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Marcuzzi O, Calcaterra F, Loza Vega A, Ortega Masagué MF, Armstrong E, Pereira Rico JA, Jara E, Olivera LH, Peral García P, Giovambattista G. Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America. Anim Genet 2024; 55:527-539. [PMID: 38716584 DOI: 10.1111/age.13435] [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: 03/25/2024] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 07/04/2024]
Abstract
The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.
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Affiliation(s)
- O Marcuzzi
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - F Calcaterra
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - A Loza Vega
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - M F Ortega Masagué
- Instituto de Investigación Animal del Chaco Semiárido, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Leales, Tucumán, Argentina
| | - E Armstrong
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - J A Pereira Rico
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - E Jara
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - L H Olivera
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - P Peral García
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
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Green BT, Welch KD, Lee ST, Davis TZ, Stonecipher CA, Stegelmeier BL, Cook D. Acute death as a result of poisoning tropical (Bos taurus indicus) but not temperate (Bos taurus taurus) cattle after oral dosing with Lupinus leucophyllus (velvet lupine). Toxicon 2024; 242:107706. [PMID: 38570167 DOI: 10.1016/j.toxicon.2024.107706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Due to climate change and increasing summer temperatures, tropical cattle may graze where temperate cattle have grazed, exposing tropical cattle to toxic plants they may be unfamiliar with. This work compared the toxicity of Lupinus leucophyllus (velvet lupine) in temperate and tropical cattle. Orally dosed velvet lupine in tropical cattle caused death. If producers opt to graze tropical cattle, additional care must be taken on rangelands where toxic lupines like velvet lupine grow.
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Affiliation(s)
- Benedict T Green
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA.
| | - Kevin D Welch
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA
| | - Stephen T Lee
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA
| | - T Zane Davis
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA
| | - Clinton A Stonecipher
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA
| | - Bryan L Stegelmeier
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA
| | - Daniel Cook
- United States Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, 1150 East 1400 North, Logan, UT, 84341, USA
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Du X, Sun Y, Fu T, Gao T, Zhang T. Research Progress and Applications of Bovine Genome in the Tribe Bovini. Genes (Basel) 2024; 15:509. [PMID: 38674443 PMCID: PMC11050176 DOI: 10.3390/genes15040509] [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: 03/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.
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Affiliation(s)
- Xingjie Du
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yu Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tianliu Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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MacPhillamy C, Ren Y, Chen T, Hiendleder S, Low WY. MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver. Front Genet 2023; 14:1329939. [PMID: 38162682 PMCID: PMC10757722 DOI: 10.3389/fgene.2023.1329939] [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: 10/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes. Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth. Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism. Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.
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Affiliation(s)
- Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Tong Chen
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
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Delsol N, Stucky BJ, Oswald JA, Cobb CR, Emery KF, Guralnick R. Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas. Sci Rep 2023; 13:12444. [PMID: 37528222 PMCID: PMC10394069 DOI: 10.1038/s41598-023-39518-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023] Open
Abstract
Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.
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Affiliation(s)
- Nicolas Delsol
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Brian J Stucky
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, USA
| | - Jessica A Oswald
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biology Department, University of Nevada, Reno, Reno, NV, 89557, USA
- U.S. Fish and Wildlife Service, National Fish and Wildlife Forensic Laboratory, Ashland, OR, 97520, USA
| | - Charles R Cobb
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Kitty F Emery
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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Martinez R, Bejarano D, Ramírez J, Ocampo R, Polanco N, Perez JE, Onofre HG, Rocha JF. Genomic variability and population structure of six Colombian cattle breeds. Trop Anim Health Prod 2023; 55:185. [PMID: 37130925 PMCID: PMC10154261 DOI: 10.1007/s11250-023-03574-8] [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: 09/03/2022] [Accepted: 03/29/2023] [Indexed: 05/04/2023]
Abstract
Analyses of the genetic diversity of indigenous cattle are essential for implementing conservation programs, promoting their sustainable use and maintaining productive advantages offered by these breeds in local conditions. The aim of this study was to investigate the genetic diversity and population structure of six Colombian cattle breeds: Blanco Orejinegro (BON), Costeño con Cuernos (CCC), Romosinuano (ROM), Sanmartinero (SAM), Casanareño (CAS), and Hartón del Valle (HDV). Two additional breed groups were included for comparison: Zebu (CEB) and a crossbreed of Colombian cattle breeds × Zebu. Genetic diversity within breeds was analyzed using expected heterozygosity (He), inbreeding coefficient (f), and runs of homozygosity (ROH). Population structure was assessed using model-based clustering (ADMIXTURE) and principal components analysis (PCA). Zebu cattle showed the lowest genetic diversity (He = 0.240). Breeds with the highest genetic diversity level were HDV and BON (He = 0.350 and 0.340, respectively). Inbreeding was lower for Colombian cattle breeds ranging between 0.005 and 0.045. Overall, the largest average genetic distance was found among the group of Colombian cattle breeds and Zebu, while the smallest was found between ROM and CCC. Model-based clustering revealed some level of admixture among HDV and CAS cattle which is consistent with their recent history. The results of the present study provide a useful insight on the genetic structure of Colombian cattle breeds.
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Affiliation(s)
- Rodrigo Martinez
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Diego Bejarano
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Julián Ramírez
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Ricardo Ocampo
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia.
| | - Nelson Polanco
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Juan Esteban Perez
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Héctor Guillermo Onofre
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Juan Felipe Rocha
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
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Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:ijms24055061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [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: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Vahedi SM, Salek Ardestani S, Pahlevan Afshari K, Ghoreishifar SM, Moghaddaszadeh-Ahrabi S, Banabazi MH, Brito LF. Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle. Front Genet 2022; 13:844653. [PMID: 35719394 PMCID: PMC9201998 DOI: 10.3389/fgene.2022.844653] [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: 12/28/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic introgression from interbreeding hybridization of European Bos taurus taurus (EBT) and Indian Bos taurus indicus (IBI) cattle breeds have been widely used to combine the climatic resilience of the IBI cattle and the higher productivity of EBT when forming new composite beef cattle (CB) populations. The subsequent breeding strategies have shifted their initial genomic compositions. To uncover population structure, signatures of selection, and potential introgression events in CB populations, high-density genotypes [containing 492,954 single nucleotide polymorphisms (SNPs) after the quality control] of 486 individuals from 15 cattle breeds, including EBT, IBI, and CB populations, along with two Bos grunniens genotypes as outgroup were used in this study. Then, in-depth population genetics analyses were performed for three CB breeds of Beefmaster, Brangus, and Santa Gertrudis. Neighbor-joining, principal components, and admixture analyses confirmed the historical introgression of EBT and IBI haplotypes into CB breeds. The fdM statistics revealed that only 12.9% of CB populations' genetic components are of IBI origin. The results of signatures of selection analysis indicated different patterns of selection signals in the three CB breeds with primary pressure on pathways involved in protein processing and stress response in Beefmaster, cell proliferation regulation and immune response in Brangus, and amino acids and glucose metabolisms in Santa Gertrudis. An average of >90% of genomic regions underlying selection signatures were of EBT origin in the studied CB populations. Investigating the CB breeds' genome allows the estimation of EBT and IBI ancestral proportions and the locations within the genome where either taurine or indicine origin alleles are under selective pressure. Such findings highlight various opportunities to control the selection process more efficiently and explore complementarity at the genomic level in CB populations.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kian Pahlevan Afshari
- Department of Animal Sciences, Islamic Azad University, Varamin-Pishva Branch, Varamin, Iran
| | - Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Mohammad Hossein Banabazi
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Luiz Fernando Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Her C, Rezaei HR, Hughes S, Naderi S, Duffraisse M, Mashkour M, Naghash HR, Bălășescu A, Luikart G, Jordan S, Özüt D, Kence A, Bruford MW, Tresset A, Vigne JD, Taberlet P, Hänni C, Pompanon F. Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros. Anim Genet 2022; 53:452-459. [PMID: 35288946 DOI: 10.1111/age.13191] [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: 03/09/2021] [Revised: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).
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Affiliation(s)
- Charlotte Her
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Hamid-Reza Rezaei
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Environmental Sciences Department, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Saeid Naderi
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Department of Environment, Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - Marilyne Duffraisse
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marjan Mashkour
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Hamid-Reza Naghash
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Adrian Bălășescu
- Department of Bioarchaeology, 'Vasile Pârvan' Institute of Archaeology, Romanian Academy, Bucharest, Romania
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, Montana, USA
| | - Steve Jordan
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Deniz Özüt
- Biology Department, Middle East Technical University, Ankara, Turkey
| | - Aykut Kence
- Biology Department, Middle East Technical University, Ankara, Turkey
| | | | - Anne Tresset
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Jean-Denis Vigne
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Pierre Taberlet
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway
| | - Catherine Hänni
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - François Pompanon
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
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10
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Population genetic diversity and genetic evaluation models reveal the maternal genetic structure and conservation priority characteristics of indigenous cattle in China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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11
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Cubric‐Curik V, Novosel D, Brajkovic V, Rota Stabelli O, Krebs S, Sölkner J, Šalamon D, Ristov S, Berger B, Trivizaki S, Bizelis I, Ferenčaković M, Rothammer S, Kunz E, Simčič M, Dovč P, Bunevski G, Bytyqi H, Marković B, Brka M, Kume K, Stojanović S, Nikolov V, Zinovieva N, Schönherz AA, Guldbrandtsen B, Čačić M, Radović S, Miracle P, Vernesi C, Curik I, Medugorac I. Large‐scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl 2021; 15:663-678. [PMID: 35505892 PMCID: PMC9046920 DOI: 10.1111/eva.13315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vlatka Cubric‐Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Dinko Novosel
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
- Department of Pathology Croatian Veterinary Institute Zagreb Croatia
| | - Vladimir Brajkovic
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Omar Rota Stabelli
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center Ludwig Maximilians University Munich Munich Germany
| | - Johann Sölkner
- Division of Livestock Sciences Department of Sustainable Agricultural Systems BOKU‐University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Dragica Šalamon
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | | | - Beate Berger
- AREC Raumberg‐Gumpenstein Institute of Organic Farming and Biodiversity of Farm Animals Thalheim Austria
| | | | - Iosif Bizelis
- Faculty of Animal Science and Aquaculture Department of Animal Breeding & Husbandry Agricultural University of Athens Athens Greece
| | - Maja Ferenčaković
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Sophie Rothammer
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Elisabeth Kunz
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Mojca Simčič
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Peter Dovč
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Gojko Bunevski
- Faculty of Agricultural Sciences and Food University Ss. Cyril and Methodius Skopje Macedonia
| | - Hysen Bytyqi
- Faculty of Agriculture and Veterinary Department of Animal Science University of Prishtina Prishtina Kosovo
| | - Božidarka Marković
- Biotechnical Faculty Department of Livestock Science University of Montenegro Podgorica Montenegro
| | - Muhamed Brka
- Faculty of Agriculture and Food Science Institute of Animal Sciences University of Sarajevo Sarajevo Bosnia and Herzegovina
| | | | - Srđan Stojanović
- Ministry of Agriculture, Forestry and Water Management Beograd Serbia
| | - Vasil Nikolov
- Executive Agency for Selection and Reproduction in Animal Breeding Sofia Bulgaria
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry Moscow Region Russia
| | | | - Bernt Guldbrandtsen
- Department of Animal Sciences Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Mato Čačić
- Croatian Agricultural Agency Zagreb Croatia
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology Croatian Academy of Sciences and Arts Zagreb Croatia
| | - Preston Miracle
- Department of Archaeology University of Cambridge Cambridge UK
| | - Cristiano Vernesi
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Ino Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Ivica Medugorac
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
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12
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Petrelli S, Buglione M, Maselli V, Troiano C, Larson G, Frantz L, Manin A, Ricca E, Baccigalupi L, Wright D, Pietri C, Fulgione D. Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs. Mol Ecol 2021; 31:220-237. [PMID: 34676935 DOI: 10.1111/mec.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.
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Affiliation(s)
- Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Naples, Italy
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Aurelie Manin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Loredana Baccigalupi
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Dominic Wright
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Christian Pietri
- Fédération Départementale des Chasseurs de Haute-Corse (FDCHC), Résidence Nouvelle-Corniche, St Joseph, Bastia, France
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
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13
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Dokan K, Kawamura S, Teshima KM. Effects of single nucleotide polymorphism ascertainment on population structure inferences. G3-GENES GENOMES GENETICS 2021; 11:6237890. [PMID: 33871576 PMCID: PMC8496283 DOI: 10.1093/g3journal/jkab128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/08/2021] [Indexed: 11/14/2022]
Abstract
Single nucleotide polymorphism (SNP) data are widely used in research on natural populations. Although they are useful, SNP genotyping data are known to contain bias, normally referred to as ascertainment bias, because they are conditioned by already confirmed variants. This bias is introduced during the genotyping process, including the selection of populations for novel SNP discovery and the number of individuals involved in the discovery panel and selection of SNP markers. It is widely recognized that ascertainment bias can cause inaccurate inferences in population genetics and several methods to address these bias issues have been proposed. However, especially in natural populations, it is not always possible to apply an ideal ascertainment scheme because natural populations tend to have complex structures and histories. In addition, it was not fully assessed if ascertainment bias has the same effect on different types of population structure. Here, we examine the effects of bias produced during the selection of population for SNP discovery and consequent SNP marker selection processes under three demographic models: the island, stepping-stone, and population split models. Results show that site frequency spectra and summary statistics contain biases that depend on the joint effect of population structure and ascertainment schemes. Additionally, population structure inferences are also affected by ascertainment bias. Based on these results, it is recommended to evaluate the validity of the ascertainment strategy prior to the actual typing process because the direction and extent of ascertainment bias vary depending on several factors.
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Affiliation(s)
- Kotaro Dokan
- Graduate School of System Life Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Sayu Kawamura
- Graduate School of System Life Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Kosuke M Teshima
- Department of Biology, Kyushu University, Fukuoka 819-0395, Japan
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14
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Jiang L, Kon T, Chen C, Ichikawa R, Zheng Q, Pei L, Takemura I, Nsobi LH, Tabata H, Pan H, Omori Y, Ogura A. Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour. Sci Rep 2021; 11:17359. [PMID: 34462508 PMCID: PMC8405626 DOI: 10.1038/s41598-021-96896-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/05/2021] [Indexed: 12/04/2022] Open
Abstract
Zhoushan cattle are an endangered cattle breed in the Zhoushan islands in China. Since Zhoushan cattle have been bred in isolation, they show unique characteristics, such as dark black coat colour. However, no studies have been conducted on the genome of Zhoushan cattle. Here, we performed whole-genome sequencing of seven individuals of Zhoushan cattle and nine cattle in Wenling, geographically close to the Zhoushan islands. By integrating our data and publicly-available data, we found that Zhoushan cattle are genetically highly similar to Bos indicus cattle in south-eastern China. Furthermore, by identifying the genomic regions shared between Zhoushan cattle and Angus cattle, a Bos taurus breed, we found that the p.F195L mutation in melanocyte-stimulating hormone receptor (MC1R) could be associated with their dark black coat colour. Taken together, our results provide a valuable resource for characterising the uniqueness of Zhoushan cattle.
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Affiliation(s)
- Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China. .,Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan.
| | - Tetsuo Kon
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Chunyan Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ryota Ichikawa
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Qiyuan Zheng
- Zhoushan Sanxing Zhoushan Cattle Protection Institute, Zhoushan City, 316000, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ikuyo Takemura
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Lauden Hagai Nsobi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Hiromasa Tabata
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Hao Pan
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Yoshihiro Omori
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Atsushi Ogura
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan.
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15
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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.
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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
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16
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Wu D, Lao S, Fan L. De-Domestication: An Extension of Crop Evolution. TRENDS IN PLANT SCIENCE 2021; 26:560-574. [PMID: 33648850 DOI: 10.1016/j.tplants.2021.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
De-domestication or feralization is an interesting phenomenon in crops and livestock. Previously, evidence for crop de-domestication was based mainly on studies using phenotypic and genotypic data from limited molecular markers or gene segments. Recent genomic studies in rice, barley, and wheat provide comprehensive landscapes of de-domestication on a whole-genome scale. Here, we summarize crop de-domestication processes, ecological roles of de-domesticates, mechanisms underlying crop de-domestication syndromes, and conditions potentially favoring de-domestication events. We further explain how recent de-domestication studies have expanded our understanding of the complexity of crop evolution, and highlight the genetic novelties of de-domesticates beneficial for modern crop breeding.
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Affiliation(s)
- Dongya Wu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sangting Lao
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China.
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17
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Geibel J, Reimer C, Weigend S, Weigend A, Pook T, Simianer H. How array design creates SNP ascertainment bias. PLoS One 2021; 16:e0245178. [PMID: 33784304 PMCID: PMC8009414 DOI: 10.1371/journal.pone.0245178] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™ Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.
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Affiliation(s)
- Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
- * E-mail:
| | - Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Torsten Pook
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
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18
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Ballard JWO, Gardner C, Ellem L, Yadav S, Kemp RI. Eye contact and sociability data suggests that Australian dingoes were never domesticated. Curr Zool 2021; 68:423-432. [PMID: 36090142 PMCID: PMC9450177 DOI: 10.1093/cz/zoab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Dogs were the first animal to become domesticated by humans, and they represent a classic model system for unraveling the processes of domestication. We compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog (GSD) breeds. Australian dingoes arrived in Australia 5,000–8,000 BP, and there is debate whether they were domesticated before their arrival. The Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process, while GSDs are a breed dog selected from existing domestic dogs in the late 1800s. We conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each canid. We found 75% of dingoes made eye contact in each phase. In contrast, 86% of Basenjis and 96% of GSDs made eye contact. Dingoes also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called actively. Sociability, quantified as a canid coming within 1 m of the experimenter, was lowest for dingoes and highest for GSDs. For sociability duration, dingoes spent less time within 1 m of the experimenter than either breed dog. When compared with previous studies, these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in Australia. However, it remains possible that the accumulation of mutations since colonization has obscured historical behaviors, and dingoes now exist in a feralized retamed cycle. Additional morphological and genetic data are required to resolve this conundrum.
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Affiliation(s)
- J William O Ballard
- Department of Ecology, Environment, and Evolution, Latrobe University, Melbourne, VIC 3086, Australia
- Department of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Chloe Gardner
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Richard I Kemp
- School of Psychology, UNSW Sydney, Sydney, NSW 2052, Australia
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19
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Ramírez-Ayala LC, Rocha D, Ramos-Onsins SE, Leno-Colorado J, Charles M, Bouchez O, Rodríguez-Valera Y, Pérez-Enciso M, Ramayo-Caldas Y. Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. Genet Sel Evol 2021; 53:3. [PMID: 33397281 PMCID: PMC7784321 DOI: 10.1186/s12711-020-00597-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/11/2020] [Indexed: 02/01/2023] Open
Abstract
Background In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. Results In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Conclusions Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle.
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Affiliation(s)
- Lino C Ramírez-Ayala
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Dominique Rocha
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France
| | - Sebas E Ramos-Onsins
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Jordi Leno-Colorado
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Mathieu Charles
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France.,INRAE, SIGENAE, Jouy-En-Josas, 78350, France
| | - Olivier Bouchez
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, US, 1426, France
| | | | - Miguel Pérez-Enciso
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain.,Institut Català de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes De Montbui, 08140, Spain.
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20
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Sudrajad P, Subiharta S, Adinata Y, Lathifah A, Lee JH, Lenstra JA, Lee SH. An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis. PLoS One 2020; 15:e0241038. [PMID: 33170846 PMCID: PMC7654832 DOI: 10.1371/journal.pone.0241038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/07/2020] [Indexed: 12/01/2022] Open
Abstract
The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.
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Affiliation(s)
- Pita Sudrajad
- Assessment Institute for Agricultural Technology–Central Java, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Kabupaten Semarang, Indonesia
- * E-mail:
| | - Subiharta Subiharta
- Assessment Institute for Agricultural Technology–Central Java, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Kabupaten Semarang, Indonesia
| | - Yudi Adinata
- Beef Cattle Research Station, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Kabupaten Semarang, Indonesia
| | | | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | | | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
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21
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Černý V, Fortes-Lima C, Tříska P. Demographic history and admixture dynamics in African Sahelian populations. Hum Mol Genet 2020; 30:R29-R36. [PMID: 33105478 DOI: 10.1093/hmg/ddaa239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
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Affiliation(s)
- Viktor Černý
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Cesar Fortes-Lima
- Subdepartment of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
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22
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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.
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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
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23
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Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History. G3-GENES GENOMES GENETICS 2020; 10:3061-3070. [PMID: 32680852 PMCID: PMC7466990 DOI: 10.1534/g3.120.400886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.
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24
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Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis. Genes (Basel) 2020; 11:genes11080940. [PMID: 32824045 PMCID: PMC7463645 DOI: 10.3390/genes11080940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 01/24/2023] Open
Abstract
Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.
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25
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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.
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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:
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26
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Chen Q, Shen J, Hanif Q, Chen N, Huang Y, Dang R, Lan X, Chen H, Lei C. Whole genome analyses revealed genomic difference between European taurine and East Asian taurine. J Anim Breed Genet 2020; 138:56-68. [PMID: 32770713 DOI: 10.1111/jbg.12501] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/29/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022]
Abstract
European taurine and East Asian taurine are two main clades in Bos taurus, but their genomic differences are not clearly elucidated. Here, we sequenced 16 Mongolian cattle genomes and compared them to the 92 genomes of 10 representative breeds worldwide. We found the highest LD level in Mishima cattle and the fastest LD decay in European taurine. Phylogenetic analysis revealed that Mongolian, Hanwoo and Mishima cattle were clustered into East Asian taurine. From selective sweep, gene annotation, functional enrichment and differential expression analysis, we identified selective signals including genes and/or pathways related to rapid growth and large body size in European taurine, and superior meat quality in East Asian taurine. Our findings will help us understand the evolutionary history and formation process of the breeds and provide theoretical materials regarding the genetic mechanism underlying breed characteristics and molecular breeding programmes of the taurine clades in the future.
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Affiliation(s)
- Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - 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
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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
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27
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Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni. Proc Natl Acad Sci U S A 2020; 117:11018-11028. [PMID: 32366649 PMCID: PMC7245135 DOI: 10.1073/pnas.1917168117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
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28
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Smaragdov MG, Kudinov AA. Assessing the power of principal components and wright's fixation index analyzes applied to reveal the genome-wide genetic differences between herds of Holstein cows. BMC Genet 2020; 21:47. [PMID: 32345235 PMCID: PMC7189535 DOI: 10.1186/s12863-020-00848-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 03/27/2020] [Indexed: 11/30/2022] Open
Abstract
Background Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright’s fixation index (Fst) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. Results Comparative analysis of the power Principal Components Analysis (PCA) and Fst were carried out to reveal genetic differences between herds of Holsteinized cows. Totally, 803 BovineSNP50 genotypes of cows from 13 herds were used in current study. Obtained Fst values were in the range of 0.002–0.012 (mean 0.0049) while for rare SNPs with MAF 0.0001–0.005 they were even smaller in the range of 0.001–0.01 (mean 0.0027). Genetic relatedness of the cows in the herds was the cause of such small Fst values. The contribution of rare alleles with MAF 0.0001–0.01 to the Fst values was much less than common alleles and this effect depends on linkage disequilibrium (LD). Despite of substantial change in the MAF spectrum and the number of SNPs we observed small effect size of LD - based pruning on Fst data. PCA analysis confirmed the mutual admixture and small genetic difference between herds. Moreover, PCA analysis of the herds based on the visualization the results of a single eigenvector cannot be used to significantly differentiate herds. Only summed eigenvectors should be used to realize full power of PCA to differentiate small between herds genetic difference. Finally, we presented evidences that the significance of Fst data far exceeds the significance of PCA data when these methods are used to reveal genetic differences between herds. Conclusions LD - based pruning had a small effect on findings of Fst and PCA analyzes. Therefore, for weakly structured populations the LD - based pruning is not effective. In addition, our results show that the significance of genetic differences between herds obtained by Fst analysis exceeds the values of PCA. Proposed, to differentiate herds or low structured populations we recommend primarily using the Fst approach and only then PCA.
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Affiliation(s)
- M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the l.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia. .,, St. Petersburg, Russian Federation.
| | - A A Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the l.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia.,Department of Agricultural Science, University of Helsinki, FI-00014, Helsinki, Finland
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29
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Lehocká K, Olšanská B, Kasarda R, Kadlečík O, Trakovická A, Moravčíková N. The Genetic Structure of Slovak Spotted Cattle Based on Genome-wide Analysis. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2020. [DOI: 10.11118/actaun202068010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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30
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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.
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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.
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31
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Paim TDP, Hay EHA, Wilson C, Thomas MG, Kuehn LA, Paiva SR, McManus C, Blackburn HD. Dynamics of genomic architecture during composite breed development in cattle. Anim Genet 2020; 51:224-234. [PMID: 31961956 PMCID: PMC7065137 DOI: 10.1111/age.12907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022]
Abstract
Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.
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Affiliation(s)
- T do P Paim
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Avenida Oeste n. 350, Iporá, 76.200-000, Brazil.,Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - E H A Hay
- US Department of Agriculture, Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, 243 Fort Keogh Road, Miles City, 59301, USA
| | - C Wilson
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
| | - M G Thomas
- Department of Animal Sciences, Colorado State University, 350 W. Pitkin St., Fort Collins, 80523-1171, USA
| | - L A Kuehn
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, Clay Center, 68933, USA
| | - S R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final) Caixa Postal 02372, Brasília, 70.770-917, Brazil
| | - C McManus
- Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - H D Blackburn
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
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Asadollahpour Nanaei H, Dehghani Qanatqestani M, Esmailizadeh A. Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle. Genomics 2020; 112:880-885. [DOI: 10.1016/j.ygeno.2019.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/02/2019] [Accepted: 06/01/2019] [Indexed: 12/23/2022]
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Salazar AN, Gorter de Vries AR, van den Broek M, Brouwers N, de la Torre Cortès P, Kuijpers NGA, Daran JMG, Abeel T. Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization. BMC Genomics 2019; 20:916. [PMID: 31791228 PMCID: PMC6889557 DOI: 10.1186/s12864-019-6263-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history. RESULTS To fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains. CONCLUSIONS Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.
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Affiliation(s)
- Alex N Salazar
- Delft Bioinformatics Lab, Delft University of Technology, 2628, CD, Delft, The Netherlands
| | - Arthur R Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Nick Brouwers
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Pilar de la Torre Cortès
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Niels G A Kuijpers
- HEINEKEN Supply Chain B.V., Global Innovation and Research, Zoeterwoude, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, 2628, CD, Delft, The Netherlands.
- Broad Institute of MIT and Harvard, Boston, MA, 02142, USA.
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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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Global selective sweep of a highly inbred genome of the cattle parasite Neospora caninum. Proc Natl Acad Sci U S A 2019; 116:22764-22773. [PMID: 31636194 DOI: 10.1073/pnas.1913531116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Neospora caninum, a cyst-forming apicomplexan parasite, is a leading cause of neuromuscular diseases in dogs as well as fetal abortion in cattle worldwide. The importance of the domestic and sylvatic life cycles of Neospora, and the role of vertical transmission in the expansion and transmission of infection in cattle, is not sufficiently understood. To elucidate the population genomics of Neospora, we genotyped 50 isolates collected worldwide from a wide range of hosts using 19 linked and unlinked genetic markers. Phylogenetic analysis and genetic distance indices resolved a single genotype of N. caninum Whole-genome sequencing of 7 isolates from 2 different continents identified high linkage disequilibrium, significant structural variation, but only limited polymorphism genome-wide, with only 5,766 biallelic single nucleotide polymorphisms (SNPs) total. Greater than half of these SNPs (∼3,000) clustered into 6 distinct haploblocks and each block possessed limited allelic diversity (with only 4 to 6 haplotypes resolved at each cluster). Importantly, the alleles at each haploblock had independently segregated across the strains sequenced, supporting a unisexual expansion model that is mosaic at 6 genomic blocks. Integrating seroprevalence data from African cattle, our data support a global selective sweep of a highly inbred livestock pathogen that originated within European dairy stock and expanded transcontinentally via unisexual mating and vertical transmission very recently, likely the result of human activities, including recurrent migration, domestication, and breed development of bovid and canid hosts within similar proximities.
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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Ahmad SF, Panigrahi M, Chhotaray S, Pal D, Parida S, Bhushan B, Gaur GK, Mishra BP, Singh RK. Revelation of genomic breed composition in a crossbred cattle of India with the help of Bovine50K BeadChip. Genomics 2019; 112:1531-1535. [PMID: 31472242 DOI: 10.1016/j.ygeno.2019.08.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 01/24/2023]
Abstract
The aim of the present study was to assess the population structure and admixture levels in the Vrindavani composite population in India by using Bovine50KSNP BeadChip data. Genotypic data were generated for randomly selected animals (n = 72) of Vrindavani population and the data for parental breeds i.e., Hariana (n = 10), Holstein-Friesian (n = 63), Jersey (n = 28) and Brown Swiss (n = 22) were retrieved from a public repository. The indices of population structure were calculated using PLINK software and R-program. The merged dataset was analysed for assessing admixture levels and population stratification using three different approaches i.e., principal component analysis (PCA), multi-dimensional scaling (MDS) approach and the model-based approach in STRUCTURE software. The average minor allele frequency (MAF) value for Vrindavani population was estimated to be 0.235. Vrindavani population was found to possess an average ancestry of 39.5, 22.9, 26.9, and 10.7% inheritance levels from Holstein Friesian, Jersey, Hariana and Brown Swiss cattle breeds, respectively.
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Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Supriya Chhotaray
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Dhan Pal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B P Mishra
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - R K Singh
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Ginja C, Gama LT, Cortés O, Burriel IM, Vega-Pla JL, Penedo C, Sponenberg P, Cañón J, Sanz A, do Egito AA, Alvarez LA, Giovambattista G, Agha S, Rogberg-Muñoz A, Lara MAC, Delgado JV, Martinez A. The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers. Sci Rep 2019; 9:11486. [PMID: 31391486 PMCID: PMC6685949 DOI: 10.1038/s41598-019-47636-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.
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Affiliation(s)
- Catarina Ginja
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Luis Telo Gama
- CIISA.Faculdade de Medicina Veterinaria, Universidade de Lisboa, Lisbon, Portugal
| | - Oscar Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.
| | - Inmaculada Martin Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Jose Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Servicio de Cría Caballar de las Fuerzas Armadas, Córdoba, Spain
| | - Cecilia Penedo
- Veterinary Genetics Laboratory, University of California, Davis, California, USA
| | - Phil Sponenberg
- Virginia-Maryland Regional College of Veterinary Medicine. Virginia Tech, Virginia, USA
| | - Javier Cañón
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Arianne Sanz
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | | | - Saif Agha
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | | | | | | | - Juan Vicente Delgado
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Amparo Martinez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Animal Beeding Consulting S.L. Universidad de Córdoba, Córdoba, Spain
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40
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Iqbal N, Liu X, Yang T, Huang Z, Hanif Q, Asif M, Khan QM, Mansoor S. Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan. PLoS One 2019; 14:e0215065. [PMID: 30973947 PMCID: PMC6459497 DOI: 10.1371/journal.pone.0215065] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.
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Affiliation(s)
- Naveed Iqbal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Department of Biotechnology & Informatics, Faculty of life Sciences, Baluchistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Baluchistan, Pakistan
| | - Xin Liu
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Ting Yang
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Ziheng Huang
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Qaiser Mahmood Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
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New world goat populations are a genetically diverse reservoir for future use. Sci Rep 2019; 9:1476. [PMID: 30728441 PMCID: PMC6365549 DOI: 10.1038/s41598-019-38812-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/30/2018] [Indexed: 01/02/2023] Open
Abstract
Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.
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42
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Pitt D, Bruford MW, Barbato M, Orozco‐terWengel P, Martínez R, Sevane N. Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics. Evol Appl 2019; 12:105-122. [PMID: 30622639 PMCID: PMC6304683 DOI: 10.1111/eva.12641] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 02/06/2023] Open
Abstract
The introduction of Iberian cattle in the Americas after Columbus' arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD) and N e Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) and population differentiation (F ST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic N e contraction. NeS analysis provided insights into short-term complexity in population change and depicted a decrease/expansion episode at the end of the ABC-inferred expansion, as well as several additional fluctuations in N e with the attainment of the current small N e only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future-proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change.
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Affiliation(s)
- Daniel Pitt
- School of BiosciencesCardiff UniversityCardiffUK
| | - Michael W. Bruford
- School of BiosciencesCardiff UniversityCardiffUK
- Sustainable Places Research InstituteCardiff UniversityCardiffUK
| | - Mario Barbato
- Institute of ZootechnicsUniversità Cattolica del Sacro CuorePiacenzaItaly
| | | | - Rodrigo Martínez
- Centro de investigaciones TibaitatáCorporación Colombiana De Investigación Agropecuaria (Corpoica)BogotáColombia
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Pitt D, Sevane N, Nicolazzi EL, MacHugh DE, Park SDE, Colli L, Martinez R, Bruford MW, Orozco‐terWengel P. Domestication of cattle: Two or three events? Evol Appl 2019; 12:123-136. [PMID: 30622640 PMCID: PMC6304694 DOI: 10.1111/eva.12674] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/19/2018] [Accepted: 06/10/2018] [Indexed: 02/06/2023] Open
Abstract
Cattle have been invaluable for the transition of human society from nomadic hunter-gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human-mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.
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Affiliation(s)
- Daniel Pitt
- School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - David E. MacHugh
- Animal Genomics LaboratoryUCD School of Agriculture and Food Science, UCD College of Health and Agricultural SciencesUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublinIreland
| | | | - Licia Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e sul DNA AnticoUniversità Cattolica del S. Cuore di PiacenzaPiacenzaItaly
| | - Rodrigo Martinez
- Corporación Colombiana De Investigación Agropecuaria (Corpoica)Centro de investigaciones TibaitatáBogotáColombia
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Zhang W, Gao X, Zhang Y, Zhao Y, Zhang J, Jia Y, Zhu B, Xu L, Zhang L, Gao H, Li J, Chen Y. Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle. BMC Genet 2018; 19:114. [PMID: 30572824 PMCID: PMC6302425 DOI: 10.1186/s12863-018-0705-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022] Open
Abstract
Background China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K). Results In principal component analysis (PCA) and neighbour-joining (NJ) tree analysis, samples of the same breeds were grouped together, leading to clear separation from other breeds. And Chinese indigenous cattle were clustered into two groups of southern and northern breeds, originated from Asian Bos indicus lineage and Eurasian Bos taurus lineage, respectively. In STRUCTURE K = 2, a clear transition occurred from the northern breeds to the southern breeds. Additionally, the northern breeds contained a smaller Eurasian taurine (62.5%) descent proportion than that reported previously (more than 90%). In STRUCTURE K = 3, a distinct descent was detected in the southern Chinese breeds, which could reflect a long-term selection history of Chinese indigenous cattle. The results from TreeMix and f3 statistic provided the evidence of an admixture history between southern breeds and northern breeds. Conclusions Consistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds. Electronic supplementary material The online version of this article (10.1186/s12863-018-0705-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wengang Zhang
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue Gao
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yang Zhang
- Xinjiang Academy of Animal Science, Urumqi, 830011, China
| | - Yumin Zhao
- Jilin Academy of Animal Science, Changchun, 130124, China
| | | | - Yutang Jia
- Institute of Animal Husbandry and Veterinary Medicine, AnhuiAcademyof Agricultural Sciences, Hefei, 230031, China
| | - Bo Zhu
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lingyang Xu
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lupei Zhang
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Huijiang Gao
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Junya Li
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Yan Chen
- Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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Colli L, Milanesi M, Talenti A, Bertolini F, Chen M, Crisà A, Daly KG, Del Corvo M, Guldbrandtsen B, Lenstra JA, Rosen BD, Vajana E, Catillo G, Joost S, Nicolazzi EL, Rochat E, Rothschild MF, Servin B, Sonstegard TS, Steri R, Van Tassell CP, Ajmone-Marsan P, Crepaldi P, Stella A. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes. Genet Sel Evol 2018; 50:58. [PMID: 30449284 PMCID: PMC6240949 DOI: 10.1186/s12711-018-0422-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. RESULTS A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. CONCLUSIONS After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.
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Affiliation(s)
- Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy. .,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy.
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,School of Veterinary Medicine, Department of Support, Production and Animal Health, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, USA.,National Institute of Aquatic Resources, Technical University of Denmark, DTU, Lyngby, Denmark
| | - Minhui Chen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark.,Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alessandra Crisà
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Kevin Gerard Daly
- Population Genetics Lab, Smurfit Institute of Genetics, Trinity College of Dublin, Dublin, Ireland
| | - Marcello Del Corvo
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Elia Vajana
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Roberto Steri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Lodi, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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Ahmad SF, Panigrahi M, Chhotaray S, Pal D, Chauhan A, Sonwane A, Parida S, Bhushan B, Gaur GK, Mishra BP, Singh RK. Population structure and admixture analysis in Frieswal crossbred cattle of India – a pilot study. Anim Biotechnol 2018; 31:86-92. [DOI: 10.1080/10495398.2018.1538013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Supriya Chhotaray
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Dhan Pal
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Anuj Chauhan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Arvind Sonwane
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Subhashree Parida
- Division of Veterinary Pharmacology, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Gyanendra Kumar Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
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Castiglione GM, Chang BS. Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision. eLife 2018; 7:35957. [PMID: 30362942 PMCID: PMC6203435 DOI: 10.7554/elife.35957] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022] Open
Abstract
Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.
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Affiliation(s)
- Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Belinda Sw Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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Lwin M, Mon SLY, Yamanaka H, Nagano Y, Mannen H, Faruque MO, Kawabe K, Okamoto S, Shimogiri T. Genetic diversities and population structures of four popular Myanmar local cattle breeds. Anim Sci J 2018; 89:1648-1655. [PMID: 30318818 DOI: 10.1111/asj.13112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022]
Abstract
Local cattle breeds are popular in Myanmar because they make excellent draught animals, so it is of fundamental importance that their genetic diversities and population structures are elucidated for breeding and conservation purposes. In this study, we characterized the genetic diversities and population structures of four popular Myanmar local cattle breeds and five native cattle populations from neighboring countries (Bangladesh, Laos, Cambodia, and Vietnam) using the GGP Bovine 50K array. The mean observed and expected heterozygosity estimates using pruned datasets ranged from 0.317 and 0.322, respectively, in Cambodia to 0.448 and 0.421, respectively, in Vietnam South. The four Myanmar local breeds exhibited similar levels of genetic diversity. However, AMOVA revealed significant genetic differentiation among the nine populations (p < 0.00001), and Neighbor-Net analysis showed that Shan Ngwar Pu was distinct from the other Myanmar local breeds. Furthermore, PCA and population structure analyses revealed that the native cattle from neighboring countries genetically influenced the Myanmar local breeds to some extent and that the genetic origins could also be observed in the local breeds. These findings highlight the importance of Myanmar local breeds as genetic resources and provide useful information for the future development of breeding strategies and conservation management plans.
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Affiliation(s)
- Moe Lwin
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Su Lai Y Mon
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Hayate Yamanaka
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Analytical Research Center for Experimental Sciences, Saga University, Honjo, Saga, Japan
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | | | - Kotaro Kawabe
- Education Center, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
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Dotsev AV, Sermyagin AA, Shakhin AV, Paronyan IA, Plemyashov KV, Reyer H, Wimmers K, Brem G, Zinovieva NA. Evaluation of current gene pool of Kholmogor and Black-and-white cattle breeds based on whole genome SNP analysis. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Conservation of local cattle genetic resources is an important strategy for achieving Russia’s food security. During last decades, in the Russian Federation, local livestock populations were either crossbred or replaced by highly productive imported breeds, which led to a loss of the major part of original breeds identities. The objective of our study was to identify genetic differences between the populations of Kholmogor and Black-and-white cattle with varying degrees of admixture with the Holstein breed. The aforementioned breeds were studied using their whole-genome single nucleotide polymorphism (SNP) genotypes. The Kholmogor breed was subdivided into three groups: purebred (KHLM, n = 3), admixed with Holsteins (KHLM-HLST, n = 4) and representatives of old-type breed (KHLM-INTA, n = 15). Blackand-white was subdivided into four groups: purebred (BLWT, n = 9), with a low (BLWT-75, n = 8) and a high (BLWT-HLST, n = 10) level of admixture with Holstein, and represented by archival samples from the 1970s and 1980s (BLWT-OLD, n = 15). The Holsteins genetic profiles (HLST, n = 27) were taken as a comparison group. PLINK 1.07, Admixture 1.3, SplitsTree 4.14.6 and R package StAMPP were used to infer genetic relationship between the studied groups. After quality control, 29 688 SNPs were selected for analysis. Multidimensional scaling (MDS), Admixture analysis and a dendrogram constructed using the Neighbor-Net method, revealed the presence of three clusters belonging to the Kholmogor, Black-and-white and Holstein breeds. The first one included KHLM and KHLM-INTA, the second – BLWT and BLWT-OLD, and the third – HLST, KHLM-HLST and BLWT-HLST. The BLWT-75 samples were placed between HLST and BLWT. Thus, our results showed that currently the populations of native cattle breeds with valuable genotypes still exist. The populations with a high level of admixture with Holsteins could be considered neither as the Kholmogor nor as Blackand-white breeds, and would rather be referred as the Holstein breed of local breeding.
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Affiliation(s)
- A. V. Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry
| | | | - A. V. Shakhin
- L.K. Ernst Federal Science Center for Animal Husbandry
| | - I. A. Paronyan
- Russian Research Institute of Farm Animal Genetics and Breeding – Subsidiary of L.K. Ernst Federal Science Center for Animal Husbandry
| | - K. V. Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding – Subsidiary of L.K. Ernst Federal Science Center for Animal Husbandry
| | - H. Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology
| | - K. Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology
| | - G. Brem
- L.K. Ernst Federal Science Center for Animal Husbandry; Institute of Animal Breeding and Genetics, University of Veterinary Medicine
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50
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Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin. Sci Rep 2018; 8:11677. [PMID: 30076315 PMCID: PMC6076285 DOI: 10.1038/s41598-018-30061-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/18/2018] [Indexed: 12/03/2022] Open
Abstract
Domestic animals play a key role in human survival and the development of civilization. However, the genetic resources of domestic animals are facing an alarming rate of erosion due to socioeconomic changes, economic globalization and financial constraints. In this study, through genome-wide SNP analysis, we estimated the heterozygosity, inbreeding coefficient, effective population size, and runs of homozygosity to identify the breeds facing the risk of extinction for sheep and cattle across the world. In particular, we quantified the contribution of 97 sheep breeds and 53 cattle breeds to genomic diversity (within-breed, between-breed and total) and prioritized the breeds for conservation. Additionally, we compared the average values of genomic diversity between breeds from regions (or countries) in different economic categories (underdeveloped, developing and developed), and found that breeds in developed regions exhibit significantly higher levels of total genomic diversity than those in underdeveloped and developing regions. Altogether, our results suggested that conservation priority should be given to breeds in developed regions to secure the future genomic diversity hotspots of domestic animal resources.
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