720612 DOI: 10.1186/s12864-020-07270-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07270-x.
Collapse
Affiliation(s)
- N Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - E M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - H Aliloo
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - K Marshall
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - J P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| |
Collapse
|
31
|
Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data. Animals (Basel) 2020; 10:E2285. [PMID: 33287320 PMCID: PMC7761732 DOI: 10.3390/ani10122285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals' pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.
Collapse
Affiliation(s)
- Filippo Biscarini
- CNR-IBBA (National Research Council, Institute of Agricultural Biology and Biotechnology), 20133 Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015 Monterotondo, Italy;
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy;
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie—Università di Pisa, 56124 Pisa, Italy;
| |
Collapse
|
32
|
Rodríguez-Valera Y, Rocha D, Naves M, Renand G, Pérez-Pineda E, Ramayo-Caldas Y, Ramos-Onsins SE. The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle. Animals (Basel) 2020; 10:ani10122233. [PMID: 33261195 PMCID: PMC7760288 DOI: 10.3390/ani10122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Charolais de Cuba cattle is a tropical adapted breed founded in Cuba around 120 years ago from Charolais French specimens. Nowadays, it is still a closed breed and remains as a small population. In this work, we analyzed the inbreeding and diversity patterns, as well as the population size, of this recent adapted breed via a run of homozygosity (ROH) analysis. We found that the genomic inbreeding levels are higher in the Charolais de Cuba breed compared to French and British Charolais populations. Nevertheless, we detected that the effective population size experienced a very similar decline during the last century in the three Charolais populations studied. Finally, a number of regions with exceptional patterns of long homozygosity were identified in this breed, and these could be related to processes of adaptation to tropical conditions. Abstract Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
Collapse
Affiliation(s)
- Yoel Rodríguez-Valera
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Dominique Rocha
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Michel Naves
- INRAE, URZ, 97170 Petit Bourg, Guadeloupe, France;
| | - Gilles Renand
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Eliecer Pérez-Pineda
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Yuliaxis Ramayo-Caldas
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
| | - Sebastian E. Ramos-Onsins
- Plant and Animal Genomics, Centre of Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
| |
Collapse
|
33
|
Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle. Sci Rep 2020; 10:19466. [PMID: 33173134 PMCID: PMC7655849 DOI: 10.1038/s41598-020-76576-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistics and 92 outlier markers based on Bayescan test. The 13 outlier windows detected by at least two approaches, harboured genes (e.g. GH1, ACE, ASIC3, HSPH1, MVD, BCL2, HIGD2A, CBFA2T3) that may be involved in physiological adaptations required to cope with environmental stressors that are typical of the North African area such as infectious diseases, extended drought periods, scarce food supply, oxygen scarcity in the mountainous areas and high-intensity solar radiation. Our data also point to candidate genes involved in transcriptional regulation suggesting that regulatory elements had also a prominent role in North African cattle response to environmental constraints. Our study yields novel insights into the unique adaptive capacity in these endangered populations emphasizing the need for the use of whole genome sequence data to gain a better understanding of the underlying molecular mechanisms.
Collapse
|
34
|
Cai C, Huang B, Qu K, Zhang J, Lei C. A novel missense mutation within KRT75 gene strongly affects heat stress in Chinese cattle. Gene 2020; 768:145294. [PMID: 33181250 DOI: 10.1016/j.gene.2020.145294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022]
Abstract
The KRT75 gene (Keratin 75) is a member of the type II epithelial α-keratin gene family which plays a key role in hair and nail formation. And the coat conformation affects heat tolarence in mammals. Therefore, the aim of this study was to identify novel single nucleotide polymorphisms (SNPs) of the KRT75 gene and further evaluate its relation to heat stress in Chinese cattle. A missense mutation (NC_037332.1: g.1052 T > C) of the bovine KRT75 was identified using the Bovine Genome Variation Database (BGVD). The g.1052 T > C variant was then genotyped in 519 individuals of 22 cattle breeds. Further analyses showed that the frequency of T allele in Chinese indigenous cattle breeds gradually diminished from northern groups to southern groups, whereas the frequency of C allele displayed a contrary patternl. Simultaneously, the frequency of the CC and CT genotype for southern groups was much greater than that of the TT genotype. Additionally, association analysis showed the genotypes were remarkably associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (P < 0.01). Our results demonstrated that the KRT75 gene might be a candidate gene associated with the heat stress in Chinese cattle.
Collapse
Affiliation(s)
- Cuicui Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Bizhi Huang
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China
| | - Kaixing Qu
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China
| | - Jicai Zhang
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
35
|
Tiemann I, Hillemacher S, Wittmann M. Are Dual-Purpose Chickens Twice as Good? Measuring Performance and Animal Welfare throughout the Fattening Period. Animals (Basel) 2020; 10:E1980. [PMID: 33126643 PMCID: PMC7692664 DOI: 10.3390/ani10111980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 01/09/2023] Open
Abstract
Chickens are the world's most widely used farm animal and have a significant genetic diversity. In the current study, we investigated three strains for their suitability as dual-purpose chickens, with a focus on the fattening ability and welfare of the cockerels: 1. layer cockerels (Lohmann Brown, LB, n = 714); 2. cockerels of a dual-purpose hybrid (Lohmann Dual, LD, n = 844); and 3. cockerels of a native breed (Rhinelander, RL, n = 458). Chicks were raised under identical conditions and marked individually to compare focus and random sampling methods for weighing birds weekly. Because chicks of dual-purpose origins are usually raised mixed-sex, cockerels and pullets were weighed and observed together until sexes the were identifiable at week 10 of their life. During the 10th to 20th week of life, investigations were continued on 100 cockerels per genotype. Key figures for growth performance, such as feed conversion ratio (FCR) and European production efficiency factor (EPEF), were also calculated at weekly intervals. LD cockerels showed considerable growth performance (p < 0.001 compared to LB, RL, 2 kg at 9 weeks), whereas LB reached a live weight of 2 kg at 13 weeks and RL at 15 weeks of age. Genotype-dependent differences were also evident, with favorable FCR and EPEF for LD, intermediate for LB, and unfavorable for RL (all p < 0.001). The results of the FCR and EPEF suggest that cockerels should be slaughtered around week 8 of life, although only the carcass of the LD might be marketable. Thus, the optimal time of slaughter based on production parameters such as FCR and EPEF is different from the time when the animal reaches a marketable 2 kg live weight. Animal-based welfare indicators revealed that the RL are not adapted to production environments, including those that are extensive. Further research aimed at adapted feed management, including better FCR, and animals adapted to the respective production environments is necessary to improve alternative poultry production in the future.
Collapse
Affiliation(s)
- Inga Tiemann
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany;
- Institute of Agricultural Engineering, University of Bonn, Nussallee 5, 53115 Bonn, Germany
| | - Sonja Hillemacher
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany;
- Institute of Agricultural Engineering, University of Bonn, Nussallee 5, 53115 Bonn, Germany
| | - Margit Wittmann
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany;
| |
Collapse
|
36
|
Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
Collapse
Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| |
Collapse
|
37
|
Mastrangelo S, Tolone M, Ben Jemaa S, Sottile G, Di Gerlando R, Cortés O, Senczuk G, Portolano B, Pilla F, Ciani E. Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle. Sci Rep 2020; 10:14522. [PMID: 32883980 PMCID: PMC7471305 DOI: 10.1038/s41598-020-71375-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were observed among domesticated bovid populations from different geographic areas, except for Bali cattle. Our findings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic differentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene flow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, reflecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived-breeds, in the past experienced a similar non-European influence, with African and indicine introgression.
Collapse
Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de La Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia
| | - Gianluca Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, 90128, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Oscar Cortés
- Departamento de Produccion Animal, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
| |
Collapse
|
38
|
Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U, Lasagna E. The genetics of phenotypic plasticity in livestock in the era of climate change: a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1809540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Giacomo Rovelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Eymen Demir
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Fabio Abeni
- Centro di ricerca Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Lodi, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | - Martino Cassandro
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
| | - Umberto Bernabucci
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Viterbo, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| |
Collapse
|
39
|
Senczuk G, Guerra L, Mastrangelo S, Campobasso C, Zoubeyda K, Imane M, Marletta D, Kusza S, Karsli T, Gaouar SBS, Pilla F, Ciani E. Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color. Genes (Basel) 2020; 11:genes11080932. [PMID: 32823527 PMCID: PMC7464420 DOI: 10.3390/genes11080932] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.
Collapse
Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy; (G.S.); (F.P.)
| | - Lorenzo Guerra
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Claudia Campobasso
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
| | - Kaouadji Zoubeyda
- Department of Biology, University Abou Bekr Bélkaid, Tlemcen 13000, Algeria; (K.Z.); (M.I.); (S.B.S.G.)
| | - Meghelli Imane
- Department of Biology, University Abou Bekr Bélkaid, Tlemcen 13000, Algeria; (K.Z.); (M.I.); (S.B.S.G.)
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, 95123 Catania, Italy;
| | - Szilvia Kusza
- Animal Genetics Laboratory, University of Debrecen, 4032 Debrecen, Hungary;
| | - Taki Karsli
- Department of Animal Science, Akdeniz University, 07070 Antalya, Turkey;
| | | | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy; (G.S.); (F.P.)
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
- Correspondence:
| | | |
Collapse
|
40
|
Papachristou D, Koutsouli P, Laliotis GP, Kunz E, Upadhyay M, Seichter D, Russ I, Gjoko B, Kostaras N, Bizelis I, Medugorac I. Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genet Sel Evol 2020; 52:43. [PMID: 32727375 PMCID: PMC7391618 DOI: 10.1186/s12711-020-00560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
Background The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
Collapse
Affiliation(s)
- Dimitris Papachristou
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - George P Laliotis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Bunevski Gjoko
- Livestock Department, Faculty of Agricultural Sciences and Food Institute of Animal Biotechnology, University Ss. Cyril and Methodius, 16-ta Makedonska Brigada 3, 1000, Skopje, North Macedonia
| | - Nikolaos Kostaras
- AMALTHIA, Network for the Protection of Greek Indigenous Farm Animals, 51 Argyrokastrou, 15669, Athens, Greece
| | - Iosif Bizelis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.
| |
Collapse
|
41
|
Hansen PJ. Prospects for gene introgression or gene editing as a strategy for reduction of the impact of heat stress on production and reproduction in cattle. Theriogenology 2020; 154:190-202. [PMID: 32622199 DOI: 10.1016/j.theriogenology.2020.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022]
Abstract
In cattle, genetic variation exists in regulation of body temperature and stabilization of cellular function during heat stress. There are opportunities to reduce the impact of heat stress on cattle production by identifying the causative mutations responsible for genetic variation in thermotolerance and transferring specific alleles that confer thermotolerance to breeds not adapted to hot climates. An example of a mutation conferring superior ability to regulate body temperature is the group of frame-sift mutations in the prolactin receptor gene (PRLR) that lead to a truncated receptor and development of cattle with a short, sleek hair coat. Slick mutations in PRLR have been found in several extant breeds derived from criollo cattle. The slick mutation in Senepol cattle has been introgressed into dairy cattle in Puerto Rico, Florida and New Zealand. An example of a mutation that confers cellular protection against elevated body temperature is a deletion mutation in the promoter region of a heat shock protein 70 gene called HSPA1L. Inheritance of the mutation results in amplification of the transcriptional response of HSPA1L to heat shock and increased cell survival. The case of PRLR provides a promising example of the efficacy of the genetic approach outlined in this paper. Identification of other mutations conferring thermotolerance at the whole-animal or cellular level will lead to additional opportunities for using genetic solutions to reduce the impact of heat stress.
Collapse
Affiliation(s)
- Peter J Hansen
- Department of Animal Sciences, D.H Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL, 32611-0910, USA.
| |
Collapse
|
42
|
Barbato M, Hailer F, Upadhyay M, Del Corvo M, Colli L, Negrini R, Kim ES, Crooijmans RPMA, Sonstegard T, Ajmone-Marsan P. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep 2020; 10:1279. [PMID: 31992729 PMCID: PMC6987186 DOI: 10.1038/s41598-020-57880-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/26/2019] [Indexed: 11/19/2022] Open
Abstract
Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
Collapse
Affiliation(s)
- Mario Barbato
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcello Del Corvo
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| |
Collapse
|
43
|
Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle. BMC Genomics 2019; 20:494. [PMID: 31200634 PMCID: PMC6570941 DOI: 10.1186/s12864-019-5822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Background Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. Results We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions. Conclusions Our results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5822-y) contains supplementary material, which is available to authorized users.
Collapse
|