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Fegraeus K, Rosengren MK, Naboulsi R, Orlando L, Åbrink M, Jouni A, Velie BD, Raine A, Egner B, Mattsson CM, Lång K, Zhigulev A, Björck HM, Franco-Cereceda A, Eriksson P, Andersson G, Sahlén P, Meadows JRS, Lindgren G. An endothelial regulatory module links blood pressure regulation with elite athletic performance. PLoS Genet 2024; 20:e1011285. [PMID: 38885195 PMCID: PMC11182536 DOI: 10.1371/journal.pgen.1011285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024] Open
Abstract
The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.
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Affiliation(s)
- Kim Fegraeus
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Maria K. Rosengren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Rakan Naboulsi
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Stockholm
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Toulouse, France
| | - Magnus Åbrink
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ahmad Jouni
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Brandon D. Velie
- School of Life & Environmental Sciences, University of Sydney, Sydney, Australia
| | - Amanda Raine
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Beate Egner
- Department of Cardio-Vascular Research, Veterinary Academy of Higher Learning, Babenhausen, Germany
| | - C Mikael Mattsson
- Silicon Valley Exercise Analytics (svexa), MenloPark, CA, United States of America
| | - Karin Lång
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Artemy Zhigulev
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Hanna M. Björck
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Anders Franco-Cereceda
- Section of Cardiothoracic Surgery, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Göran Andersson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
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Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J. Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. PLoS One 2024; 19:e0299109. [PMID: 38442089 PMCID: PMC10914290 DOI: 10.1371/journal.pone.0299109] [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: 07/19/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.
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Affiliation(s)
- B. Bazvand
- Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran
| | - A. Rashidi
- Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran
| | - M. B. Zandi
- Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - M. H. Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - J. Rostamzadeh
- Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran
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3
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Howe NS, Hale MC, Waters CD, Schaal SM, Shedd KR, Larson WA. Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. Evol Appl 2024; 17:e13656. [PMID: 38357359 PMCID: PMC10866082 DOI: 10.1111/eva.13656] [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: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.
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Affiliation(s)
- Natasha S. Howe
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Charles D. Waters
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Sara M. Schaal
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Kyle R. Shedd
- Alaska Department of Fish and Game, Division of Commercial FisheriesGene Conservation LaboratoryAnchorageAlaskaUSA
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
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4
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Sharko FS, Boulygina ES, Tsygankova SV, Slobodova NV, Rastorguev SM, Krasivskaya AA, Belinsky AB, Härke H, Kadieva AA, Demidenko SV, Malashev VY, Shvedchikova TY, Dobrovolskaya MV, Reshetova IK, Korobov DS, Nedoluzhko AV. Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus. Eur J Hum Genet 2024:10.1038/s41431-023-01524-4. [PMID: 38177408 DOI: 10.1038/s41431-023-01524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.
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Affiliation(s)
- Fedor S Sharko
- European University at St. Petersburg, 6/1A Gagarinskaya Street, 191187, St. Petersburg, Russia
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
| | - Eugenia S Boulygina
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
| | - Svetlana V Tsygankova
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
| | - Natalia V Slobodova
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
- HSE University, Profsoyuznaya st. 33, bld. 4, Moscow, 117418, Russia
| | - Sergey M Rastorguev
- N. I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation Ostrovityanova st. 1, Moscow, 117997, Russia
| | - Anna A Krasivskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Andrej B Belinsky
- Limited liability company Nasledie, K. Marx av., 56, Stavropol', 355017, Russia
| | - Heinrich Härke
- Centre for Classical and Oriental Archaeology, National Research University Higher School of Economics, ul. Staraya Basmannaya 21/4c1, Moscow, 105066, Russia
- Department of Medieval Archaeology, University of Tübingen, Schloss Hohentübingen, D-72070, Tübingen, Germany
| | - Anna A Kadieva
- Department of Archaeology, State Historical Museum, Krasnaya pl., 1, Moscow, 109012, Russia
| | - Sergej V Demidenko
- Department of Scythian and Sarmatian Archaeology, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Vladimir Yu Malashev
- Department of Scythian and Sarmatian Archaeology, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Tatiana Yu Shvedchikova
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Maria V Dobrovolskaya
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Irina K Reshetova
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Dmitry S Korobov
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia.
| | - Artem V Nedoluzhko
- European University at St. Petersburg, 6/1A Gagarinskaya Street, 191187, St. Petersburg, Russia.
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5
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Benítez-Burraco A, Uriagereka J, Nataf S. The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development. Dev Genes Evol 2023; 233:123-135. [PMID: 37552321 PMCID: PMC10746608 DOI: 10.1007/s00427-023-00709-7] [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: 02/26/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain.
- Área de Lingüística General, Departamento de Lengua Española, Lingüística y Teoría de la Literatura, Facultad de Filología, Universidad de Sevilla, C/ Palos de la Frontera s/n., 41007-, Sevilla, España.
| | - Juan Uriagereka
- Department of Linguistics and School of Languages, Literatures & Cultures, University of Maryland, College Park, MD, USA
| | - Serge Nataf
- Stem-cell and Brain Research Institute, 18 avenue de Doyen Lépine, F-69500, Bron, France
- University of Lyon 1, 43 Bd du 11 Novembre 1918, F-69100, Villeurbanne, France
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d'Arsonval, F-69003, Lyon, France
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6
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Chen J, Zhang S, Liu S, Dong J, Cao Y, Sun Y. Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds. Anim Biotechnol 2023; 34:1828-1839. [PMID: 35382683 DOI: 10.1080/10495398.2022.2053145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.
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Affiliation(s)
- Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, China
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Yanhang Cao
- Modern Animal Husbandry Development Service Center of Dongying, Dongying, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
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7
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Moyers BA, Loupe JM, Felker SA, Lawlor JM, Anderson AG, Rodriguez-Nunez I, Bunney WE, Bunney BG, Cartagena PM, Sequeira A, Watson SJ, Akil H, Mendenhall EM, Cooper GM, Myers RM. Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561245. [PMID: 37873117 PMCID: PMC10592666 DOI: 10.1101/2023.10.06.561245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors. Using graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signal between alleles at heterozygous variants within each tissue sample from each donor. Comparison of results from different brain regions within donors and the same regions between donors provided measures of allele bias reproducibility. We identified thousands of DNA variants that show reproducible bias in ChIP-seq for at least one TF. We found that alleles that are rarer in the general population were more likely than common alleles to exhibit large biases, and more frequently led to reduced TF binding. Combining ChIP-seq with RNA-seq, we identified TF-allele interaction biases with RNA bias in a phased allele linked to 6,709 eQTL variants identified in GTEx data, 3,309 of which were found in neural contexts. Our results provide insights into the effects of both common and rare variation on gene regulation in the brain. These findings can facilitate mechanistic understanding of cis-regulatory variation associated with biological traits, including disease.
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Affiliation(s)
| | - Jacob M. Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville AL, USA
| | | | | | | | | | - William E. Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine CA, USA
| | - Blynn G. Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine CA, USA
| | - Preston M. Cartagena
- Department of Psychiatry and Human Behavior, University of California, Irvine CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California, Irvine CA, USA
| | - Stanley J. Watson
- The Michigan Neuroscience Institute, University of Michigan, Ann Arbor MI, USA
| | - Huda Akil
- The Michigan Neuroscience Institute, University of Michigan, Ann Arbor MI, USA
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Gu J, Li S, Zhu B, Liang Q, Chen B, Tang X, Chen C, Wu DD, Li Y. Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing. Mol Ecol Resour 2023; 23:1656-1672. [PMID: 37259205 DOI: 10.1111/1755-0998.13818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.
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Affiliation(s)
- Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Sheng Li
- Maxun Biotechnology Institute, Changsha, China
| | - Bo Zhu
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiqi Liang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Bin Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Xiangwei Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Chujie Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, China
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May-Davis S, Dzingle D, Saber E, Blades Eckelbarger P. Characterization of the Caudal Ventral Tubercle in the Sixth Cervical Vertebra in Modern Equus ferus caballus. Animals (Basel) 2023; 13:2384. [PMID: 37508161 PMCID: PMC10376820 DOI: 10.3390/ani13142384] [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: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
This study examined the anomalous variations of the ventral process of C6 in modern E. ferus caballus. The aim was to provide an incremental grading protocol measuring the absence of the caudal ventral tubercle (CVT) in this ventral process. The findings revealed the most prevalent absent CVT (aCVT) was left unilateral (n = 35), with bilateral (n = 29) and right unilateral (n = 12). Grading was determined in equal increments of absence 1/4, 2/4, 3/4, with 4/4 representing a complete aCVT in 56/76, with a significance of p = 0.0013. This also applied to bilateral specimens. In those C6 osseous specimens displaying a 4/4 grade aCVT, 41/56 had a partial absence of the caudal aspect of the cranial ventral tubercle (CrVT). Here, grading absent CrVTs (aCrVT) followed similarly to aCVTs, though 4/4 was not observed. The significance between 4/4 grade aCVTs and the presentation of an aCrVT was left p = 0.00001 and right p = 0.00018. In bilateral specimens, C6 morphologically resembled C5, implying a homeotic transformation that limited the attachment sites for the cranial and thoracal longus colli muscle. This potentially diminishes function and caudal cervical stability. Therefore, it is recommended that further studies examine the morphological extent of this equine complex vertebral malformation (ECVM) as well as its interrelationships and genetic code/blueprint.
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Affiliation(s)
- Sharon May-Davis
- Canine and Equine Research Group, University of New England, Armidale, NSW 2351, Australia
| | - Diane Dzingle
- Equus Soma-Equine Osteology and Anatomy Learning Center, Aiken, SC 29805, USA
| | - Elle Saber
- Biological Data Science Institute, Australian National University, Canberra, ACT 2601, Australia
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10
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Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding. iScience 2023; 26:107104. [PMID: 37416458 PMCID: PMC10319840 DOI: 10.1016/j.isci.2023.107104] [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: 01/03/2023] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023] Open
Abstract
Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.
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Affiliation(s)
- Evelyn T. Todd
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aurore Fromentier
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Richard Sutcliffe
- Glasgow Museums Resource Centre, 200 Woodhead Road, Nitshill, G53 7NN Glasgow, UK
| | - Yvette Running Horse Collin
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Camille Èche
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Ted Kalbfleisch
- MH Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska-Lincoln, 3940 Fair St, Lincoln, NE 68583-0908, USA
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
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11
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Vasoya D, Tzelos T, Benedictus L, Karagianni AE, Pirie S, Marr C, Oddsdóttir C, Fintl C, Connelley T. High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure. Genes (Basel) 2023; 14:1422. [PMID: 37510326 PMCID: PMC10379315 DOI: 10.3390/genes14071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
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Affiliation(s)
- Deepali Vasoya
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Thomas Tzelos
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lindert Benedictus
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Anna Eleonora Karagianni
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Scott Pirie
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Celia Marr
- Rossdales Equine Hospital, Cotton End Road, Exning, Newmarket CD8 7NN, UK
| | - Charlotta Oddsdóttir
- The Institute for Experimental Pathology at Keldur, University of Iceland Keldnavegur 3, 112 Reykjavík, Iceland
| | - Constanze Fintl
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
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12
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Gleeson BT, Wilson LAB. Shared reproductive disruption, not neural crest or tameness, explains the domestication syndrome. Proc Biol Sci 2023; 290:20222464. [PMID: 36946116 PMCID: PMC10031412 DOI: 10.1098/rspb.2022.2464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Altered neural crest cell (NCC) behaviour is an increasingly cited explanation for the domestication syndrome in animals. However, recent authors have questioned this explanation, while others cast doubt on whether domestication syndrome even exists. Here, we review published literature concerning this syndrome and the NCC hypothesis, together with recent critiques of both. We synthesize these contributions and propose a novel interpretation, arguing shared trait changes under ancient domestication resulted primarily from shared disruption of wild reproductive regimes. We detail four primary selective pathways for 'reproductive disruption' under domestication and contrast these succinct and demonstrable mechanisms with cryptic genetic associations posited by the NCC hypothesis. In support of our perspective, we illustrate numerous important ways in which NCCs contribute to vertebrate reproductive phenotypes, and argue it is not surprising that features derived from these cells would be coincidentally altered under major selective regime changes, as occur in domestication. We then illustrate several pertinent examples of Darwin's 'unconscious selection' in action, and compare applied selection and phenotypic responses in each case. Lastly, we explore the ramifications of reproductive disruption for wider evolutionary discourse, including links to wild 'self-domestication' and 'island effect', and discuss outstanding questions.
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Affiliation(s)
- Ben Thomas Gleeson
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
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13
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Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annu Rev Anim Biosci 2023; 11:93-114. [PMID: 36332644 PMCID: PMC9933137 DOI: 10.1146/annurev-animal-080522-093311] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.
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Affiliation(s)
- Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, California, USA;
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Stella C Yuan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , , .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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14
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Everett R, Cribdon B. MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.888421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.
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15
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Schoenecker KA, Esmaeili S, King SRB. Seasonal resource selection and movement ecology of free‐ranging horses in the western United States. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kathryn A. Schoenecker
- U.S. Geological Survey, Fort Collins Science Center 2150 Centre Avenue, Building C Fort Collins CO 80526 USA
| | - Saeideh Esmaeili
- Colorado State University, Natural Resources Ecology Laboratory 1213 Libbie Coy Way Fort Collins CO 80523 USA
| | - Sarah R. B. King
- Colorado State University, Natural Resources Ecology Laboratory 1213 Libbie Coy Way Fort Collins CO 80523 USA
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16
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Han H, McGivney BA, Allen L, Bai D, Corduff LR, Davaakhuu G, Davaasambuu J, Dorjgotov D, Hall TJ, Hemmings AJ, Holtby AR, Jambal T, Jargalsaikhan B, Jargalsaikhan U, Kadri NK, MacHugh DE, Pausch H, Readhead C, Warburton D, Dugarjaviin M, Hill EW. Common protein-coding variants influence the racing phenotype in galloping racehorse breeds. Commun Biol 2022; 5:1320. [PMID: 36513809 PMCID: PMC9748125 DOI: 10.1038/s42003-022-04206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.
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Affiliation(s)
- Haige Han
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Beatrice A. McGivney
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Lucy Allen
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Dongyi Bai
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Leanne R. Corduff
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Gantulga Davaakhuu
- grid.425564.40000 0004 0587 3863Institute of Biology, Mongolian Academy of Sciences, Peace Avenue 54B, Ulaanbaatar, 13330 Mongolia
| | - Jargalsaikhan Davaasambuu
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Dulguun Dorjgotov
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Thomas J. Hall
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Andrew J. Hemmings
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Amy R. Holtby
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Tuyatsetseg Jambal
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Badarch Jargalsaikhan
- grid.444534.60000 0000 8485 883XDepartment of Obstetrics and Gynecology, Mongolian National University of Medical Sciences, Ulaanbaatar, 14210 Mongolia
| | - Uyasakh Jargalsaikhan
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Naveen K. Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - David E. MacHugh
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland ,grid.7886.10000 0001 0768 2743UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Carol Readhead
- grid.20861.3d0000000107068890Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - David Warburton
- grid.42505.360000 0001 2156 6853The Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027 USA
| | - Manglai Dugarjaviin
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Emmeline W. Hill
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland ,grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
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17
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Wilson LAB. Developmental instability in domesticated mammals. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:484-494. [PMID: 34813170 DOI: 10.1002/jez.b.23108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.
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Affiliation(s)
- Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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18
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Xu B, Yang G, Jiao B, Zhu H. Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication. Front Genet 2022; 13:944933. [PMID: 36276948 PMCID: PMC9579347 DOI: 10.3389/fgene.2022.944933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs’ potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.
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Affiliation(s)
- Baoyan Xu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Medical Engineering Department, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Guixian Yang
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Hao Zhu,
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19
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Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science 2022; 377:1172-1180. [PMID: 36074859 DOI: 10.1126/science.abo3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
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Affiliation(s)
- Evelyn T Todd
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Pierre Clavel
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Lucía Pérez Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
| | | | - Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - John Southon
- Earth System Science Department, University of California, Irvine, CA 92697, USA
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Emmanuelle Vila
- Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Giovanna Bagnasco Gianni
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | | | - Vincenzo Tinè
- Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy
| | | | - João Luís Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.,Universidade Aberta, Lisbon 1269-001, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.,School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France
| | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara 06100, Turkey
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey
| | - Benoît Clavel
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran
| | - Hossein Davoudi
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Azadeh Mohaseb
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.,Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
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20
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Salek Ardestani S, Zandi MB, Vahedi SM, Mahboudi H, Mahboudi F, Meskoob A. Detection of common copy number of variation underlying selection pressure in Middle Eastern horse breeds using whole-genome sequence data. J Hered 2022; 113:421-430. [PMID: 35605262 DOI: 10.1093/jhered/esac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/21/2022] [Indexed: 11/14/2022] Open
Abstract
Dareshouri, Arabian, and Akhal-Teke are three Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole-genome of four Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n=3) and Akhal-Teke (n=3) horses . Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size=100kb, step size=50kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8,837,950 single nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and three quantitative trait loci (QTLs), including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted p-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs which were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Canada
| | - Hossein Mahboudi
- Department of Biotechnology, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
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21
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Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. eLife 2022; 11:73346. [PMID: 35543411 PMCID: PMC9142152 DOI: 10.7554/elife.73346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
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Affiliation(s)
- Dawei Cai
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Siqi Zhu
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Mian Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Naifan Zhang
- Bioarchaeology Laboratory, Jilin University, Changchuin, China
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiyao Liang
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Weilu Sun
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Xinyue Shao
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yaqi Guo
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiaoyang Wang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - He Tian
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Youqian Li
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Wei Liu
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Miaomiao Yang
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Jian Yang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ludovic Orlando
- 7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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22
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Genetic load: genomic estimates and applications in non-model animals. Nat Rev Genet 2022; 23:492-503. [PMID: 35136196 DOI: 10.1038/s41576-022-00448-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/11/2022]
Abstract
Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.
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23
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Demystifying the genetic origins of the Mangalarga Horse through the influential stallion Turbante J.O. J Equine Vet Sci 2022; 113:103910. [DOI: 10.1016/j.jevs.2022.103910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/20/2022]
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24
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Smith EG, Hazzouri KM, Choi JY, Delaney P, Al-Kharafi M, Howells EJ, Aranda M, Burt JA. Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs. SCIENCE ADVANCES 2022; 8:eabl7287. [PMID: 35020424 PMCID: PMC10954036 DOI: 10.1126/sciadv.abl7287] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Coral populations in the world’s warmest reefs, the Persian/Arabian Gulf (PAG), represent an ideal model system to understand the evolutionary response of coral populations to past and present environmental change and to identify genomic loci that contribute to elevated thermal tolerance. Here, we use population genomics of the brain coral Platygyra daedalea to show that corals in the PAG represent a distinct subpopulation that was established during the Holocene marine transgression, and identify selective sweeps in their genomes associated with thermal adaptation. We demonstrate the presence of positive and disruptive selection and provide evidence for selection of differentially methylated haplotypes. While demographic analyses suggest limited potential for genetic rescue of neighboring Indian Ocean reefs, the presence of putative targets of selection in corals outside of the PAG offers hope that loci associated with thermal tolerance may be present in the standing genetic variation.
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Affiliation(s)
- Edward G. Smith
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Khaled M. Hazzouri
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Abu Dhabi, UAE
| | - Jae Young Choi
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Patrice Delaney
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Mohammed Al-Kharafi
- Department of Fisheries Resource Development, Public Authority of Agriculture and Fisheries Resources, Kuwait City, Kuwait
| | - Emily J. Howells
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Manuel Aranda
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - John A. Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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25
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Wolfsberger WW, Ayala NM, Castro-Marquez SO, Irizarry-Negron VM, Potapchuk A, Shchubelka K, Potish L, Majeske AJ, Oliver LF, Lameiro AD, Martínez-Cruzado JC, Lindgren G, Oleksyk TK. Genetic diversity and selection in Puerto Rican horses. Sci Rep 2022; 12:515. [PMID: 35017609 PMCID: PMC8752667 DOI: 10.1038/s41598-021-04537-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/23/2021] [Indexed: 11/21/2022] Open
Abstract
Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.
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Affiliation(s)
- Walter W Wolfsberger
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Nikole M Ayala
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Stephanie O Castro-Marquez
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | | | - Antoliy Potapchuk
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Khrystyna Shchubelka
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Ludvig Potish
- Department of Forestry, Uzhhorod National University, Uzhhorod, Ukraine
| | - Audrey J Majeske
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Luis Figueroa Oliver
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Alondra Diaz Lameiro
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Taras K Oleksyk
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine.
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26
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Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. JOURNAL OF GENETIC MUTATION DISORDERS 2022; 1:103. [PMID: 35465405 PMCID: PMC9031527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 controls from other horse breeds identified variants uniquely shared amongst the case cohort. Further validation via targeted resequencing of these variants, that pertain to non-intergenic regions, on additional eleven case individuals revealed a single 19bp deletion coupled with a triple-C insertion (Δ19InsCCC) within the TRIM39-RPP21 gene readthrough that was uniquely shared across all case individuals, and absent from three additional Arabian controls. Furthermore, we have confirmed recent findings refuting potential linkage between JIE and other inherited diseases in the Arabian lineage, and refuted the potential linkage between JIE and genes predisposing a similar disorder in human newborns. This is the first study to report a genetic variant to be shared in a sub-population cohort of Arabian foals diagnosed with JIE. Further evaluation of the sensitivity and specificity of the Δ19InsCCC allele within additional cohorts of the Arabian horse is warranted in order to validate its credibility as a marker for JIE, and to ascertain whether it has been introduced into other horse breeds by Arabian ancestry.
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Affiliation(s)
- S Polani
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - M Dean
- National Cancer Institute, Division of Cancer Epidemiology & Genetics, Laboratory of Translational Genomics, USA
| | - A Lichter-Peled
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - S Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, USA
| | | | - X Fang
- BGI-Shenzhen, Shenzhen, China
| | - Y Feng
- BGI-Shenzhen, Shenzhen, China
| | - W Qiao
- BGI-Shenzhen, Shenzhen, China
| | - G Avni
- Medisoos Equine Clinic, Kibutz Magal, Israel
| | - G Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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27
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Niego A, Benítez-Burraco A. Are feralization and domestication truly mirror processes? ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2021.1975314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amy Niego
- PhD Program, Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain (E-mail: )
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28
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Lovász L, Fages A, Amrhein V. Konik, Tarpan, European wild horse: An origin story with conservation implications. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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30
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Kis J, Rózsa L, Husvéth F, Zsolnai A, Anton I. Role of genes related to performance and reproduction of Thoroughbreds in training and breeding - A review. Acta Vet Hung 2021; 69:315-323. [PMID: 34739392 DOI: 10.1556/004.2021.00045] [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: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022]
Abstract
Thoroughbreds have been selected for speed and stamina since the 1700s. This selection resulted in structural and functional system-wide adaptations that enhanced physiological characteristics for outstanding speed of 61-71 kph (38-44 mph) between 1,000 and 3,200 m (5 furlongs - 2 miles). At present, horseracing is still an economically important industrial sector, therefore intensive research is underway to explore genes that allow the utilisation of genetic abilities and are significant in breeding and training. This study aims to provide an overview of genetic research and its applicability related to Thoroughbreds.
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Affiliation(s)
- Judit Kis
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
| | - László Rózsa
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
| | - Ferenc Husvéth
- 2Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Hungary
| | - Attila Zsolnai
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
| | - István Anton
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
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Deleterious protein-coding variants in diverse cattle breeds of the world. Genet Sel Evol 2021; 53:80. [PMID: 34654372 PMCID: PMC8518297 DOI: 10.1186/s12711-021-00674-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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33
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Wanner NM, Faulk C. Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. Genes (Basel) 2021; 12:genes12081223. [PMID: 34440397 PMCID: PMC8391136 DOI: 10.3390/genes12081223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 02/01/2023] Open
Abstract
Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human-animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.
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Affiliation(s)
- Nicole M. Wanner
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA;
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agriculture, and Natural Resource Sciences, University of Minnesota, 277 Coffey Hall, 1420 Eckles Avenue, St. Paul, MN 55108, USA
- Correspondence:
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Wilson LAB, Balcarcel A, Geiger M, Heck L, Sánchez‐Villagra MR. Modularity patterns in mammalian domestication: Assessing developmental hypotheses for diversification. Evol Lett 2021; 5:385-396. [PMID: 34367663 PMCID: PMC8327948 DOI: 10.1002/evl3.231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/14/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
The neural crest hypothesis posits that selection for tameness resulted in mild alterations to neural crest cells during embryonic development, which directly or indirectly caused the appearance of traits associated with the "domestication syndrome" (DS). Although representing an appealing unitary explanation for the generation of domestic phenotypes, support for this hypothesis from morphological data and for the validity of the DS remains a topic of debate. This study used the frameworks of morphological integration and modularity to assess patterns that concern the embryonic origin of the skull and issues around the neural crest hypothesis. Geometric morphometric landmarks were used to quantify cranial trait interactions between six pairs of wild and domestic mammals, comprising representatives that express between five and 17 of the traits included in the DS, and examples from each of the pathways by which animals entered into relationships with humans. We predicted the presence of neural crest vs mesoderm modular structure to the cranium, and that elements in the neural crest module would show lower magnitudes of integration and higher disparity in domestic forms compared to wild forms. Our findings support modular structuring based on tissue origin (neural crest, mesoderm) modules, along with low module integration magnitudes for neural crest cell derived cranial elements, suggesting differential capacity for evolutionary response among those elements. Covariation between the neural crest and mesoderm modules accounted for major components of shape variation for most domestic/wild pairs. Contra to our predictions, however, we find domesticates share similar integration magnitudes to their wild progenitors, indicating that higher disparity in domesticates is not associated with magnitude changes to integration among either neural crest or mesoderm derived elements. Differences in integration magnitude among neural crest and mesoderm elements across species suggest that developmental evolution preserves a framework that promotes flexibility under the selection regimes of domestication.
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Affiliation(s)
- Laura A. B. Wilson
- School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
- School of Archaeology and AnthropologyThe Australian National UniversityCanberraAustralia
| | - Ana Balcarcel
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - Madeleine Geiger
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - Laura Heck
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
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Benítez-Burraco A, Chekalin E, Bruskin S, Tatarinova T, Morozova I. Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis. Ann Hum Biol 2021; 48:313-320. [PMID: 34241552 DOI: 10.1080/03014460.2021.1936634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND AND AIM Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. METHODS In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans. RESULTS We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. CONCLUSION We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
| | - Evgeny Chekalin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Tatarinova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, University of La Verne, La Verne, CA, USA.,A. A. Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Department of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
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36
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From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management. Animals (Basel) 2021; 11:ani11071859. [PMID: 34206575 PMCID: PMC8300240 DOI: 10.3390/ani11071859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Horses were domesticated later than any other major livestock species. Their role in shaping ancient civilizations cannot be overestimated. As a primary means of transportation, an essential asset in warfare, and later one of the key elements of circus entertainment, horses quickly became luxurious goods. Vast amounts of money were invested in the horse industry resulted resulting in the rapid development of horse breeding and husbandry. This review examines paleogenetic, archeological, and classical studies on managing horses in antiquity. Many ancient approaches and practices in horse management are still relevant today and some of them, now abandoned, are worth re-examination. Abstract The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.
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Wang MS, Zhang JJ, Guo X, Li M, Meyer R, Ashari H, Zheng ZQ, Wang S, Peng MS, Jiang Y, Thakur M, Suwannapoom C, Esmailizadeh A, Hirimuthugoda NY, Zein MSA, Kusza S, Kharrati-Koopaee H, Zeng L, Wang YM, Yin TT, Yang MM, Li ML, Lu XM, Lasagna E, Ceccobelli S, Gunwardana HGTN, Senasig TM, Feng SH, Zhang H, Bhuiyan AKFH, Khan MS, Silva GLLP, Thuy LT, Mwai OA, Ibrahim MNM, Zhang G, Qu KX, Hanotte O, Shapiro B, Bosse M, Wu DD, Han JL, Zhang YP. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biol 2021; 19:118. [PMID: 34130700 PMCID: PMC8207802 DOI: 10.1186/s12915-021-01052-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/19/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.
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Affiliation(s)
- Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Rachel Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hidayat Ashari
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Bogor, 16911, Indonesia.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Zhu-Qing Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Mukesh Thakur
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Phayao, 56000, Thailand.,Unit of Excellence on Biodiversity and Natural Resources Management, University of Phayao, Phayao, 56000, Thailand
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Department of Animal Science, Shahid Bahonar University of Kerman, P.O. Box 76169133, Kerman, Iran
| | - Nalini Yasoda Hirimuthugoda
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Moch Syamsul Arifin Zein
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Bogor, 16911, Indonesia
| | - Szilvia Kusza
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, H-4032, Hungary
| | - Hamed Kharrati-Koopaee
- Department of Animal Science, Shahid Bahonar University of Kerman, P.O. Box 76169133, Kerman, Iran.,Institute of Biotechnology, School of Agriculture, Shiraz University, P.O. Box 1585, Shiraz, Iran
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yun-Mei Wang
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xue-Mei Lu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, 06123, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentarie Ambientali, University of Perugia, 06123, Perugia, Italy
| | | | | | - Shao-Hong Feng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Hao Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Ministry of Agriculture of China, Beijing, 100193, China
| | | | | | | | - Le Thi Thuy
- National Institute of Animal Husbandry, Hanoi, Vietnam
| | - Okeyo A Mwai
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | | | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-1870, Copenhagen, Denmark
| | - Kai-Xing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Livestock Genetics Program, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mirte Bosse
- Wageningen University & Research - Animal Breeding and Genomics, 6708 PB, Wageningen, The Netherlands.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. .,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650204, China. .,State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, China.
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol Ecol 2021; 30:6144-6161. [PMID: 33971056 DOI: 10.1111/mec.15977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/24/2021] [Accepted: 04/27/2021] [Indexed: 01/02/2023]
Abstract
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.
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Affiliation(s)
- Alisa O Vershinina
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | - Grant Zazula
- Collections and Research, Canadian Museum of Nature, Station D, Ottawa, ON, Canada.,Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Shelby G Dunn
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Luca Ermini
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Mann
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, CA, USA
| | - Mathias Stiller
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Division Molecular Pathology, Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Marine Biology, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Dmitry Gimranov
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia.,Ural Federal University named after the first President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Eric Scott
- California State University, San Bernardino, CA, USA
| | - Elizabeth Hall
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Susan Hewitson
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Kosintsev
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia
| | | | - Hao-Wen Tong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | | | | | - Beth Shapiro
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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41
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Sharko FS, Boulygina ES, Tsygankova SV, Slobodova NV, Alekseev DA, Krasivskaya AA, Rastorguev SM, Tikhonov AN, Nedoluzhko AV. Steller's sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans. Nat Commun 2021; 12:2215. [PMID: 33850161 PMCID: PMC8044168 DOI: 10.1038/s41467-021-22567-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
Anthropogenic activity is the top factor directly related to the extinction of several animal species. The last Steller's sea cow (Hydrodamalis gigas) population on the Commander Islands (Russia) was wiped out in the second half of the 18th century due to sailors and fur traders hunting it for the meat and fat. However, new data suggests that the extinction process of this species began much earlier. Here, we present a nuclear de novo assembled genome of H. gigas with a 25.4× depth coverage. Our results demonstrate that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago. Besides, as a matter of consideration, our findings also demonstrate that the extinction of this marine mammal starts along the North Pacific coastal line much earlier than the first Paleolithic humans arrived in the Bering sea region.
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Affiliation(s)
- Fedor S Sharko
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia.,Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Eugenia S Boulygina
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Svetlana V Tsygankova
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Natalia V Slobodova
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Dmitry A Alekseev
- Russian Presidential Academy of National Economy and Public Administration, Prospect Vernadskogo, 82, Moscow, Russia
| | | | - Sergey M Rastorguev
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Alexei N Tikhonov
- Zoological Institute Russian Academy of Sciences, Universitetskaya nab., 1, Saint-Petersburg, Russia.,Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Russia
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42
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Brooks SA. Genomics in the Horse Industry: Discovering New Questions at Every Turn. J Equine Vet Sci 2021; 100:103456. [PMID: 34030792 DOI: 10.1016/j.jevs.2021.103456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
The sheer diversity of heritable physiological traits, and the ingenuity of genome derived research technologies, extends the study of genetics to impact diverse scientific fields. Equine science is no exception, experiencing a number of genome-enabled discoveries that spur further research in areas like nutrition, reproduction, and exercise physiology. Yet unexpected findings, especially those that over-turn commonly held beliefs in the horse industry, can create challenges in outreach, education and communication with stakeholders. For example, studies of ancient DNA revealed that the oldest domesticated equids in the archeological record were in fact another species, the Przewalski's horse, leaving the origins of our modern horses a mystery yet to be solved. Genomic analysis of ancestry can illuminate relationships older than our prized pedigree records, and in some cases, identify unexpected inconsistencies in those pedigrees. Even our interpretation of what constitutes a genetic disease is changing, as we re-examine common disease alleles; how these alleles impact equine physiology, and how they are perceived by breeders and professionals in the industry. Effectively translating genetic tools for utilization in horse management and preparing our community for the debate surrounding ethical questions that may arise from genomic studies, may be the next great challenges we face as scientists and educators.
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Affiliation(s)
- Samantha A Brooks
- Department of Animal Sciences and the UF Genetics Institute, University of Florida, Gainesville Fl.
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43
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Al Abri MA, Brooks SA, Al-Saqri N, Alkharousi K, Johnson EH, Alqaisi O, Al-Rawahi A, Al Marzooqi W. Investigating the population structure and genetic diversity of Arabian horses in Oman using SNP markers. Anim Genet 2021; 52:304-310. [PMID: 33730759 DOI: 10.1111/age.13056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 11/27/2022]
Abstract
Arabian horses were selected for metabolic efficiency, beauty, efficiency and endurance. Therefore, Bedouins have for centuries traced their prized horses' ancestries. With the establishment of the World Arabian Horse Organization (WAHO), registration of Arabian horses became centralized and countries worldwide registered them in its database. Most existing Arabian horses in Oman today were imported after the 1970s and are predominantly flat-racing Arabians. This work aimed at revealing the genetic background and diversity of Omani Arabian horses by comparing them with Arabian horses from a diverse genetic background. To that end, we genotyped 63 randomly sampled Arabian horses from Oman using the Illumina Equine SNP70. For comparison, SNP genotypes of 12 Saudi Arabian horses, 27 French, 77 Egyptian, 11 Polish and 36 US Arabians were included in the study. We additionally included 17 Thoroughbred horses and 21 horses representing large and small breeds as an outgroup. Our MDS analysis and phylogenetic analysis showed that the Arabian horses in Oman cluster primarily with French Arabian horses, with a few horses clustering within the Polish/US Arabians. The French Arabian horse cluster was the closest to the Thoroughbred horses. Amongst the Arabian horses, plink average genomic inbreeding levels were highest in the Egyptian Arabian (0.169) followed by the Saudi Arabian horses (0.137) and lowest in the Omani and French Arabian horses, -0.041 and -0.079 respectively. To our knowledge, this is the first report on the genetic background and diversity of Arabian horses in Oman. Our results demonstrated a definite subpopulation structure among Arabian horses and this information should advise future decision-making on Arabian horse breeding.
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Affiliation(s)
- M A Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - S A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - N Al-Saqri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - K Alkharousi
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - E H Johnson
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - O Alqaisi
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - A Al-Rawahi
- The Royal Cavalry of Oman, PO Box 70, Al Seeb, Muscat, 111, Oman
| | - W Al Marzooqi
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
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44
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Diaz-Maroto P, Rey-Iglesia A, Cartajena I, Núñez L, Westbury MV, Varas V, Moraga M, Campos PF, Orozco-terWengel P, Marin JC, Hansen AJ. Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes. eLife 2021; 10:63390. [PMID: 33724183 PMCID: PMC8032396 DOI: 10.7554/elife.63390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.
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Affiliation(s)
| | - Alba Rey-Iglesia
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Isabel Cartajena
- Faculty of Social Sciences, University of Chile, Santiago de Chile, Chile
| | - Lautaro Núñez
- Institute of Archaeological Research and Museum, Católica del Norte University, San Pedro de Atacama, Chile
| | - Michael V Westbury
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Valeria Varas
- School of Science Ecology and Evolution, Faculty of Sciences, Austral of Chile University, Valdivia, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Paula F Campos
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom
| | - Juan Carlos Marin
- ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom.,Genomic and Biodiversity Laboratory, Basic Sciences Department, Faculty of Sciences, Bio-Bio University, Chillán, Chile
| | - Anders J Hansen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Kusliy MA, Vorobieva NV, Tishkin AA, Makunin AI, Druzhkova AS, Trifonov VA, Iderkhangai TO, Graphodatsky AS. Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations. Genes (Basel) 2021; 12:genes12030412. [PMID: 33809280 PMCID: PMC8000342 DOI: 10.3390/genes12030412] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged.
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Affiliation(s)
- Mariya A. Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (N.V.V.); (A.I.M.); (A.S.D.); (V.A.T.); (A.S.G.)
- Correspondence:
| | - Nadezhda V. Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (N.V.V.); (A.I.M.); (A.S.D.); (V.A.T.); (A.S.G.)
| | - Alexey A. Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, 656049 Barnaul, Russia;
| | - Alexey I. Makunin
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (N.V.V.); (A.I.M.); (A.S.D.); (V.A.T.); (A.S.G.)
| | - Anna S. Druzhkova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (N.V.V.); (A.I.M.); (A.S.D.); (V.A.T.); (A.S.G.)
| | - Vladimir A. Trifonov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (N.V.V.); (A.I.M.); (A.S.D.); (V.A.T.); (A.S.G.)
| | - Tumur-O. Iderkhangai
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 13343, Mongolia;
| | - Alexander S. Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (N.V.V.); (A.I.M.); (A.S.D.); (V.A.T.); (A.S.G.)
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Oleksyk TK, Wolfsberger WW, Weber AM, Shchubelka K, Oleksyk OT, Levchuk O, Patrus A, Lazar N, Castro-Marquez SO, Hasynets Y, Boldyzhar P, Neymet M, Urbanovych A, Stakhovska V, Malyar K, Chervyakova S, Podoroha O, Kovalchuk N, Rodriguez-Flores JL, Zhou W, Medley S, Battistuzzi F, Liu R, Hou Y, Chen S, Yang H, Yeager M, Dean M, Mills RE, Smolanka V. Genome diversity in Ukraine. Gigascience 2021; 10:6079618. [PMID: 33438729 PMCID: PMC7804371 DOI: 10.1093/gigascience/giaa159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.
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Affiliation(s)
- Taras K Oleksyk
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Walter W Wolfsberger
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khrystyna Shchubelka
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA.,Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Olga T Oleksyk
- A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, Ukraine
| | | | | | | | - Stephanie O Castro-Marquez
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Yaroslava Hasynets
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine
| | - Patricia Boldyzhar
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Mikhailo Neymet
- Velyka Kopanya Family Hospital, Transcarpatia 90330, Ukraine
| | | | | | - Kateryna Malyar
- I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, Ukraine
| | | | | | - Natalia Kovalchuk
- Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, Ukraine
| | | | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Medley
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Fabia Battistuzzi
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Ryan Liu
- BGI Shenzhen, Shenzhen, 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen, 518083, China
| | - Siru Chen
- BGI Shenzhen, Shenzhen, 518083, China
| | | | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Volodymyr Smolanka
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
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Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes. Nature 2021; 598:634-640. [PMID: 34671162 PMCID: PMC8550961 DOI: 10.1038/s41586-021-04018-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/10/2021] [Indexed: 01/13/2023]
Abstract
Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.
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Affiliation(s)
- Pablo Librado
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Naveed Khan
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.440522.50000 0004 0478 6450Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Antoine Fages
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Mariya A. Kusliy
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.415877.80000 0001 2254 1834Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Tomasz Suchan
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.413454.30000 0001 1958 0162W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Laure Tonasso-Calvière
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Stéphanie Schiavinato
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Duha Alioglu
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Aurore Fromentier
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Aude Perdereau
- grid.460789.40000 0004 4910 6535Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Evry, France
| | - Charleen Gaunitz
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Lorelei Chauvey
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Clio Der Sarkissian
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - John Southon
- grid.266093.80000 0001 0668 7243Earth System Science Department, University of California, Irvine, Irvine, CA USA
| | - Beth Shapiro
- grid.205975.c0000 0001 0740 6917Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA USA
| | - Alexey A. Tishkin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Alexey A. Kovalev
- grid.465449.e0000 0001 1214 1108Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Saleh Alquraishi
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed H. Alfarhan
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Khaled A. S. Al-Rasheid
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Timo Seregély
- grid.7359.80000 0001 2325 4853Institute for Archaeology, Heritage Conservation Studies and Art History, University of Bamberg, Bamberg, Germany
| | | | - Rune Iversen
- grid.5254.60000 0001 0674 042XSaxo Institute, section of Archaeology, University of Copenhagen, Copenhagen, Denmark
| | - Olivier Bignon-Lau
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | - Pierre Bodu
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | - Monique Olive
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | | | - Myriam Boudadi-Maligne
- grid.412041.20000 0001 2106 639XUMR 5199 De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Nadir Alvarez
- grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mietje Germonpré
- grid.20478.390000 0001 2171 9581OD Earth & History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Magdalena Moskal-del Hoyo
- grid.413454.30000 0001 1958 0162W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Jarosław Wilczyński
- grid.413454.30000 0001 1958 0162Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- grid.413454.30000 0001 1958 0162Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Anna Lasota-Kuś
- grid.413454.30000 0001 1958 0162Institute of Archaeology and Ethnology Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- grid.413454.30000 0001 1958 0162Institute of Archaeology and Ethnology Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- grid.5522.00000 0001 2162 9631Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | - Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, Tartu, Estonia
| | - Urmas Saarma
- grid.10939.320000 0001 0943 7661Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Gennady Boeskorov
- Diamond and Precious Metals Geology Institute, SB RAS, Yakutsk, Russia
| | - Lembi Lōugas
- grid.8207.d0000 0000 9774 6466Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - René Kyselý
- grid.447879.10000 0001 0792 540XDepartment of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | - Adrian Bălășescu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Valentin Dumitrașcu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Roxana Dobrescu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Daniel Gerber
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary ,grid.5591.80000 0001 2294 6276Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Viktória Kiss
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Anna Szécsényi-Nagy
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Balázs G. Mende
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | | | | | - Gabriella Kulcsár
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Erika Gál
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Robin Bendrey
- grid.4305.20000 0004 1936 7988School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Edinburgh, UK
| | - Morten E. Allentoft
- grid.1032.00000 0004 0375 4078Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia Australia ,grid.5254.60000 0001 0674 042XLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ghenadie Sirbu
- grid.435140.7Department of Academic Management, Academy of Science of Moldova, Chișinău, Republic of Moldova
| | - Valentin Dergachev
- grid.435140.7Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, Chișinău, Republic of Moldova
| | - Henry Shephard
- grid.446391.d0000 0001 2190 3450Archaeological Institute of America, Boston, MA USA
| | - Noémie Tomadini
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sandrine Grouard
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Aleksei Kasparov
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | | | - Mikhail A. Anisimov
- grid.424187.c0000 0001 1942 9788Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Pavel A. Nikolskiy
- grid.465388.4Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Elena Y. Pavlova
- grid.424187.c0000 0001 1942 9788Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Vladimir Pitulko
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - Gottfried Brem
- grid.6583.80000 0000 9686 6466Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Barbara Wallner
- grid.6583.80000 0000 9686 6466Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- grid.466489.10000 0001 2151 4674Department of Prehistory and Western Asian/Northeast African Archaeology, Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Marcel Keller
- grid.10939.320000 0001 0943 7661Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia ,grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Keiko Kitagawa
- grid.10392.390000 0001 2190 1447SFB 1070 Resource Cultures, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany ,grid.4444.00000 0001 2112 9282UMR 7194 Muséum National d’Histoire Naturelle, CNRS, UPVD, Paris, France
| | - Alexander N. Bessudnov
- grid.459698.f0000 0000 8989 8101Semenov-Tyan-Shanskii Lipetsk State Pedagogical University, Lipetsk, Russia
| | - Alexander Bessudnov
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - William Taylor
- grid.266190.a0000000096214564Museum of Natural History, University of Colorado-Boulder, Boulder, CO USA
| | - Jérome Magail
- Musée d’Anthropologie préhistorique de Monaco, Monaco, Monaco
| | - Jamiyan-Ombo Gantulga
- grid.425564.40000 0004 0587 3863Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Jamsranjav Bayarsaikhan
- grid.469873.70000 0004 4914 1197Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany ,Chinggis Khaan Museum, Ulaanbaatar, Mongolia
| | | | - Kubatbeek Tabaldiev
- grid.444269.90000 0004 0387 4627Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia
| | - Bazartseren Boldgiv
- grid.260731.10000 0001 2324 0259Department of Biology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Turbat Tsagaan
- grid.425564.40000 0004 0587 3863Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Mélanie Pruvost
- grid.412041.20000 0001 2106 639XUMR 5199 De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Sandra Olsen
- grid.266515.30000 0001 2106 0692Division of Archaeology, Biodiversity Institute, University of Kansas, Lawrence, KS USA
| | - Cheryl A. Makarewicz
- grid.9764.c0000 0001 2153 9986Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany ,grid.9764.c0000 0001 2153 9986ROOTS Excellence Cluster, Kiel University, Kiel, Germany
| | - Silvia Valenzuela Lamas
- grid.4711.30000 0001 2183 4846Archaeology of Social Dynamics, Institució Milà i Fontanals d’Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Silvia Albizuri Canadell
- grid.5841.80000 0004 1937 0247Departament d’Història i Arqueologia–SERP, Universitat de Barcelona, Barcelona, Spain
| | - Ariadna Nieto Espinet
- grid.15043.330000 0001 2163 1432Grup d’Investigació Prehistòrica, Universitat de Lleida, PID2019-110022GB-I00, Lleida, Spain
| | | | - Jaime Lira Garrido
- grid.8393.10000000119412521Departamento de Medicina Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain ,Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | | | - Sebastián Celestino
- grid.454770.50000 0001 1945 3489Instituto de Arqueología (CSIC–Junta de Extremadura), Mérida, Spain
| | - Carmen Olària
- grid.9612.c0000 0001 1957 9153Laboratori d’Arqueologia Prehistòrica, Universitat Jaume I, Castelló de la Plana, Spain
| | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain ,grid.4795.f0000 0001 2157 7667Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Nadiia Kotova
- grid.418751.e0000 0004 0385 8977Department of Eneolithic and Bronze Age, Institute of Archaeology National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alexander Pryor
- grid.8391.30000 0004 1936 8024Department of Archaeology, University of Exeter, Exeter, UK
| | - Pam Crabtree
- grid.137628.90000 0004 1936 8753Center for the Study of Human Origins, Anthropology Department, New York University, New York, NY USA
| | - Rinat Zhumatayev
- grid.77184.3d0000 0000 8887 5266Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Abdesh Toleubaev
- grid.77184.3d0000 0000 8887 5266Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Nina L. Morgunova
- grid.445474.20000 0001 1092 7131Scientific Research Department, Orenburg State Pedagogical University, Orenburg, Russia
| | - Tatiana Kuznetsova
- grid.14476.300000 0001 2342 9668Department of paleontology, Faculty of Geology, Moscow State University, Moscow, Russia ,grid.77268.3c0000 0004 0543 9688Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan, Russia
| | - David Lordkipanize
- grid.452450.20000 0001 0739 408XGeorgian National Museum, Tbilisi, Georgia ,grid.26193.3f0000 0001 2034 6082Tbilisi State University, Tbilisi, Georgia
| | - Matilde Marzullo
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Ornella Prato
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Giovanna Bagnasco Gianni
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Umberto Tecchiati
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Benoit Clavel
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Hossein Davoudi
- grid.46072.370000 0004 0612 7950University of Tehran, Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, Tehran, Iran
| | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France ,grid.46072.370000 0004 0612 7950University of Tehran, Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, Tehran, Iran
| | - Natalia Ya. Berezina
- grid.14476.300000 0001 2342 9668Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Philipp W. Stockhammer
- grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.5252.00000 0004 1936 973XInstitute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Munich, Germany
| | - Johannes Krause
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Haak
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.1010.00000 0004 1936 7304School of Biological Sciences, The University of Adelaide, Adelaide, South Australia Australia
| | - Arturo Morales-Muñiz
- grid.5515.40000000119578126Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Norbert Benecke
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Michael Hofreiter
- grid.11348.3f0000 0001 0942 1117Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Science, University of Potsdam, Potsdam, Germany
| | - Arne Ludwig
- grid.418779.40000 0001 0708 0355Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Alexander S. Graphodatsky
- grid.415877.80000 0001 2254 1834Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Joris Peters
- grid.5252.00000 0004 1936 973XArchaeoBioCenter and Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany ,grid.452781.d0000 0001 2203 6205SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Kirill Yu. Kiryushin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Nikolay A. Bokovenko
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - Sergey K. Vasiliev
- grid.415877.80000 0001 2254 1834ArchaeoZOOlogy in Siberia and Central Asia—ZooSCAn International Research Laboratory, Institute of Archeology and Ethnography of the Siberian Branch of the RAS, Novosibirsk, Russia
| | - Nikolai N. Seregin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Konstantin V. Chugunov
- grid.426493.e0000 0004 1800 742XDepartment of Eastern European and Siberian Archaeology, State Hermitage Museum, St Petersburg, Russia
| | - Natalya A. Plasteeva
- grid.482778.60000 0001 2197 0186Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Gennady F. Baryshnikov
- grid.439287.30000 0001 2314 7601Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Ekaterina Petrova
- grid.6441.70000 0001 2243 2806Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Mikhail Sablin
- grid.439287.30000 0001 2314 7601Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Elina Ananyevskaya
- grid.6441.70000 0001 2243 2806Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Andrey Logvin
- grid.443586.8Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Irina Shevnina
- grid.443586.8Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Victor Logvin
- Department of History and Archaeology, Surgut Governmental University, Surgut, Russia
| | - Saule Kalieva
- Department of History and Archaeology, Surgut Governmental University, Surgut, Russia
| | - Valeriy Loman
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Igor Kukushkin
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Ilya Merz
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Victor Merz
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Sergazy Sakenov
- grid.55380.3b0000 0004 0398 5415Faculty of History, L. N. Gumilev Eurasian National University, Nur-Sultan, Kazakhstan
| | - Victor Varfolomeyev
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Emma Usmanova
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Viktor Zaibert
- grid.77184.3d0000 0000 8887 5266Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Benjamin Arbuckle
- grid.10698.360000000122483208Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | | | | | - Sabine Reinhold
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Aleksandr I. Yudin
- Research Center for the Preservation of Cultural Heritage, Saratov, Russia
| | - Alekandr A. Vybornov
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Andrey Epimakhov
- grid.440724.10000 0000 9958 5862Russian and Foreign History Department, South Ural State University, Chelyabinsk, Russia ,grid.465317.20000 0001 2224 8785South Ural Department, Institute of History and Archaeology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Natalia S. Berezina
- Archaeological School, Chuvash State Institute of Humanities, Cheboksary, Russia
| | - Natalia Roslyakova
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel A. Kosintsev
- grid.482778.60000 0001 2197 0186Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia ,grid.412761.70000 0004 0645 736XDepartment of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - Pavel F. Kuznetsov
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - David Anthony
- grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.418410.80000 0001 0115 6427Anthropology Faculty, Hartwick College, Oneonta NY, USA
| | - Guus J. Kroonen
- grid.5254.60000 0001 0674 042XDepartment of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark ,grid.5132.50000 0001 2312 1970Leiden University Center for Linguistics, Leiden University, Leiden, The Netherlands
| | - Kristian Kristiansen
- grid.8761.80000 0000 9919 9582Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden ,grid.452548.a0000 0000 9817 5300Present Address: Lundbeck Foundation GeoGenetics Centre, Copenhagen, Denmark
| | - Patrick Wincker
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Evry, France
| | - Alan Outram
- grid.8391.30000 0004 1936 8024Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
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48
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Wang M, Lin Y, Zhou S, Cui Y, Feng Q, Yan W, Xiang H. Genetic Mapping of Climbing and Mimicry: Two Behavioral Traits Degraded During Silkworm Domestication. Front Genet 2020; 11:566961. [PMID: 33391338 PMCID: PMC7773896 DOI: 10.3389/fgene.2020.566961] [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: 05/29/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
Behavioral changes caused by domestication in animals are an important issue in evolutionary biology. The silkworm, Bombyx mori, is an ideal fully domesticated insect model for studying both convergent domestication and behavior evolution. We explored the genetic basis of climbing for foraging and mimicry, two degraded behaviors during silkworm domestication, in combination of bulked segregant analysis (BSA) and selection sweep screening. One candidate gene, ASNA1, located in the 3-5 Mb on chromosome 19, harboring a specific non-synonymous mutation in domestic silkworm, might be involved in climbing ability. This mutation was under positive selection in Lepidoptera, strongly suggesting its potential function in silkworm domestication. Nine candidate domesticated genes related to mimicry were identified on chromosomes 13, 21, and 27. Most of the candidate domesticated genes were generally expressed at higher levels in the brain of the wild silkworm. This study provides valuable information for deciphering the molecular basis of behavioral changes associated with silkworm domestication.
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Affiliation(s)
- Man Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yongjian Lin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shiyi Zhou
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yong Cui
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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49
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Variability of ACOX1 Gene Polymorphisms across Different Horse Breeds with Regard to Selection Pressure. Animals (Basel) 2020; 10:ani10122225. [PMID: 33260884 PMCID: PMC7761022 DOI: 10.3390/ani10122225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The genetic mechanisms occurring in organisms are shaped by selection pressure. Features that ought to be useful under given conditions leave their marks on the genome in the form of mutations, thereby creating different alleles. In this study, five different horse breeds were examined to find the connection between an individual’s lifestyle and the presence of the peroxisomal acyl-coenzyme A oxidase 1 (ACOX1) gene, which is necessary for some metabolic pathways. Results indicated that different ACOX1 gene alleles play various roles in primitive breeds and domesticated horses. This led to the conclusion that the DNA profile can be rated on the basis of adaptation to living conditions, opening the gate for further investigation. Abstract The ACOX1 gene encodes peroxisomal acyl-coenzyme A oxidase 1, the first enzyme in the fatty acid β-oxidation pathway, which could be significant for organisms exposed to long periods of starvation and harsh living conditions. We hypothesized that variations within ACOX1, revealed by RNA Sequencing (RNA-Seq), might be based on adaptation to living conditions and had resulted from selection pressure. There were five different horse breeds used in this study, representing various utility types: Arabian, Thoroughbred, Polish Konik, draft horses, and Hucul. The single-nucleotide polymorphism (SNP) located in the ACOX1 (rs782885985) was used as a marker and was identified using the PCR restriction fragment length polymorphism method (PCR-RFLP). Results indicated extremely different genotype and allele distributions of the ACOX1 gene across breeds. A predominance of the G allele was exhibited in horses that had adapted to difficult environmental conditions, namely, Polish Konik and Huculs, which are considered to be primitive breeds. The prevalence of the T allele in Thoroughbreds indicated that ACOX1 is significant in energy metabolism during flat racing.
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50
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Kvist L, Honka J, Niskanen M, Liedes O, Aspi J. Selection in the Finnhorse, a native all-around horse breed. J Anim Breed Genet 2020; 138:188-203. [PMID: 33226152 PMCID: PMC7894145 DOI: 10.1111/jbg.12524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 12/19/2022]
Abstract
Selection by breeders modifies the morphology, behaviour and performance of domesticated species. Here, we examined signs of selection in Finnhorse, the only native horse breed in Finland. We first searched divergent genomic regions between Finnhorses and other breeds, as well as between different breeding sections of the Finnhorse with data from Illumina Equine SNP70 BeadChip, and then studied several of the detected regions in more detail. We found altogether 35 common outlier SNPs between Finnhorses and other breeds using two different selection tests. Many of the SNPs were located close to genes affecting coat colour, performance, size, sugar metabolism, immune response and olfaction. We selected genes affecting coat colour (KIT, MITF, PMEL), performance (MSTN) and locomotion (DMRT3) for a more detailed examination. In addition, we looked for, and found, associations with height at withers and SNPs located close to gene LCORL. Among the four breeding sections of Finnhorses (harness trotters, riding horses, draught horses and pony‐sized horses), a single SNP located close to the DMRT3 gene was significantly differentiated and only between harness trotters and pony‐sized horses.
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Affiliation(s)
- Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Johanna Honka
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Markku Niskanen
- Research Unit of History, Culture and Communications, University of Oulu, Oulu, Finland
| | - Oona Liedes
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jouni Aspi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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