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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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2
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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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3
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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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4
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Ono T, Inoue Y, Hisaeda K, Yamada Y, Hata A, Miyama TS, Shibano K, Kitagawa H, Ohzawa E, Iwata E. Effect of seasons and sex on the physical, hematological, and blood biochemical parameters of Noma horses. J Equine Sci 2021; 32:21-25. [PMID: 33776537 PMCID: PMC7984912 DOI: 10.1294/jes.32.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/01/2021] [Indexed: 11/21/2022] Open
Abstract
This study aimed to evaluate the influence of seasons and sex on body size and
hematological and biochemistry parameters of Noma horses, a native Japanese breed. Body
size was larger in winter than in summer. Laboratory testing variables, including
erythrocytic parameters and urea nitrogen, total cholesterol, and creatinine kinase
levels, were higher in winter, while the eosinophil count was higher in summer. These
seasonal differences may be related to increased energy consumption of horses due to heat
stress. The higher eosinophil counts may have been related to the dermatitis observed in
summer. Stallions tended to have smaller bodies compared with mares. Future studies are
necessary to investigate the effect of stress in seasonal and sex-based groups.
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Affiliation(s)
- Tetsushi Ono
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Yoichi Inoue
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Keiichi Hisaeda
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Yutaka Yamada
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Akihisa Hata
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | | | - Kenichi Shibano
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Hitoshi Kitagawa
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Emi Ohzawa
- Noma Horse Preservation Society, Ehime 794-0082, Japan
| | - Eri Iwata
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
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5
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Nguyen TB, Paul RC, Okuda Y, LE TNA, Pham PTK, Kaissar KJ, Kazhmurat A, Bibigul S, Bakhtin M, Kazymbet P, Maratbek SZ, Meldebekov A, Nishibori M, Ibi T, Tsuji T, Kunieda T. Genetic characterization of Kushum horses in Kazakhstan based on haplotypes of mtDNA and Y chromosome, and genes associated with important traits of the horses. J Equine Sci 2020; 31:35-43. [PMID: 33061782 PMCID: PMC7538259 DOI: 10.1294/jes.31.35] [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: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
The Kushum is a relatively new breed of horses in Kazakhstan that was established in the
middle of the 20th century through a cross between mares of Kazakhstan local horses and
stallions of Thoroughbred, Trotter, and Russian Don breeds to supply military horses. To
reveal the genetic characteristics of this breed, we investigated haplotypes of
mitochondrial DNA (mtDNA) and single-nucleotide polymorphisms of the Y chromosome, as well
as genotypes of five functional genes associated with coat color, body composition, and
locomotion traits. We detected 10 mtDNA haplotypes that fell into 8 of the 17 major
haplogroups of horse mtDNA, indicating a unique haplotype composition with high genetic
diversity. We also found two Y-chromosomal haplotypes in Kushum horses, which likely
originated from Trotter and/or Don breeds. The findings regarding the mtDNA and
Y-chromosomal haplotypes are concordant with the documented maternal and paternal origins
of the Kushum horses. The allele frequencies of ASIP, MC1R, and MATP associated with coat
color were consistent with the coat color variations of Kushum horses. The allele
frequencies of MSTN associated with endurance performance and those of DMRT3 associated
with gait suggested that the observed allele frequencies of these genes were the result of
selective breeding for these traits. As a result of this study, we were able to obtain
useful information for a better understanding of the origin and breeding history of the
Kushum horse breed using molecular markers.
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Affiliation(s)
- Trung B Nguyen
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,An Giang University, Vietnam National University, An Giang, Vietnam
| | - Ripon C Paul
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Patuakhali Science and Technology University, Barishal, Bangladesh
| | - Yu Okuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Okayama University of Science, Okayama 700-0005, Japan
| | - Thu N A LE
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,University of Agriculture & Forestry, Hue University, Hue, Vietnam
| | - Phuong T K Pham
- An Giang University, Vietnam National University, An Giang, Vietnam
| | - Kushaliye J Kaissar
- Zhangir Khan West Kazakhstan Agrarian-Technical University, Uralsk, Kazakhstan
| | | | | | - Meirat Bakhtin
- Radiobiological Research Institute, JSC Astana Medical University, Astana, Kazakhstan
| | - Polat Kazymbet
- Radiobiological Research Institute, JSC Astana Medical University, Astana, Kazakhstan
| | | | | | - Masahide Nishibori
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takehito Tsuji
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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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: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Lancioni H, Cardinali I, Giontella A, Antognoni MT, Miglio A. Mitochondrial DNA variation in the Italian Heavy Draught Horse. PeerJ 2020; 8:e8996. [PMID: 32461825 PMCID: PMC7233276 DOI: 10.7717/peerj.8996] [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: 11/28/2019] [Accepted: 03/26/2020] [Indexed: 12/28/2022] Open
Abstract
Background In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook. Methodology To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds. Results Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.
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Affiliation(s)
- Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | | | - Arianna Miglio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
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8
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Ono T, Yamada Y, Hata A, Shimokawa Miyama T, Shibano K, Iwata E, Ohzawa E, Kitagawa H. Reference values of hematological and blood biochemical parameters for the Noma horse. J Equine Sci 2019; 30:69-73. [PMID: 31592225 PMCID: PMC6773617 DOI: 10.1294/jes.30.69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/23/2019] [Indexed: 11/17/2022] Open
Abstract
The Noma horse is a Japanese breed from the Noma region of Imabari City, Ehime
Prefecture. To obtain reference hematological and biochemical values, we performed
examinations in 39 clinically healthy, mature Noma horses managed at the Imabari public
ranch. Hematological and biochemical results of Noma horses were close to the normal
ranges of horses in the U.S.A. The erythrocyte parameters and hepatobiliary enzyme levels
in Noma and Kiso horses were lower than those in Japanese racehorses. Noma horses showed
higher erythrocyte parameters and triglyceride concentrations and a lower creatinine
concentration compared with those in Kiso horses. These data represent the first report of
reference values for Noma horses and may be useful to improve their management.
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Affiliation(s)
- Tetsushi Ono
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Yutaka Yamada
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Akihisa Hata
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | | | - Kenichi Shibano
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Eri Iwata
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
| | - Emi Ohzawa
- Noma Horse Preservation Society, Ehime 794-0082, Japan
| | - Hitoshi Kitagawa
- Faculty of Veterinary Medicine, Okayama University of Science, Ehime 794-8555, Japan
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9
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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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Tozaki T, Kikuchi M, Kakoi H, Hirota K, Nagata S, Yamashita D, Ohnuma T, Takasu M, Kobayashi I, Hobo S, Manglai D, Petersen JL. Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data. Anim Genet 2019; 50:449-459. [PMID: 31282588 DOI: 10.1111/age.12819] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2019] [Indexed: 11/29/2022]
Abstract
Eight horse breeds-Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni-are native to Japan. Although Japanese native breeds are believed to have originated from ancient Mongolian horses imported from the Korean Peninsula, the phylogenetic relationships among these breeds are not well elucidated. In the present study, we compared genetic diversity among 32 international horse breeds previously evaluated by the Equine Genetic Diversity Consortium, the eight Japanese native breeds and Japanese Thoroughbreds using genome-wide SNP genotype data. The proportion of polymorphic loci and expected heterozygosity showed that the native Japanese breeds, with the exception of the Hokkaido, have relatively low diversity compared to the other breeds sampled. Phylogenetic and cluster analyses demonstrated relationships among the breeds that largely reflect their geographic distribution in Japan. Based on these data, we suggest that Japanese horses originated from Mongolian horses migrating through the Korean Peninsula. The Japanese Thoroughbreds were distinct from the native breeds, and although they maintain similar overall diversity as Thoroughbreds from outside Japan, they also show evidence of uniqueness relative to the other Thoroughbred samples. This is the first study to place the eight native Japanese breeds and Japanese Thoroughbred in context with an international sample of diverse breeds.
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Affiliation(s)
- T Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.,College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - M Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan
| | - H Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan
| | - K Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan
| | - S Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan
| | - D Yamashita
- Japan Equine Affairs Association, Chuo-ku, Tokyo, 104-0033, Japan
| | - T Ohnuma
- Japan Equine Affairs Association, Chuo-ku, Tokyo, 104-0033, Japan
| | - M Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - I Kobayashi
- Sumiyoshi Livestock Science Station, Field Science Center, University of Miyazaki, Miyazaki, 880-0121, Japan
| | - S Hobo
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, 890-0065, Japan
| | - D Manglai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - J L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583-0908, USA
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