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Chen J, Wang H, Li J, Liu S, Li B, Sun Y, Wang H, Manglai D. CKM intron: an appropriate marker for the determination of the genetic relationships among horse populations and breeds. Anim Biotechnol 2023; 34:3962-3970. [PMID: 37593944 DOI: 10.1080/10495398.2023.2247445] [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: 08/19/2023]
Abstract
To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; CKM) variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse sequences. From these, 40 haplotypes were inferred. Haplotype diversity (H) values differed from 0.6424 to 0.7881 and nucleotide diversity (π) values ranged from 0.00150 to 0.00211. The differences between Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations with respect to CKM intron sequences suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and CMH are very closely related and the introgression (interbreeding) between them is serious. Our results suggest that Sanhe and Wushen require prompt and powerful protection. Overall, CKM intron was an appropriate marker for the determination of genetic relationships among horse populations and breeds.
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Affiliation(s)
- Jianxing Chen
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Huidong Wang
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Jing Li
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Shuqin Liu
- Gene Bank for Equine Genetic Resources of Shandong Province, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Benke Li
- Binzhou Refferral Center for Agricultural Technologies, Binzhou, China
| | - Yujiang Sun
- Gene Bank for Equine Genetic Resources of Shandong Province, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
| | - Huaidong Wang
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
| | - Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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Giontella A, Cardinali I, Sarti FM, Silvestrelli M, Lancioni H. Y-Chromosome Haplotype Report among Eight Italian Horse Breeds. Genes (Basel) 2023; 14:1602. [PMID: 37628653 PMCID: PMC10454838 DOI: 10.3390/genes14081602] [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] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique traits and socio-cultural peculiarities. Here, for the first time, we report the genetic variation of three loci of the male-specific region of the Y chromosome (MSY) of four local breeds and another one (Lipizzan, UNESCO) well-represented in the Italian Peninsula. The analysis also includes data from three Sardinian breeds and another forty-eight Eurasian and Mediterranean horse breeds retrieved from GenBank for comparison. Three haplotypes (HT1, HT2, and HT3) were found in Italian stallions, with different spatial distributions between breeds. HT1 (the ancestral haplotype) was frequent, especially in Bardigiano and Monterufolino, HT2 (Neapolitan/Oriental wave) was found in almost all local breeds, and HT3 (Thoroughbred wave) was detected in Maremmano and two Sardinian breeds (Sardinian Anglo-Arab and Sarcidano). This differential distribution is due to three paternal introgressions of imported stallions from foreign countries to improve local herds; however, further genetic analyses are essential to reconstruct the genetic history of native horse breeds, evaluate the impact of selection events, and enable conservation strategies.
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Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (A.G.); (M.S.)
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy;
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (A.G.); (M.S.)
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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3
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Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. Refining the evolutionary tree of the horse Y chromosome. Sci Rep 2023; 13:8954. [PMID: 37268661 DOI: 10.1038/s41598-023-35539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.
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Affiliation(s)
- Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lara Radovic
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Viktoria Remer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lucy Allen
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Caitlin Castaneda
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Gus Cothran
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Terje Raudsepp
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Okuda
- Museum of Dinosaur Research, Okayama University of Science, Okayama, Japan
| | - Kyaw Kyaw Moe
- Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Hla Hla Moe
- Department of Genetics and Animal Breeding, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Bounthavone Kounnavongsa
- National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center, Xaythany District, Vientiane, Laos
| | - Soukanh Keonouchanh
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Nguyen Huu Van
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Van Hai Vu
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Manoj Kumar Shah
- Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Rampur, 44209, Nepal
| | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Polat Kazymbet
- Radiobiological Research Institute, JSC Astana Medical University, Astana, 010000, Republic of Kazakhstan
| | - Meirat Bakhtin
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic
| | - Asankadyr Zhunushov
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic
| | - Ripon Chandra Paul
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
- Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal, Bangladesh
| | - Bumbein Dashnyam
- Institute of Biological Sciences, Mongolian Academy of Sciences, Ulaan Baator, Mongolia
| | - Ken Nozawa
- Primate Research Institute, Kyoto University, Aichi, Japan
| | - Saria Almarzook
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Gudrun A Brockmann
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Monika Reissmann
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Donald C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Raheleh Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Ines von Butler-Wemken
- Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V., Kirchgasse 11, 67718, Schmalenberg, Germany
| | | | - Haige Han
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500, Osh, Kyrgyzstan
| | - Boldbaatar Sukhbaatar
- Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory, Ulaanbaatar, 17024, Mongolia
| | - Katarzyna Ropka-Molik
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047, Cracow, Poland
| | | | - Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores, 9700-042, Angra do Heroísmo, Portugal
| | | | | | - Liliya Kalinkova
- All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia
| | - Alexander M Zaitev
- All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia
| | - Miguel Novoa-Bravo
- Genética Animal de Colombia SAS., Av. Calle 26 #69-76, 111071, Bogotá, Colombia
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Samantha Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Laura Patterson Rosa
- Department of Agriculture and Industry, Sul Ross State University, Alpine, TX, 79832, USA
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Rytis Juras
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan.
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
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Han H, Randhawa IAS, MacHugh DE, McGivney BA, Katz LM, Dugarjaviin M, Hill EW. Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health. BMC Genomics 2023; 24:35. [PMID: 36658473 PMCID: PMC9854188 DOI: 10.1186/s12864-023-09116-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection. RESULTS We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade. CONCLUSIONS Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.
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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 Centre, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Imtiaz A. S. Randhawa
- grid.1003.20000 0000 9320 7537Animal Genetics Laboratory, School of Veterinary Science, University of Queensland, Brisbane, Australia
| | - 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, D04V1W8 Ireland
| | - Beatrice A. McGivney
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Lisa M. Katz
- grid.7886.10000 0001 0768 2743UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04V1W8 Ireland
| | - Manglai Dugarjaviin
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Emmeline W. Hill
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8 Ireland ,grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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6
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MSTN Regulatory Network in Mongolian Horse Muscle Satellite Cells Revealed with miRNA Interference Technologies. Genes (Basel) 2022; 13:genes13101836. [PMID: 36292721 PMCID: PMC9601437 DOI: 10.3390/genes13101836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 12/05/2022] Open
Abstract
Myostatin (MSTN), a member of the transforming growth factor-β superfamily, inhibits the activation of muscle satellite cells. However, the role and regulatory network of MSTN in equine muscle cells are not well understood yet. We discovered that MSTN knockdown significantly reduces the proliferation rate of equine muscle satellite cells. In addition, after the RNA sequencing of equine satellite cells transfected with MSTN-interference plasmid and control plasmid, an analysis of the differentially expressed genes was carried out. It was revealed that MSTN regulatory networks mainly involve genes related to muscle function and cell-cycle regulation, and signaling pathways, such as Notch, MAPK, and WNT. Subsequent real-time PCR in equine satellite cells and immunohistochemistry on newborn and adult muscle also verified the MSTN regulatory network found in RNA sequencing analysis. The results of this study provide new insight into the regulatory mechanism of equine MSTN.
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Y Chromosome Haplotypes Enlighten Origin, Influence, and Breeding History of North African Barb Horses. Animals (Basel) 2022; 12:ani12192579. [PMID: 36230320 PMCID: PMC9559282 DOI: 10.3390/ani12192579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb region and European subpopulations. All detected HTs belonged to the Crown haplogroup, and the broad MSY spectrum reflects the wide variety of influential stallions throughout the breed’s history. Distinct HTs and regional disparities were characterized and a remarkable number of early introduced lineages were observed. The data indicate recent refinement with Thoroughbred and Arabian patrilines, while 57% of the dataset supports historical migrations between North Africa and the Iberian Peninsula. In the Barb horse, we detected the HT linked to Godolphin Arabian, one of the Thoroughbred founders. Hence, we shed new light on the question of the ancestry of one Thoroughbred patriline. We show the strength of the horse Y chromosome as a genealogical tool, enlighten recent paternal history of North African horses, and set the foundation for future studies on the breed and the formation of conservation breeding programs.
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8
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Zhang FL, Zhang XY, Zhao JX, Zhu KX, Liu SQ, Zhang T, Sun YJ, Wang JJ, Shen W. Multispecies comparative analysis reveals transcriptional specificity during Mongolian horse testicular development. Reprod Domest Anim 2022; 57:1295-1306. [PMID: 35789122 DOI: 10.1111/rda.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 12/01/2022]
Abstract
Mongolian horses have been bred and used for labor and transport for centuries. Nevertheless, traits of testicular development in Mongolian horses have rarely been studied; particularly, studies regarding the transcriptional regulation characteristics of testicular development are lacking. In this paper, transcription specificity during testicular development in Mongolian horses is highlighted via a multispecies comparative analysis and weighted gene co-expression network analysis (WGCNA). Interestingly, the results showed that most genes were up-regulated in the testes after sexual maturity, which is a phenomenon conserved across species. Moreover, we observed nine key genes involved in regulating Mongolian horse testicular development. Notably, unique transcription signatures of testicular development in Mongolian horses are emphasized, which provides a novel insight into the mechanistic study of their testicular development.
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Affiliation(s)
- Fa-Li Zhang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, China.,College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xiao-Yuan Zhang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, China
| | - Jin-Xin Zhao
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, China
| | - Ke-Xin Zhu
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, China
| | - Shu-Qin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Teng Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yu-Jiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Dongying Vocational Institute, Dongying, China
| | - Jun-Jie Wang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, China
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9
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Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes (Basel) 2022; 13:genes13020229. [PMID: 35205275 PMCID: PMC8871751 DOI: 10.3390/genes13020229] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
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10
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Liu S, Fu C, Yang Y, Zhang Y, Ma H, Xiong Z, Ling Y, Zhao C. Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms. G3 (BETHESDA, MD.) 2021; 11:jkab008. [PMID: 33604674 PMCID: PMC8022964 DOI: 10.1093/g3journal/jkab008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/14/2020] [Indexed: 12/04/2022]
Abstract
To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 loci, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in the present study. The polymorphic Y chromosomal microsatellite markers result in 19 haplotypes in the studied horses and formed 24 paternal lines when merged with the 14 Y chromosomal SNPs reported previously. The haplotypes CHT18 and SS24 harboring AMELY gene mutation were the ancestral haplotypes, and other haplotypes were derived from them by one or more mutation steps. The horse populations in mountainous and remote areas of southwestern China have the most ancient paternal lines, which suggests that ancient paternal lines preserved in local populations attributed to less human interventions. Our results also showed that the northern local breeds had higher mtDNA diversity than the southern ones in China. The frequency of haplogroup B, F, and G of mtDNA in Chinese indigenous horses has declined in recent years, and some breeds are in endangered status mainly due to small population sizes. Urgent actions should be taken to conserve the genetic diversity of the indigenous horse populations, especially the rare paternal lines. Our findings help to elucidate the genetic diversity and evolutionary history of Chinese domestic horses, which will facilitate the conservation of the indigenous horses in the future.
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Affiliation(s)
- Shuqin Liu
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Qingdao Agricultural University, Shandong, China
| | - Chunzheng Fu
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yunzhou Yang
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuanyuan Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongying Ma
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhiyao Xiong
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Ling
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, China
- Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China
| | - Chunjiang Zhao
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, China
- Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China
- National Engineering Laboratory for Animal Breeding. Beijing, China
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11
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A Genetic Window on Sardinian Native Horse Breeds through Uniparental Molecular Systems. Animals (Basel) 2020; 10:ani10091544. [PMID: 32882901 PMCID: PMC7552234 DOI: 10.3390/ani10091544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The horse is a mammalian species showing a high variation among maternal lineages but a limited variability in the paternal inheritance. The female phylogenetic history is commonly investigated by analyzing the maternally transmitted mitochondrial DNA (mtDNA), while the male perspective is provided by the paternally inherited portion of the Y chromosome (NRY). Here we explored the variation of both non-recombining genetic systems in three horse breeds present in Sardinia: Giara, Sarcidano, and Sardinian Anglo-Arab. The analysis of 34 stallions revealed three differentially distributed NRY types: (i) the first and most ancestral one is typical of Sarcidano; (ii) the second is well represented in Giara and seems to derive from Neapolitan/Oriental stallions; (iii) the third confirms the Thoroughbred influence in the Sardinian Anglo-Arab breed. By extending the analysis to 178 mtDNAs, we observed a common maternal origin for Giara and Sarcidano. Contrarily, the outlier behavior of the Sardinian Anglo-Arab is due to its higher mitochondrial variability, testifying for multiple maternal lineages in its current population. Our preliminary findings highlight the importance of a parallel molecular screening of NRYs and mtDNAs to reconstruct both paternal and maternal phylogenetic histories and to fully evaluate the extent of autochthonous genetic resources in the island. Abstract Sardinia, an island located to the west of Italy in the Mediterranean Sea, boasts three native horse breeds: Giara, Sarcidano, and Sardinian Anglo-Arab. Here, we have investigated for the first time three loci of the non-recombining region of the Y chromosome (NRY) in 34 stallions from these breeds and performed a phylogenetic analysis of the maternal relationships among 178 previously published mitochondrial control regions. We found that the current NRY diversity of Sardinian horse breeds is linked to three haplotypes (HT), all identified within Sarcidano. Each breed showed a typical HT: HT1 (ancestral) was the most represented in Sarcidano, HT2 (Neapolitan/Oriental wave) in Giara, and HT3 (Thoroughbred wave) in Sardinian Anglo-Arab. The specificity of each haplotype suggests the influence of independent breeding strategies and the effect of genetic drift in each Sardinian population. The female counterpart, extended to 178 horses, showed a low genetic variability and a common maternal origin for Giara and Sarcidano. The higher variability of the Sardinian Anglo-Arab indicates multiple mare lineages in its current population. Further genetic analyses will be crucial to understand the paternal history of male horses, preserve the endangered mares’ and stallions’ lineages, and improve the enhancement of autochthonous genetic resources on this island.
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12
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Han H, Bryan K, Shiraigol W, Bai D, Zhao Y, Bao W, Yang S, Zhang W, MacHugh DE, Dugarjaviin M, Hill EW. Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations. J Hered 2020; 110:769-781. [PMID: 31628847 DOI: 10.1093/jhered/esz032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 08/01/2019] [Indexed: 01/02/2023] Open
Abstract
The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.
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Affiliation(s)
- Haige Han
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kenneth Bryan
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Wunierfu Shiraigol
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Dongyi Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Yiping Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Wuyingga Bao
- Vocational and Technical College of Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Siqin Yang
- Inner Mongolia University for the Nationalities, Tongliao, P.R. China
| | - Wengang Zhang
- Institute of Animal Science, Chinese Academy of Agriculture Sciences, Beijing, P.R. China
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Emmeline W Hill
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
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13
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Liu S, Yang Y, Pan Q, Sun Y, Ma H, Liu Y, Wang M, Zhao C, Wu C. Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers. Front Genet 2020; 11:467. [PMID: 32508879 PMCID: PMC7253630 DOI: 10.3389/fgene.2020.00467] [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: 08/29/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
Extremely low nucleotide diversity of modern horse Y-chromosome has been reported, and only poor phylogenetic resolution could be resulted from limited Y-chromosome markers. In this study, three types of horse Y-chromosome markers, including Single-nucleotide polymorphisms (SNPs), copy number variants (CNVs), and allele-specific CNVs, were developed by screening more than 300 male horses from 23 indigenous Chinese horse populations and 4 imported horse breeds. Fourteen segregating sites including a novel SNP in the AMELY gene were found in approximately 53 kb of male-specific Y-chromosome sequences. CNVs were detected at 11 of 14 sites, while allele-specific CNVs at 6 polymorphic sites in repeated fragments were also determined. The phylogenetic analyses with the SNPs identified in this study and previously published 51 SNPs obtained mainly from European horses showed that indigenous Chinese horses exhibit much deeper divergence than European and Middle Eastern horses, while individuals of Chinese horses with the C allele of the AMELY gene constituted the most ancient group. Via SNPs, CNVs, and allele-specific CNVs, much higher diversity of paternal lines can be detected than those identified with merely SNPs. Our results indicated that there are ancient paternal horse lines preserved in southwestern China, which sheds new light on the domestication and immigration of horses, and suggest that the priorities of the conservation should be given to the ancient and rare paternal lines. These three marker types provided finer phylogenetic resolution of horse patrilineal lines, and the strategies used in the present study also provide valuable reference for the genetic studies of other mammalian patrilineages.
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Affiliation(s)
- Shuqin Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Yunzhou Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Qingjie Pan
- School of Animal Science and Technology, Qingdao Agricultural University, Shandong, China
| | - Yujiang Sun
- School of Animal Science and Technology, Qingdao Agricultural University, Shandong, China
| | - Hongying Ma
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Yu Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Animal Genetic Improvement, Beijing, China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Animal Genetic Improvement, Beijing, China
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14
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Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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