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Maciel SVSA, Oliveira IPP, Senes BB, Silva JAIDV, Feitosa FLB, Alves JS, Costa RB, de Camargo GMF. Genomic regions associated with coat color in Gir cattle. Genome 2024; 67:233-242. [PMID: 38579337 DOI: 10.1139/gen-2023-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.
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Baker KH, Miller H, Doherty S, Gray HWI, Daujat J, Çakırlar C, Spassov N, Trantalidou K, Madgwick R, Lamb AL, Ameen C, Atici L, Baker P, Beglane F, Benkert H, Bendrey R, Binois-Roman A, Carden RF, Curci A, De Cupere B, Detry C, Gál E, Genies C, Kunst GK, Liddiard R, Nicholson R, Perdikaris S, Peters J, Pigière F, Pluskowski AG, Sadler P, Sicard S, Strid L, Sudds J, Symmons R, Tardio K, Valenzuela A, van Veen M, Vuković S, Weinstock J, Wilkens B, Wilson RJA, Evans JA, Hoelzel AR, Sykes N. The 10,000-year biocultural history of fallow deer and its implications for conservation policy. Proc Natl Acad Sci U S A 2024; 121:e2310051121. [PMID: 38346198 PMCID: PMC10895352 DOI: 10.1073/pnas.2310051121] [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: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024] Open
Abstract
Over the last 10,000 y, humans have manipulated fallow deer populations with varying outcomes. Persian fallow deer (Dama mesopotamica) are now endangered. European fallow deer (Dama dama) are globally widespread and are simultaneously considered wild, domestic, endangered, invasive and are even the national animal of Barbuda and Antigua. Despite their close association with people, there is no consensus regarding their natural ranges or the timing and circumstances of their human-mediated translocations and extirpations. Our mitochondrial analyses of modern and archaeological specimens revealed two distinct clades of European fallow deer present in Anatolia and the Balkans. Zooarchaeological evidence suggests these regions were their sole glacial refugia. By combining biomolecular analyses with archaeological and textual evidence, we chart the declining distribution of Persian fallow deer and demonstrate that humans repeatedly translocated European fallow deer, sourced from the most geographically distant populations. Deer taken to Neolithic Chios and Rhodes derived not from nearby Anatolia, but from the Balkans. Though fallow deer were translocated throughout the Mediterranean as part of their association with the Greco-Roman goddesses Artemis and Diana, deer taken to Roman Mallorca were not locally available Dama dama, but Dama mesopotamica. Romans also initially introduced fallow deer to Northern Europe but the species became extinct and was reintroduced in the medieval period, this time from Anatolia. European colonial powers then transported deer populations across the globe. The biocultural histories of fallow deer challenge preconceptions about the divisions between wild and domestic species and provide information that should underpin modern management strategies.
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Affiliation(s)
- Karis H. Baker
- Department of Biosciences, Durham University, DurhamDH1 3LE, United Kingdom
| | - Holly Miller
- Department of Classics and Archaeology, University of Nottingham, NottinghamNG7 2RD, United Kingdom
| | - Sean Doherty
- Department of Archaeology and History, University of Exeter, ExeterEX4 4QE, United Kingdom
| | - Howard W. I. Gray
- Department of Biosciences, Durham University, DurhamDH1 3LE, United Kingdom
| | - Julie Daujat
- Department of Classics and Archaeology, University of Nottingham, NottinghamNG7 2RD, United Kingdom
| | - Canan Çakırlar
- Groningen Institute of Archaeology, University of Groningen, Groningen9712 ER, The Netherlands
| | - Nikolai Spassov
- Department of Paleontology, National Museum of Natural History, Bulgarian Academy of Sciences, Sofia1000, Bulgaria
| | - Katerina Trantalidou
- Ephorate for Palaeoanthropology-Speleology, Hellenic Ministry of Culture, Athens106 82, Greece
| | - Richard Madgwick
- School of History, Archaeology and Religion, Cardiff University, CardiffCF10 3EU, United Kingdom
| | - Angela L. Lamb
- National Environmental Isotope Facility, British Geological Survey, NottinghamNG12 5GG, United Kingdom
| | - Carly Ameen
- Department of Archaeology and History, University of Exeter, ExeterEX4 4QE, United Kingdom
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, NV89154
| | | | - Fiona Beglane
- Centre for Environmental Research Innovation and Sustainability, Atlantic Technological University, Sligo F91 YW50, Ireland
| | - Helene Benkert
- Department of Archaeology and History, University of Exeter, ExeterEX4 4QE, United Kingdom
| | - Robin Bendrey
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - Annelise Binois-Roman
- School of Art History and Archaeology, University of Paris 1 Panthéon-Sorbonne, Paris75006, France
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, DublinD04 V1W8, Ireland
| | - Antonio Curci
- Department of History and Cultures, University of Bologna, Bologna40124, Italy
| | - Bea De Cupere
- Operational Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels1000, Belgium
| | - Cleia Detry
- Center of Archaeology of the University of Lisbon, Department of History, School of Arts and Humanities of the University of Lisbon, Alameda da Universidade, Lisboa1600-214, Portugal
| | - Erika Gál
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest1097, Hungary
| | - Chloé Genies
- Bureau d’études, Éveha, Saint-Avertin, Tour37550, France
| | - Günther K. Kunst
- Vienna Institute for Archaeological Science, Research Network Human Evolution and Archaeological Sciences, University of Vienna, Vienna1090, Austria
| | - Robert Liddiard
- School of History, University of East Anglia, Norwich Research Park, NorwichNR4 7TJX, United Kingdom
| | | | - Sophia Perdikaris
- School of Global Integrative Studies, University of Nebraska-Lincoln, Lincoln, NE68588
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Munich80539, Germany
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, Munich80333, Germany
| | - Fabienne Pigière
- Department of Geography, Royal Holloway, University of London, EghamTW20 0EX, United Kingdom
| | | | - Peta Sadler
- Independent Researcher, Buckinghamshire, Greater MissendenHP16 0LF, United Kingdom
| | - Sandra Sicard
- Département de la Charente, Angouleme Cedex 91616917, France
| | - Lena Strid
- Department of Archaeology and Ancient History, Lund University, Lund223 62, Sweden
| | - Jack Sudds
- Department of Archaeology and History, University of Exeter, ExeterEX4 4QE, United Kingdom
| | - Robert Symmons
- Fishbourne Roman Palace, ChichesterPO19 3QR, United Kingdom
| | - Katie Tardio
- Department of Classics and Ancient Mediterranean Studies, Bucknell University, Lewisburg, PA17837
| | - Alejandro Valenzuela
- Mediterranean Institute for Advanced Studies, Ecology and Evolution, Miquel Marquès Street, Esporles, Illes Balears2107190, Spain
| | - Monique van Veen
- Department of Archaeology, Municipality of The Hague, Den Haag2500 DP, The Netherlands
| | - Sonja Vuković
- Laboratory for Bioarchaeology, Archaeology Department, University of Belgrade, Belgrade11000, Serbia
| | - Jaco Weinstock
- Department of Archaeology, University of Southampton, School of Humanities, SouthamptonSO171BF, United Kingdom
| | | | - Roger J. A. Wilson
- Department of Ancient Mediterranean and Near Eastern Studies, V6T 1Z1, Canada
| | - Jane A. Evans
- National Environmental Isotope Facility, British Geological Survey, NottinghamNG12 5GG, United Kingdom
| | - A. Rus Hoelzel
- Department of Biosciences, Durham University, DurhamDH1 3LE, United Kingdom
| | - Naomi Sykes
- Department of Archaeology and History, University of Exeter, ExeterEX4 4QE, United Kingdom
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Pallotti S, Antonini M, Napolioni V, Renieri C. Whole-genome sequencing of alpaca revealed variants in KIT gene potentially associated with the white coat phenotype. Anim Genet 2023; 54:816-817. [PMID: 37778745 DOI: 10.1111/age.13366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
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, Rome, Italy
| | - Valerio Napolioni
- Genomic and Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
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Platzer JM, Gunter LM, Feuerbacher EN. Exploring the Domestication Syndrome Hypothesis in Dogs: Pigmentation Does Not Predict Cortisol Levels. Animals (Basel) 2023; 13:3095. [PMID: 37835701 PMCID: PMC10571964 DOI: 10.3390/ani13193095] [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: 07/28/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Previous research has found connections between pigmentation, behavior, and the physiological stress response in both wild and domestic animals; however, to date, no extensive research has been devoted to answering these questions in domestic dogs. Modern dogs are exposed to a variety of stressors; one well-studied stressor is residing in an animal shelter. To explore the possible relationships between dogs' responses to stress and their pigmentation, we conducted statistical analyses of the cortisol:creatinine ratios of 208 American shelter dogs as a function of their coat color/pattern, eumelanin pigmentation, or white spotting. These dogs had been enrolled in previous welfare studies investigating the effect of interventions during which they left the animal shelter and spent time with humans. In the current investigation, we visually phenotype dogs based on photographs in order to classify their pigmentation and then conduct post hoc analyses to examine whether they differentially experience stress as a function of pigmentation. We found that the dogs did not differ significantly in their urinary cortisol:creatinine ratios based on coat color/pattern, eumelanin pigmentation, or white spotting, either while they were residing in the animal shelter or during the human interaction intervention. These preliminary data suggest that pigmentation alone does not predict the stress responses of shelter dogs; however, due to the small sample size and retrospective nature of the study, more research is needed.
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Affiliation(s)
- JoAnna M. Platzer
- School of Animal Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA; (L.M.G.); (E.N.F.)
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Zhang K, Wang G, Wang L, Wen B, Fu X, Liu N, Yu Z, Jian W, Guo X, Liu H, Chen SY. A genome-wide association study of coat color in Chinese Rex rabbits. Front Vet Sci 2023; 10:1184764. [PMID: 37655262 PMCID: PMC10467280 DOI: 10.3389/fvets.2023.1184764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Coat color is an important phenotypic characteristic of the domestic rabbit (Oryctolagus cuniculus) and has specific economic importance in the Rex rabbit industry. Coat color varies considerably among different populations of rabbits, and several causal genes for this variation have been thoroughly studied. Nevertheless, the candidate genes affecting coat color variation in Chinese Rex rabbits remained to be investigated. In this study, we collected blood samples from 250 Chinese Rex rabbits with six different coat colors. We performed genome sequencing using a restriction site-associated DNA sequencing approach. A total of 91,546 single nucleotide polymorphisms (SNPs), evenly distributed among 21 autosomes, were identified. Genome-wide association studies (GWAS) were performed using a mixed linear model, in which the individual polygenic effect was fitted as a random effect. We detected a total of 24 significant SNPs that were located within a genomic region on chromosome 4 (OCU4). After re-fitting the most significant SNP (OCU4:13,434,448, p = 1.31e-12) as a covariate, another near-significant SNP (OCU4:11,344,946, p = 7.03e-07) was still present. Hence, we conclude that the 2.1-Mb genomic region located between these two significant SNPs is significantly associated with coat color in Chinese Rex rabbits. The well-studied coat-color-associated agouti signaling protein (ASIP) gene is located within this region. Furthermore, low genetic differentiation was also observed among the six coat color varieties. In conclusion, our results confirmed that ASIP is a putative causal gene affecting coat color variation in Chinese Rex rabbits.
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Affiliation(s)
- Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Guozhi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lihuan Wang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Bin Wen
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiangchao Fu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Ning Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Zhiju Yu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Wensu Jian
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiaolin Guo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Hanzhong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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6
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Barash A, Preiss-Bloom S, Machluf Y, Fabbri E, Malkinson D, Velli E, Mucci N, Barash A, Caniglia R, Dayan T, Dekel Y. Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus). Sci Rep 2023; 13:7388. [PMID: 37149712 PMCID: PMC10164184 DOI: 10.1038/s41598-023-34533-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the context of the jackal as an overabundant species in Israel, the rural nature of the surveyed area, the abundance of anthropogenic waste, and molecular and morphological findings, the possibility of an individual presenting incipient stages of domestication should also be considered.
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Affiliation(s)
- Ayelet Barash
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Shlomo Preiss-Bloom
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Yossy Machluf
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Dan Malkinson
- Department of Geography and Environmental Studies, University of Haifa, 3498838, Haifa, Israel
| | - Edoardo Velli
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Alon Barash
- The Azrieli Faculty of Medicine, Bar Ilan University, 8 Henrietta Szold St, Safed, Israel
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Tamar Dayan
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel.
| | - Yaron Dekel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel.
- The Cheryl Spencer Department of Nursing and The Cheryl Spencer Institute of Nursing Research, University of Haifa, 3498838, Haifa, Israel.
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Zhang F, Wang C, Xu H, Xia X, Luo X, Li K, Han J, Lei C, Chen N, Yue X. Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype in yak. J Anim Breed Genet 2023; 140:330-342. [PMID: 36789788 DOI: 10.1111/jbg.12761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.
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Affiliation(s)
- Fengwei Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chong Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaihui Li
- Extending Station for Animal Husbandry and Veterinary Technology of Tianzhu Tibetan Autonomous County, Tianzhu, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 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
| | - 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
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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8
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Fontanesi L. Genetics and genomics of pigmentation variability in pigs: A review. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Characterization of the Sarcidano Horse Coat Color Genes. Animals (Basel) 2022; 12:ani12192677. [PMID: 36230420 PMCID: PMC9558981 DOI: 10.3390/ani12192677] [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: 08/30/2022] [Revised: 09/24/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
The goal of this study was to contribute to the general knowledge of the Sarcidano Horse, both by the identification of the genetic basis of the coat color and by updating the exact locations of the genotyping sites, based on the current EquCab3.0 genome assembly version. One-hundred Sarcidano Horses, living in semi-feral condition, have been captured to perform health and biometric checks. From that total number, 70 individual samples of whole blood were used for DNA extraction, aimed to characterize the genetic basis of the coat color. By genotyping and sequencing analyses of the MC1R Exon 1 and ASIP Exon 3, a real image of the coat color distribution in the studied population has been obtained. Chestnut and Black resulted in the most representative coat colors both from a phenotypic and genotypic point of view, that is suggestive of no human domestication or crossbreeding with domestic breed. Due to its ancient origin and genetic isolation, an active regional plan for the conservation of this breed would be desirable, focused on maintenance of resident genotypes and genetic resources. Collection and management of DNA, sperm, embryos, with the involvement of research centers and Universities, could be a valid enhancing strategy.
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Ji RL, Tao YX. Melanocortin-1 receptor mutations and pigmentation: Insights from large animals. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:179-213. [PMID: 35595349 DOI: 10.1016/bs.pmbts.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The melanocortin-1 receptor (MC1R) is a G protein-coupled receptor expressed in cutaneous and hair follicle melanocytes, and plays a central role in coat color determination in vertebrates. Numerous MC1R variants have been identified in diverse species. Some of these variants have been associated with specific hair and skin color phenotypes in humans as well as coat color in animals. Gain-of-function mutations of the MC1R gene cause dominant or partially dominant black/dark coat color, and loss-of-function mutations of the MC1R gene cause recessive or partially recessive red/yellow/pale coat color phenotypes. These have been well documented in a large number of mammals, including human, dog, cattle, horse, sheep, pig, and fox. Higher similarities between large mammals and humans makes them better models to understand pathogenesis of human diseases caused by MC1R mutations. High identities in MC1Rs and similar variants identified in both humans and large mammals also provide an opportunity for receptor structure and function study. In this review, we aim to summarize the naturally occurring mutations of MC1R in humans and large animals.
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Affiliation(s)
- Ren-Lei Ji
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.
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Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids. Curr Biol 2022; 32:889-897.e9. [PMID: 35090588 PMCID: PMC8891063 DOI: 10.1016/j.cub.2021.12.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 12/30/2022]
Abstract
Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.
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12
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Altman A, Shennan S, Odling-Smee J. Ornamental plant domestication by aesthetics-driven human cultural niche construction. TRENDS IN PLANT SCIENCE 2022; 27:124-138. [PMID: 34629220 DOI: 10.1016/j.tplants.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Unlike plants that were domesticated to secure food, the domestication and breeding of ornamental plants are driven by aesthetic values. Here, we examine the major elements of the extended evolutionary synthesis (EES) theory that bridges the gap between the biology of ornamental plant domestication and the sociocultural motivations behind it. We propose that it involves specific elements of cumulative cultural evolution (CCE), plant gene-human culture coevolution (PGHCC), and niche construction (NC). Moreover, ornamental plant domestication represents an aesthetics-driven dimension of human niche construction that coevolved with socioeconomic changes and the adoption of new scientific technologies. Initially functioning as symbolic and aesthetic assets, ornamental plants became globally marketed material commodities as a result of the co-dependence of human CCE and prestige-competition motivations.
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Affiliation(s)
- Arie Altman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel; Institute of Archaeology, University College of London, WC1H 0PY, London, UK.
| | - Stephen Shennan
- Institute of Archaeology, University College of London, WC1H 0PY, London, UK
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13
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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14
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Anderson H, Honkanen L, Ruotanen P, Mathlin J, Donner J. Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation associated with partial recessive red phenotypes in dog. Canine Med Genet 2020; 7:16. [PMID: 33292722 PMCID: PMC7643265 DOI: 10.1186/s40575-020-00095-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/19/2020] [Indexed: 11/23/2022] Open
Abstract
Background The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in various species and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1–3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs. Results Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient red”. Phenotype analysis of owner-provided dog pictures reveals that the eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the phenotypic expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle. Conclusions This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-020-00095-7.
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15
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Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 2020; 16:e1008274. [PMID: 32433666 PMCID: PMC7239393 DOI: 10.1371/journal.pgen.1008274] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons. The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.
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Affiliation(s)
- Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Hannah Van Hollebeke
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward J. Osborne
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Zev Kronenberg
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Emily Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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16
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Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
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17
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Genetic heterogeneity of white markings in Quarter Horses. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Fogelholm J, Henriksen R, Höglund A, Huq N, Johnsson M, Lenz R, Jensen P, Wright D. CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken. Sci Rep 2020; 10:1161. [PMID: 31980681 PMCID: PMC6981141 DOI: 10.1038/s41598-020-57710-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 12/28/2019] [Indexed: 01/12/2023] Open
Abstract
Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic × wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.
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Affiliation(s)
- J Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - R Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - A Höglund
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - N Huq
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - M Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, United Kingdom.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - R Lenz
- ITN Dept of Science and Technology, Linköping University, Linköping, 58183, Sweden
| | - P Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden
| | - D Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58183, Sweden.
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19
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Rochus CM, Westberg Sunesson K, Jonas E, Mikko S, Johansson AM. Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations. Anim Genet 2019; 50:712-717. [PMID: 31475378 DOI: 10.1111/age.12837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 01/03/2023]
Abstract
By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D5 ) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.
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Affiliation(s)
- C M Rochus
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden.,UFR Génétique, Élevage et Reproduction, Sciences de la Vie et Santé, AgroParisTech, Université Paris Saclay, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France.,Génétique Physiologie Systèmes d'Elevage, Animal Genetics Division, INRA, 24 chemin de Borde-Rouge-Auzeville Tolosane, F-31326 Castanet-Tolosan, France
| | - K Westberg Sunesson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - E Jonas
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - A M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
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20
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Goud TS, Upadhyay RC, Onteru SK, Pichili VBR, Chadipiralla K. Identification and sequence characterization of melanocortin 1 receptor gene ( MC1R) in Bos indicus versus ( Bos taurus X Bos indicus). Anim Biotechnol 2019; 31:283-294. [PMID: 30890019 DOI: 10.1080/10495398.2019.1585866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Melanocortin 1 receptor (MC1R) plays a vital role in melanogenesis and determines coat color of mammals. Polymorphic variants in MC1R, causing coat color variation, were described in few mammals; however, such studies were not done in cattle. The objective of the study was to explore the association of MC1R gene polymorphism within Tharparkar (Bos indicus) and Karan Fries (B. indicus X Bos taurus) cattle. Genomic DNA isolated from blood samples of Tharparkar breed by modified Phenol: Chloroform; Isoamyl alcohol method. Using genomic DNA as template for PCR, MC1R gene was amplified and sequenced. The sequences were analyzed and submitted to Genbank with Acc.No MG373615-MG373644. Comparison of sequence alignment with other bovine species using ClustalW revealed 99-96% similarity. MC1R gene phylogenetic analyses were analyzed using MEGA X. The MC1R gene tree, protein domains and genetic variation of cattle were retrieved from Ensemble Asia Cattle Genome Browser. Eight single nucleotide polymorphisms (SNPs) (c.296T > C, c.583T > C, c.663C > T, c.830T > C, c.853G > A, c.880G > A, c.906C > G, c.927C > T) in CDS reveal high genetic variability. Subsequent to amino acid changes p.L99P, p.F195L, p.F277S, p.A285T and p.D293N, p.R302S, respectively found in seven-transmembrane. Mutations appeared in MC1R of B. taurus with white and black coat color as compared to B. indicus with white coat.
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Affiliation(s)
- Talla Sridhar Goud
- Climate Resilient Live Stock Research Centre, ICAR-National Dairy Research Institute, Karnal, India.,Department of Biotechnology, Vikrama Simhapuri University, Nellore, India
| | - Ramesh Chandra Upadhyay
- Climate Resilient Live Stock Research Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Suneel Kumar Onteru
- Molecular Endocrinology and Structural Biology, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
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21
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Kumar C, Song S, Dewani P, Kumar M, Parkash O, Ma Y, Malhi KK, Yang N, Mwacharo JM, He X, Jiang L. Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations. Anim Genet 2018; 49:592-604. [PMID: 30229969 DOI: 10.1111/age.12722] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).
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Affiliation(s)
- C Kumar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan.,Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - S Song
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - P Dewani
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - M Kumar
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - O Parkash
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - Y Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - K K Malhi
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - N Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - J M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - X He
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - L Jiang
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
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22
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Population study of the Pura Raza Español Horse regarding its coat colour. ANNALS OF ANIMAL SCIENCE 2018. [DOI: 10.2478/aoas-2018-0016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Coat colour has always been a valuable trait for horse breeders. However, preferences for this feature have changed over the years. In this research, the Pura Raza Español horse (PRE) population was divided into four subpopulations (Grey, Bay, Black and Others), according to the most frequent coat colours and those of their ancestors. The purpose was to analyse genetic variability, reproductive parameters and distances among subpopulations during three key periods in the history of the breed: before 1960, from 1960 to 2000 and after 2000. The subpopulations composed of animals with ancestors with the same coat colour showed higher values of recent inbreeding (ranging from 7.13% to 10.44%) and a greater Nei’s minimum distance between them, as a result of more inbred matings than those carried out in families with members with different coat colours. Non-pure subpopulations also showed more similar recent inbreeding values (between 6.63% and 6.74%). Strikingly, the productive life of Pure bay, Pure black and other subpopulations with minority coat colours was considerably longer (10.79, 10.08 and 9.11 years, respectively) compared to the values of grey PRE horses (6.01 and 7.98 years), which is the subpopulation with the highest census. These results, together with shorter generation intervals of black stallion-offspring (5.51 years via father-son and 6.39 years via father-daughter) and the fact that this coat colour was not present in the breed until two decades ago, highlight the recent trend towards the breeding of black animals.
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23
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Wutke S, Benecke N, Sandoval-Castellanos E, Döhle HJ, Friederich S, Gonzalez J, Hallsson JH, Hofreiter M, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Ruttkay M, Trinks A, Ludwig A. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci Rep 2016; 6:38548. [PMID: 27924839 PMCID: PMC5141471 DOI: 10.1038/srep38548] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/09/2016] [Indexed: 01/08/2023] Open
Abstract
Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
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Affiliation(s)
- Saskia Wutke
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, 10315 Berlin, Germany
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | | | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Javier Gonzalez
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Jón Hallsteinn Hallsson
- The Agricultural University of Iceland, Faculty of Land and Animal Resources, IS-112 Reykjavik, Iceland
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Ola Magnell
- National Historical Museums, Contract Archaeology, 226 60 Lund, Sweden
| | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Albína Hulda Pálsdóttir
- The Agricultural University of Iceland, Faculty of Land and Animal Resources, IS-112 Reykjavik, Iceland
| | - Monika Reissmann
- Humboldt University Berlin, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, 10115 Berlin, Germany
| | - Matej Ruttkay
- Slovak Academy of Sciences, Institute of Archaeology, 949 21 Nitra, Slovak Republic
| | - Alexandra Trinks
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Arne Ludwig
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, 10315 Berlin, Germany
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24
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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Linderholm A, Spencer D, Battista V, Frantz L, Barnett R, Fleischer RC, James HF, Duffy D, Sparks JP, Clements DR, Andersson L, Dobney K, Leonard JA, Larson G. A novel MC1R allele for black coat colour reveals the Polynesian ancestry and hybridization patterns of Hawaiian feral pigs. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160304. [PMID: 27703696 PMCID: PMC5043315 DOI: 10.1098/rsos.160304] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook's arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs. Although populations of feral pigs today are an important source of recreational hunting on all of the major islands, they also negatively impact native plants and animals. As a result, understanding the origins of these feral pig populations has significant ramifications for discussions concerning conservation management, identity and cultural continuity on the islands. Here, we analysed a neutral mitochondrial marker and a functional nuclear coat colour marker in 57 feral Hawaiian pigs. Through the identification of a new mutation in the MC1R gene that results in black coloration, we demonstrate that Hawaiian feral pigs are mostly the descendants of those originally introduced during Polynesian settlement, though there is evidence for some admixture. As such, extant Hawaiian pigs represent a unique historical lineage that is not exclusively descended from feral pigs of European origin.
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Affiliation(s)
- Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
- The Bioarchaeology and Genomics Laboratory, Department of Anthropology, Texas A&M University, MS 4352 TAMU, College Station, TX 77843-4352, USA
| | - Daisy Spencer
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
- Discipline of Archaeology, National University of Ireland, University Road, Galway, Ireland
| | - Vincent Battista
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Laurent Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Ross Barnett
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Robert C. Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5508, Washington, DC 20013-7012, USA
| | - Helen F. James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Dave Duffy
- Botany Department, University of Hawaìi at Manoa, 3190 Maile Way, Room 101, Honolulu, HI 96822, USA
| | - Jed P. Sparks
- Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
| | - David R. Clements
- Department of Biology, Trinity Western University, Langley, BC, CanadaV2Y 1Y1
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12–14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio, s/n, 41092 Seville, Spain
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
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Sánchez-Villagra MR, Geiger M, Schneider RA. The taming of the neural crest: a developmental perspective on the origins of morphological covariation in domesticated mammals. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160107. [PMID: 27429770 PMCID: PMC4929905 DOI: 10.1098/rsos.160107] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/03/2016] [Indexed: 05/02/2023]
Abstract
Studies on domestication are blooming, but the developmental bases for the generation of domestication traits and breed diversity remain largely unexplored. Some phenotypic patterns of human neurocristopathies are suggestive of those reported for domesticated mammals and disrupting neural crest developmental programmes have been argued to be the source of traits deemed the 'domestication syndrome'. These character changes span multiple organ systems and morphological structures. But an in-depth examination within the phylogenetic framework of mammals including domesticated forms reveals that the distribution of such traits is not universal, with canids being the only group showing a large set of predicted features. Modularity of traits tied to phylogeny characterizes domesticated mammals: through selective breeding, individual behavioural and morphological traits can be reordered, truncated, augmented or deleted. Similarly, mammalian evolution on islands has resulted in suites of phenotypic changes like those of some domesticated forms. Many domesticated mammals can serve as valuable models for conducting comparative studies on the evolutionary developmental biology of the neural crest, given that series of their embryos are readily available and that their phylogenetic histories and genomes are well characterized.
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Affiliation(s)
| | - Madeleine Geiger
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Street 4, 8006 Zurich, Switzerland
| | - Richard A. Schneider
- Department of Orthopaedic Surgery, University of Californiaat San Francisco, 513 Parnassus Avenue, S-1161, San Francisco, CA, USA
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San-Jose LM, Ducrest AL, Ducret V, Béziers P, Simon C, Wakamatsu K, Roulin A. Effect of the MC1R gene on sexual dimorphism in melanin-based colorations. Mol Ecol 2015; 24:2794-808. [PMID: 25857339 DOI: 10.1111/mec.13193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 02/04/2023]
Abstract
Variants of the melanocortin-1 receptor (MC1R) gene result in abrupt, naturally selected colour morphs. These genetic variants may differentially affect sexual dimorphism if one morph is naturally selected in the two sexes but another morph is naturally or sexually selected only in one of the two sexes (e.g. to confer camouflage in reproductive females or confer mating advantage in males). Therefore, the balance between natural and sexual selections can differ between MC1R variants, as suggest studies showing interspecific correlations between sexual dimorphism and the rate of nonsynonymous vs. synonymous amino acid substitutions at the MC1R. Surprisingly, how MC1R is related to within-species sexual dimorphism, and thereby to sex-specific selection, has not yet been investigated. We tackled this issue in the barn owl (Tyto alba), a species showing pronounced variation in the degree of reddish pheomelanin-based coloration and in the number and size of black feather spots. We found that a valine (V)-to-isoleucine (I) substitution at position 126 explains up to 30% of the variation in the three melanin-based colour traits and in feather melanin content. Interestingly, MC1R genotypes also differed in the degree of sexual colour dimorphism, with individuals homozygous for the II MC1R variant being 2 times redder and 2.5 times less sexually dimorphic than homozygous individuals for the VV MC1R variant. These findings support that MC1R interacts with the expression of sexual dimorphism and suggest that a gene with major phenotypic effects and weakly influenced by variation in body condition can participate in sex-specific selection processes.
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Affiliation(s)
- Luis M San-Jose
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Anne-Lyse Ducrest
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Valérie Ducret
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Paul Béziers
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Céline Simon
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi, 470-1192, Japan
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
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Bianco E, Soto HW, Vargas L, Pérez-Enciso M. The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity. Mol Ecol 2015; 24:2364-78. [DOI: 10.1111/mec.13182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 01/27/2023]
Affiliation(s)
- E. Bianco
- Centre for Research in Agricultural Genomics (CRAG); CSIC-IRTA-UAB-UB Consortium; 08193 Bellaterra Spain
- Department of Animal Science; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - H. W. Soto
- Escuela de Zootecnia; Universidad de Costa Rica; 10501 San José Costa Rica
| | - L. Vargas
- Sistema Nacional de Áreas de Conservación (SINAC); Ministerio de Ambiente y Energía (MINAE); Avenida 15, Calle 1, San José Costa Rica
| | - M. Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG); CSIC-IRTA-UAB-UB Consortium; 08193 Bellaterra Spain
- Department of Animal Science; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
- Institut Català de Recerca I Estudis Avançats (ICREA); Carrer de Lluís Companys 23 Barcelona 08010 Spain
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Zouganelis GD, Ogden R, Nahar N, Runfola V, Bonab M, Ardalan A, Radford D, Barnett R, Larson G, Hildred A, Jones M, Scarlett G. An old dog and new tricks: Genetic analysis of a Tudor dog recovered from the Mary Rose wreck. Forensic Sci Int 2014; 245:51-7. [DOI: 10.1016/j.forsciint.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/23/2014] [Accepted: 10/04/2014] [Indexed: 11/25/2022]
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Batista N, Souza B, Oliveira G, Roberto J, Araújo R, Ribeiro T, Silva R. Tolerância ao Calor em Ovinos de Pelames Claro e Escuro Submetidos ao Estresse Térmico. JOURNAL OF ANIMAL BEHAVIOUR AND BIOMETEOROLOGY 2014. [DOI: 10.14269/2318-1265/jabb.v2n3p102-108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Våge DI, Nieminen M, Anderson DG, Røed KH. Two missense mutations in melanocortin 1 receptor (MC1R) are strongly associated with dark ventral coat color in reindeer (Rangifer tarandus). Anim Genet 2014; 45:750-3. [PMID: 25039753 DOI: 10.1111/age.12187] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2014] [Indexed: 12/01/2022]
Abstract
The protein-coding region of melanocortin 1 receptor (MC1R) was sequenced to identify potential variation affecting coat color in reindeer (Rangifer tarandus). A T→C sequence variation at nucleotide position 218 (c.218T>C) causing an amino acid (aa) change from methionine to threonine at aa position 73 (p.Met73Thr) was identified. In addition, a T→G sequence variation was found at nucleotide position 839 (c.839T>G), causing phenylalanine to be exchanged by cysteine at aa position 280 (p.Phe280Cys). The two sequence variants (c.218C and c.839G) were found to be closely associated with a darker belly coat compared with animals not having any of these two variants. The aa acid change p.Met73Thr affects the same position as p.Met73Lys previously reported to give constitutive activation of MC1R in black sheep (Ovis aries), whereas p.Phe280Cys is identical to one of two variants previously reported to be associated with dark coat color in Arctic fox (Alopex lagopus), supporting that the two variants found in reindeer are functional. The complete absence of Thr73 and Cys280 among the 51 wild reindeer analyzed provides some evidence that these variants are more common in the domestic herds.
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Affiliation(s)
- D I Våge
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences (NMBU), Ås, N-1432, Norway
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Zhang MQ, Xu X, Luo SJ. The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens). Anim Genet 2014; 45:652-9. [PMID: 24989079 DOI: 10.1111/age.12191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2014] [Indexed: 11/28/2022]
Abstract
Domestic yaks (Bos grunniens) exhibit two major coat color variations: a brown vs. wild-type black pigmentation and a white spotting vs. wild-type solid color pattern. The genetic basis for these variations in color and distribution remains largely unknown and may be complicated by a breeding history involving hybridization between yaks and cattle. Here, we investigated 92 domestic yaks from China using a candidate gene approach. Sequence variations in MC1R, PMEL and TYRP1 were surveyed in brown yaks; TYRP1 was unassociated with the coloration and excluded. Recessive mutations from MC1R, or p.Gln34*, p.Met73Leu and possibly p.Arg142Pro, are reported in bovids for the first time and accounted for approximately 40% of the brown yaks in this study. The remaining 60% of brown individuals correlated with a cattle-derived deletion mutation from PMEL (p.Leu18del) in a dominant manner. Degrees of white spotting found in yaks vary from color sidedness and white face, to completely white. After examining the candidate gene KIT, we suggest that color-sided and all-white yaks are caused by the serial translations of KIT (Cs6 or Cs29 ) as reported for cattle. The white-faced phenotype in yaks is associated with the KIT haplotype S(wf) . All KIT mutations underlying the serial phenotypes of white spotting in yaks are identical to those in cattle, indicating that cattle are the likely source of white spotting in yaks. Our results reveal the complex genetic origins of domestic yak coat color as either native in yaks through evolution and domestication or as introduced from cattle through interspecific hybridization.
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Affiliation(s)
- M-Q Zhang
- College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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Abstract
It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
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34
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Hofreiter M. Genetic basis and evolutionary causes of colour variation in vertebrates. Semin Cell Dev Biol 2013; 24:515. [PMID: 23685126 DOI: 10.1016/j.semcdb.2013.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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