1
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Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia. Saudi J Biol Sci 2023; 30:103741. [PMID: 37575470 PMCID: PMC10413190 DOI: 10.1016/j.sjbs.2023.103741] [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: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and Seglawi) from the previous study for phylogenetic comparison. The whole mitochondrial genome sequencing resulted in intra and inter mtDNA variations between the studied horses. Interestingly, the Hamdani horse has nucleotide substitutions similar to those of the Hadban horse, which is reflected in the phylogenetic tree as a significantly close relationship. This type of study provides a better understanding of mitogenome structure and conservation of livestock species genetic data.
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Affiliation(s)
- Abdullah Sheikh
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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2
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Voronkova VN, Nikolaeva EA, Piskunov AK, Babayan OV, Takasu M, Tozaki T, Svishcheva GR, Stolpovsky YA. Assessment of Genetic Diversity and Structure of Russian and Mongolian Autochthonous Horse Breeds Using Nuclear and Mitochondrial DNA Markers. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Khrabrova LA, Blohina NV, Belousova NF, Cothran EG. Estimation of the Genealogical Structure of Vyatka Horse Breed (Equus ferus caballus) Using DNA Analysis. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Khrabrova LA, Blohina NV, Bazaron BZ, Khamiruev TN. Вариабельность последовательности D-петли митохондриальной ДНК у лошадей забайкальской породы. Vavilovskii Zhurnal Genet Selektsii 2021; 25:486-491. [PMID: 34595371 PMCID: PMC8453366 DOI: 10.18699/vj21.055] [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: 01/29/2021] [Revised: 03/28/2021] [Accepted: 04/08/2021] [Indexed: 11/20/2022] Open
Abstract
The Zabaikalskaya horse is an indigenous breed of horses from Siberia with diverse use. It is characterized by endurance
and good adaptability to year-round herd maintenance in the harsh conditions of the Baikal steppes. To determine
the genetic characteristics of the maternal lineage of the Zabaikalskaya horse breed based on mitochondrial DNA polymorphisms,
we collected hair samples from 31 horses belonging to breeding farms in the Trans-Baikal Territory. Analysis of the
530 bp sequence of the mtDNA D-loop was performed using the maximum composite likelihood (MCL) model in combination
with bootstrap analysis. When studying the polymorphism of the hypervariable region of the mtDNA D- loop in Zabaikalskaya
horses, we identif ied 31 haplotypes representing 8 haplogroups: B, C, G, H, L, M, Q and R according to modern
classif ication. The sequenced fragment of the D-loop from nucleotide position 15471 to 16000 contained 17 polymorphic
sites, mainly represented by the A→G, G→A and T→C transitions. The haplogroups Q (25.81 %), B (19.35 %), G (16.13 %)
and H (12.90 %) were prevailing in the mtDNA structure of this breed. Genetic analysis of the mitochondrial genome of
the Zabaikalskaya horse revealed a high level of diversity of haplotypes and haplogroups, which are typical for the horse
populations of Eurasia.
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Affiliation(s)
- L A Khrabrova
- All-Russian Research Institute for Horse Breeding, Divovo, Ryazan Region, Russia
| | - N V Blohina
- All-Russian Research Institute for Horse Breeding, Divovo, Ryazan Region, Russia
| | - B Z Bazaron
- Scientif ic Research Institute of Veterinary Medicine of Eastern Siberia - Branch of the Siberian Federal Scientif ic Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Chita, Russia
| | - T N Khamiruev
- Scientif ic Research Institute of Veterinary Medicine of Eastern Siberia - Branch of the Siberian Federal Scientif ic Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Chita, Russia
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5
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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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6
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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7
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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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8
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Giontella A, Cardinali I, Lancioni H, Giovannini S, Pieramati C, Silvestrelli M, Sarti FM. Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records. Animals (Basel) 2020; 10:E839. [PMID: 32408648 PMCID: PMC7278429 DOI: 10.3390/ani10050839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/30/2020] [Accepted: 05/09/2020] [Indexed: 11/16/2022] Open
Abstract
* Correspondence: andrea [...].
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Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via - Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via - Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (S.G.); (F.M.S.)
| | - Camillo Pieramati
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (S.G.); (F.M.S.)
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9
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Winton CL, McMahon R, Hegarty MJ, McEwan NR, Davies‐Morel MCG, Morgan C, Nash DM. Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies. Ecol Evol 2020; 10:1352-1367. [PMID: 32076519 PMCID: PMC7029099 DOI: 10.1002/ece3.5989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin. This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyze the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected (a total of 485 animals were used for mtDNA analysis and 450 for microsatellite analysis), and previously published data were used to place the British and Irish ponies in a global context. The native ponies of Britain and Ireland were found to have had a complex history, and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were maintained in native breeds, although some reduction was evident in small or isolated populations (Shetland, Carneddau, and Section C). Unusual mitochondrial diversity distribution patterns were apparent for the Carneddau and Dartmoor, although among breeds and global haplogroups there was a high degree of haplotype sharing evident, well-represented within British and Irish ponies. Ancestral maternal diversity was maintained by most populations, particularly the Fells and Welsh ponies, which exhibited rare and ancient lineages. The maternal and paternal histories of the breeds are distinct, with male-biased crossings between native breeds, and other shared influences, likely Arabs and Thoroughbreds, are apparent. The data generated herein provide valuable information to guide and implement the conservation of increasingly rare native genetic resources.
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Affiliation(s)
- Clare L. Winton
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Robert McMahon
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- Molecular HaematologyHaematology LaboratoryRoyal Infirmary of EdinburghEdinburghUK
| | - Matthew J. Hegarty
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- School of Pharmacy and Life SciencesRobert Gordon UniversityAberdeenUK
| | | | - Charly Morgan
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Deborah M. Nash
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
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10
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Mitochondrial Profiles of the East Bulgarian and the Pleven Horse Breeds. J Equine Vet Sci 2020; 88:102933. [PMID: 32303312 DOI: 10.1016/j.jevs.2020.102933] [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: 11/06/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 11/23/2022]
Abstract
It is well known that horse breeding in Bulgaria is a cultural heritage in Bulgaria, dating from prehistoric and historic times. Until now, molecular data on Bulgarian horses from the plain regions of the country were not available. Therefore, for the first time, we have collected genetic information about some modern horse breeds from the plain regions in Bulgaria. A total of 50 horses originating from different families from two different breeds were investigated: the first one was the Pleven horse (n = 11, breeding in the Danubian Plain), and the second one was the East Bulgarian horse breed (n = 39, Shumen district). These breeds were genotyped according to the mitochondrial D-loop region. The results showed that the Pleven horse particularly carries the European haplogroup L (45.45%), followed by the Middle East haplogroup C (27.27%). In contrast to the Pleven horse, the East Bulgarian horse breed revealed almost equal frequencies of the European specific haplogroup L (33.33%) and the Central Asiatic haplogroup Q (35.90%). Analyses of these two horse breeds revealed a specific genetic profile, but it is obvious that the East Bulgarian horse showed an unusual, mixed profile-a massive admixture with the Asiatic-type haplogroup Q and a high haplogroup diversity. In conclusion, the differences in genetic structure of the two plain horse breeds may be explained with the various horse breeds involved in their formation.
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11
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Lu H, Bai H, Wang L, Zhang T. Abundant genetic diversity and maternal origins of modern horses. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To clarify the origin and genetic diversity of modern horses, mitochondrial DNA (mtDNA) D-loop sequences were generated for 3965 horses from 12 geographical regions. From these sequences, we observed 439 haplotypes defined by 138 polymorphic nucleotide sites. All horses were genetically diverse (HD = 0.973 ± 0.001, π = 0.0243 ± 0.0005), which showed that maternal lineages of the domestic horse are worldwide highly diverse. In general, all 18 haplogroups were presented in the Asian horse. The majority of modern horse sequences belong to haplogroups L, Q, and A. At the same time, 194 archaeological samples from four geographical regions were obtained. Indeed, haplogroup distributions are overlapping in modern and ancient samples, indicating that most haplogroups were already present in ancient times at least in Europe and Asia. The network showed that breeds of Asian and Europe regions overlapped, suggesting that extensive gene flow had occurred between different horse breeds in Asian and European regions.
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Affiliation(s)
- Hongzhao Lu
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
| | - Hao Bai
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
| | - Ling Wang
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
| | - Tao Zhang
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, People’s Republic of China
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12
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Ning T, Ling Y, Hu S, Ardalan A, Li J, Mitra B, Chaudhuri TK, Guan W, Zhao Q, Ma Y, Savolainen P, Zhang Y. Local origin or external input: modern horse origin in East Asia. BMC Evol Biol 2019; 19:217. [PMID: 31775623 PMCID: PMC6882189 DOI: 10.1186/s12862-019-1532-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite decades of research, the horse domestication scenario in East Asia remains poorly understood. RESULTS The study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial genomes of 317 horse samples. The time to the most recent common ancestor of the 16 haplogroups ranges from [0.8-3.1] thousand years ago (KYA) to [7.9-27.1] KYA. With combined analyses of the mitochondrial control region for 35 extant Przewalski's horses, 3544 modern and 203 ancient horses across the world, researchers provide evidence for that East Asian prevalent haplogroups Q and R were indigenously domesticated or they were involved in numerous distinct genetic components from wild horses in the southern part of East Asia. These events of haplotypes Q and R occurred during 4.7 to 16.3 KYA and 2.1 to 11.5 KYA, respectively. The diffusion of preponderant European haplogroups L from west to East Asia is consistent with the external gene input. Furthermore, genetic differences were detected between northern East Asia and southern East Asia cohorts by Principal Component Analysis, Analysis of Molecular Variance test, the χ2 test and phylogeographic analyses. CONCLUSIONS All results suggest a complex picture of horse domestication, as well as geographic pattern in East Asia. Both local origin and external input occurred in East Asia horse populations. And besides, there are at least two different domestication or hybridization centers in East Asia.
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Affiliation(s)
- Tiao Ning
- College of Agriculture, Kunming University, Kunming, 650214, Yunnan, China. .,Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, Yunnan, China.
| | - Yinghui Ling
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Shaoji Hu
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650214, Yunnan, China
| | - Arman Ardalan
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65, Solna, Sweden
| | - Jing Li
- College of Agriculture, Kunming University, Kunming, 650214, Yunnan, China.,The Research Center for Urban Modern Agricultural Engineering of Yunnan Tertiary Education, Kunming University, Kunming, 650214, Yunnan, China
| | - Bikash Mitra
- Department of Zoology, University of North Bengal, Cellular Immunology Laboratory, Siliguri, West Bengal, 734013, India
| | - Tapas Kumar Chaudhuri
- Department of Zoology, University of North Bengal, Cellular Immunology Laboratory, Siliguri, West Bengal, 734013, India
| | - Weijun Guan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65, Solna, Sweden.
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, Yunnan, China. .,State Key Laboratory of Genetic Resources and Evolution Kunming, Yunnan, Kunming Institute of Zoology, Chinese Academy of Sciences, Wuhua, 650223, Yunnan, China.
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13
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Yoon SH, Lee W, Ahn H, Caetano-Anolles K, Park KD, Kim H. Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives. PLoS One 2018; 13:e0203917. [PMID: 30216366 PMCID: PMC6138400 DOI: 10.1371/journal.pone.0203917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/30/2018] [Indexed: 11/26/2022] Open
Abstract
The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski’s horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski’s horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500–11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution.
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Affiliation(s)
- Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Wonseok Lee
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyoung-Do Park
- The Animal Molecular Genetics & Breeding Center, Chonbuk National University, Jeonju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- * E-mail:
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14
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Cozzi MC, Strillacci MG, Valiati P, Rogliano E, Bagnato A, Longeri M. Genetic variability of Akhal-Teke horses bred in Italy. PeerJ 2018; 6:e4889. [PMID: 30202639 PMCID: PMC6129384 DOI: 10.7717/peerj.4889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.
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Affiliation(s)
- Maria C Cozzi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Valiati
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Elisa Rogliano
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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15
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Yang L, Kong X, Yang S, Dong X, Yang J, Gou X, Zhang H. Haplotype diversity in mitochondrial DNA reveals the multiple origins of Tibetan horse. PLoS One 2018; 13:e0201564. [PMID: 30052677 PMCID: PMC6063445 DOI: 10.1371/journal.pone.0201564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
The Tibetan horse is a species endemic to the Tibetan plateau, with considerable economic value in the region. However, we currently have little genetic evidence to verify whether the breed originated in Tibet or if it entered the area via an ancient migratory route. In the present study, we analyzed the hypervariable segment I sequences of mitochondrial DNA (mtDNA) in 2,050 horses, including 290 individuals from five Tibetan populations and 1,760 from other areas across Asia. Network analysis revealed multiple maternal lineages in the Tibetan horse. Component analysis of sub-lineage F3 indicated that it decreased in frequency from east to west, a trend reflected both southward and northward from Inner Mongolia. Analysis of population genetics showed that the Deqen horse of eastern Tibet was more closely related to the Ningqiang horse of northern China than to other Tibetan horses or the Yunnan horse. These results indicated that the Tibetan horse migrated first from Central Asia to Mongolia, moved south to eastern Tibet (near Deqen), then finally westward to other regions of Tibet. We also identified a novel lineage K that mainly comprises Tibetan and Yunnan horses, suggesting autochthonous domesticated origin for some Tibetan horse breeds from local wild horses. In conclusion, our study demonstrated that modern Tibetan horse breeds originated from the introgression of local wild horses with exotic domesticated populations outside China.
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Affiliation(s)
- Lin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoyan Kong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Shuli Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jianfa Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- * E-mail: (HZ); (XG)
| | - Hao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail: (HZ); (XG)
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16
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Ma H, Wu Y, Xiang H, Yang Y, Wang M, Zhao C, Wu C. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences. PeerJ 2018; 6:e4896. [PMID: 29868288 PMCID: PMC5985762 DOI: 10.7717/peerj.4896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/13/2018] [Indexed: 11/20/2022] Open
Abstract
Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35-10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.
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Affiliation(s)
- Hongying Ma
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Yajiang Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Hai Xiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing, China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
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17
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Khaudov AD, Duduev AS, Kokov ZA, Amshokov KK, Zhekamukhov MK, Zaitsev AM, Reissmann M. Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers. Open Vet J 2018; 8:40-46. [PMID: 29445620 PMCID: PMC5806666 DOI: 10.4314/ovj.v8i1.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/23/2018] [Indexed: 11/17/2022] Open
Abstract
Studies of mitochondrial DNA (mtDNA) as well as the non-recombining part of the Y chromosome help to understand the origin and distribution of maternal and paternal lineages. The Kabardian horse from Northern Caucasia which is well-known for strength, stamina and endurance in distance riding has a large gap in its breeding documentation especially in the recent past. A 309 bp fragment of the mitochondrial D-loop (156 Kabardian horses) and six mutations in Y chromosome (49 Kabardian stallions), respectively, were analyzed to get a better insight into breeding history, phylogenetic relationship to related breeds, maternal and paternal diversity and genetic structure. We found a high mitochondrial diversity represented by 64 D-loop haplotypes out of 14 haplogroups. The most frequent haplogroups were G (19.5%), L (12.3%), Q (11.7%), and B (11.0%). Although these four haplogroups are also frequently found in Asian riding horses (e.g. Buryat, Kirghiz, Mongolian, Transbaikalian, Tuvinian) the percentage of the particular haplogroups varies sometimes remarkable. In contrast, the obtained haplogroup pattern from Kabardian horse was more similar to that of breeds reared in the Middle East. No specific haplotype cluster was observed in the phylogenetic tree for Kabardian horses. On Kabardian Y chromosome, two mutations were found leading to three haplotypes with a percentage of 36.7% (haplotype HT1), 38.8% (haplotype HT2) and 24.5% (haplotype HT3), respectively. The high mitochondrial and also remarkable paternal diversity of the Kabardian horse is caused by its long history with a widely spread maternal origin and the introduction of Arabian as well as Thoroughbred influenced stallions for improvement. This high genetic diversity provides a good situation for the ongoing breed development and performance selection as well as avoiding inbreeding.
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Affiliation(s)
- Aliybek D. Khaudov
- Institute of Chemistry and Biology, Kabardino-Balkarian State University, Chernyshevskovo 173, 360004 Nalchik, Russia
| | - Astemir S. Duduev
- Institute of Chemistry and Biology, Kabardino-Balkarian State University, Chernyshevskovo 173, 360004 Nalchik, Russia
| | - Zaur A. Kokov
- Institute of Physics and Mathematics, Kabardino-Balkarian State University, Chernyshevskovo 173, 360004 Nalchik, Russia
| | - Khazhismel K. Amshokov
- Kabardino-Balkarian Research Institute of Agriculture, Kirova 224, 360004 Nalchik, Russia
| | | | - Alexander M. Zaitsev
- All-Russian Research Institute of Horse Breeding, Ryazan region, Rybnoye district, 391105 Divovo, Russia
| | - Monika Reissmann
- Abrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University, Unter den Linden 6, 10099 Berlin, Germany
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18
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Csizmár N, Mihók S, Jávor A, Kusza S. Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing. PeerJ 2018; 6:e4198. [PMID: 29404201 PMCID: PMC5797449 DOI: 10.7717/peerj.4198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/05/2017] [Indexed: 11/20/2022] Open
Abstract
Background The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed. Results One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected. Discussion Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.
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Affiliation(s)
- Nikolett Csizmár
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Sándor Mihók
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - András Jávor
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Szilvia Kusza
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
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19
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Ianella P, Albuquerque MDSM, Paiva SR, Egito AAD, Almeida LD, Sereno FTPS, Carvalho LFR, Mariante ADS, McManus CM. D-loop haplotype diversity in Brazilian horse breeds. Genet Mol Biol 2017; 40:604-609. [PMID: 28863209 PMCID: PMC5596364 DOI: 10.1590/1678-4685-gmb-2016-0166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 03/25/2017] [Indexed: 12/03/2022] Open
Abstract
The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for FST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making.
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Affiliation(s)
- Patrícia Ianella
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
| | | | - Samuel Rezende Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
| | | | | | - Fabiana T P S Sereno
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | | | - Concepta Margaret McManus
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
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20
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Elsner J, Hofreiter M, Schibler J, Schlumbaum A. Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum. PLoS One 2017; 12:e0177458. [PMID: 28542345 PMCID: PMC5443500 DOI: 10.1371/journal.pone.0177458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
On large geographical scales, changes in animal population distribution and abundance are driven by environmental change due to climatic and anthropogenic processes. However, so far, little is known about population dynamics on a regional scale. We have investigated 92 archaeological horse remains from nine sites mainly adjacent to the Swiss Jura Mountains dating from c. 41,000-5,000 years BP. The time frame includes major environmental turning points such as the Last Glacial Maximum (LGM), followed by steppe vegetation, afforestation and initial re-opening of the landscape by human agricultural activities. To investigate matrilinear population dynamics, we assembled 240 base pairs of the mitochondrial d-loop. FST values indicate large genetic differentiation of the horse populations that were present during and directly after the LGM. After the retreat of the ice, a highly diverse population expanded as demonstrated by significantly negative results for Tajima's D, Fu's FS and mismatch analyses. At the same time, a different development took place in Asia where populations declined after the LGM. This first comprehensive investigation of wild horse remains on a regional scale reveals a discontinuous colonisation of succeeding populations, a pattern that diverges from the larger Eurasian trend.
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Affiliation(s)
- Julia Elsner
- Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
- * E-mail:
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörg Schibler
- Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
| | - Angela Schlumbaum
- Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
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21
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Yoon SH, Kim J, Shin D, Cho S, Kwak W, Lee HK, Park KD, Kim H. Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics. Mol Biol Rep 2017; 44:233-242. [PMID: 28432484 DOI: 10.1007/s11033-017-4101-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022]
Abstract
The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.
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Affiliation(s)
- Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Jaemin Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Seoae Cho
- C&K Genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea
| | - Woori Kwak
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Hak-Kyo Lee
- The Animal Genomics and Breeding Center, Chonbuk National University, Jeonju, 561-756, Republic of Korea
| | - Kyoung-Do Park
- Genomic Informatics Center, Hankyong National University, Anseong, 456-749, Republic of Korea.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea. .,C&K Genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea.
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22
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Yang Y, Zhu Q, Liu S, Zhao C, Wu C. The origin of Chinese domestic horses revealed with novel mtDNA variants. Anim Sci J 2016; 88:19-26. [PMID: 27071843 DOI: 10.1111/asj.12583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/29/2015] [Accepted: 11/09/2015] [Indexed: 11/27/2022]
Abstract
The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe.
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Affiliation(s)
- Yunzhou Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Qiyun Zhu
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Shuqin Liu
- College of Animal Science and Technology, 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.,Key laboratory of Animal Breeding and Genetics of Ministry of Agriculture, P.R. China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key laboratory of Animal Breeding and Genetics of Ministry of Agriculture, P.R. China
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23
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Cardinali I, Lancioni H, Giontella A, Capodiferro MR, Capomaccio S, Buttazzoni L, Biggio GP, Cherchi R, Albertini E, Olivieri A, Cappelli K, Achilli A, Silvestrelli M. An Overview of Ten Italian Horse Breeds through Mitochondrial DNA. PLoS One 2016; 11:e0153004. [PMID: 27054850 PMCID: PMC4824442 DOI: 10.1371/journal.pone.0153004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The climatic and cultural diversity of the Italian Peninsula triggered, over time, the development of a great variety of horse breeds, whose origin and history are still unclear. To clarify this issue, analyses on phenotypic traits and genealogical data were recently coupled with molecular screening. METHODOLOGY To provide a comprehensive overview of the horse genetic variability in Italy, we produced and phylogenetically analyzed 407 mitochondrial DNA (mtDNA) control-region sequences from ten of the most important Italian riding horse and pony breeds: Bardigiano, Esperia, Giara, Lipizzan, Maremmano, Monterufolino, Murgese, Sarcidano, Sardinian Anglo-Arab, and Tolfetano. A collection of 36 Arabian horses was also evaluated to assess the genetic consequences of their common use for the improvement of some local breeds. CONCLUSIONS In Italian horses, all previously described domestic mtDNA haplogroups were detected as well as a high haplotype diversity. These findings indicate that the ancestral local mares harbored an extensive genetic diversity. Moreover, the limited haplotype sharing (11%) with the Arabian horse reveals that its impact on the autochthonous mitochondrial gene pools during the final establishment of pure breeds was marginal, if any. The only significant signs of genetic structure and differentiation were detected in the geographically most isolated contexts (i.e. Monterufolino and Sardinian breeds). Such a geographic effect was also confirmed in a wider breed setting, where the Italian pool stands in an intermediate position together with most of the other Mediterranean stocks. However, some notable exceptions and peculiar genetic proximities lend genetic support to historical theories about the origin of specific Italian breeds.
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Affiliation(s)
- Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Andrea Giontella
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
| | | | - Stefano Capomaccio
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
| | - Luca Buttazzoni
- Centro di ricerca per la produzione delle carni e il miglioramento genetico, Sede centrale–Monterotondo, Roma, Italy
| | | | - Raffaele Cherchi
- Agenzia per la ricerca in agricoltura–AGRIS Sardegna, Sassari, Italy
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università di Perugia, Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Katia Cappelli
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail:
| | - Maurizio Silvestrelli
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
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Han H, Zhang Q, Gao K, Yue X, Zhang T, Dang R, Lan X, Chen H, Lei C. Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1066-74. [PMID: 26104513 PMCID: PMC4478473 DOI: 10.5713/ajas.14.0784] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/16/2014] [Accepted: 03/04/2015] [Indexed: 11/27/2022]
Abstract
In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10(-4)) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.
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Affiliation(s)
- Haoyuan Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kexin Gao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangpeng Yue
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Zhang
- Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ruihua Dang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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Zhang T, Lu H, Chen C, Jiang H, Wu S. Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:921-6. [PMID: 25049645 PMCID: PMC4092969 DOI: 10.5713/ajas.2011.11483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 05/04/2012] [Accepted: 02/16/2012] [Indexed: 11/27/2022]
Abstract
In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.
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26
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Zhao Q, Kang Y, Pu Y, Niu L, Guan W, He X, Zhang H, Lim H, Ma Y, Zhong T. Primer effect in the detection of mtDNA heteroplasmy: insights from horse Cytochrome b gene. ACTA ACUST UNITED AC 2014; 26:178-81. [PMID: 24409928 DOI: 10.3109/19401736.2013.855924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Heteroplasmy, the presence of bi-allelic mtDNA types within an individual, has been previously detected in the D-loop region and Cytochrome b gene (Cytb) of mitochondrial DNA using PCR-RFLP. However, heteroplasmy was absent in thousands of equine mtDNA sequences deposited in GenBank. To address whether heteroplasmy widely exists in mitochondria of Chinese indigenous horses, we generated the data set of the target sites in Cytb region with Sanger sequencing and PCR-RFLP method as well. In this study, 23 heteroplasmic individuals were detected in 430 Chinese local horses. Both site and length heteroplasmy were identified in horse Cytb, especially in Xinihe and Ujumqin breeds. Our data provide evidence that the forward and reverse primers seem to produce a similar approximation to the proportion of mutation base call. However, locations of primers affected the proper detection of mtDNA heteroplasmy. The data obtained in this study highlight the importance of the primers in the accurate detection of heteroplasmy.
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Affiliation(s)
- Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing , China
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27
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Devi KM, Ghosh SK. Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop. Mol Biol Rep 2013; 40:5861-7. [DOI: 10.1007/s11033-013-2692-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 09/14/2013] [Indexed: 12/01/2022]
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Yang SL, Li AP, Xu LX, Yang H. Short Communication: Mitochondrial DNA D-loop sequence diversity and origin of Chinese pony breeds (Equus caballus). CANADIAN JOURNAL OF ANIMAL SCIENCE 2013. [DOI: 10.4141/cjas2012-160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Yang, S.-l., Li, A.-P., Xu, L.-x. and Yang, H. 2013. Short Communication: Mitochondrial DNA D-loop sequence diversity and origin of Chinese pony breeds ( Equus caballus ). Can. J. Anim. Sci. 93: 313–319. Previous studies based on mitochondrial DNA (mtDNA) data have shown that Chinese horses have high genetic diversity. However, little is known about the genetic diversity of mtDNA D-loop sequences and maternal origin of five Chinese pony breeds. In the present study, genetic diversity of 343-bp D-loop sequences for136 individuals representing five Chinese pony breeds was analyzed. To address the question of the single and multiple maternal origin of Chinese pony populations, 13 partial mtDNA D-loop reference sequences from GenBank representing eight ancient and modern horse breeds (Connemara, Garrano, Sorraia, Pottok, Losino, Cheju, Tuva and a Swedish horse) were added to conduct the phylogenetic analyses. A total of 59 haplotypes and 50 polymorphic loci were detected, the haplotype diversity (h) ranged from 0.894 to 0.947 and nucleotide diversity (π) ranged from 0.0184 to 0.0229, suggesting relatively abundant genetic diversity in the Debao, Yunnan and the Guizhou breeds. The phylogenetic tree and median-joining network show multiple maternal origins of the five Chinese pony breeds.
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Affiliation(s)
- Sheng-lin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Educational Ministry in Guizhou Mountainous Area, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Ai-Ping Li
- Station of Animal Husbandry and Veterinarian of Kaili, Kaili, Guizhou 560000, China
| | - Long-xing Xu
- Research Institute of Animal and Veterinary Science, Guiyang, Guizhou province
| | - Haibing Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Educational Ministry in Guizhou Mountainous Area, Guizhou University, Guiyang, 550025, Guizhou Province, China
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29
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Winton CL, Hegarty MJ, McMahon R, Slavov GT, McEwan NR, Davies-Morel MC, Morgan CM, Powell W, Nash DM. Genetic diversity and phylogenetic analysis of native mountain ponies of Britain and Ireland reveals a novel rare population. Ecol Evol 2013; 3:934-47. [PMID: 23610635 PMCID: PMC3631405 DOI: 10.1002/ece3.507] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 11/08/2022] Open
Abstract
The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free-living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free-living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats.
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Affiliation(s)
- Clare L Winton
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, UK
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Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MCT, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One 2013; 8:e54997. [PMID: 23383025 PMCID: PMC3559798 DOI: 10.1371/journal.pone.0054997] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/20/2012] [Indexed: 11/18/2022] Open
Abstract
Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.
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Affiliation(s)
- Jessica L Petersen
- University of Minnesota, College of Veterinary Medicine, St Paul, MN, USA.
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Bower MA, Whitten M, Nisbet RER, Spencer M, Dominy KM, Murphy AM, Cassidy R, Barrett E, Hill EW, Binns M. Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records. J Anim Breed Genet 2012; 130:227-35. [PMID: 23679948 DOI: 10.1111/j.1439-0388.2012.01018.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/16/2012] [Indexed: 11/27/2022]
Abstract
The potential future earnings and therefore value of Thoroughbred foals untested in the racing arena are calculated based on the performance of their forebears. Thus, lineage is of key importance. However, previous research indicates that maternally inherited mitochondrial DNA (mtDNA) does not correspond to maternal lineage according to recorded pedigree, casting doubt on the voracity of historic pedigrees. We analysed mtDNA of 296 Thoroughbred horses from 33 maternal lineages and identified an interesting trend. Subsequent to the founding of the Thoroughbred breed in the 16th century, well-populated maternal lineages were divided into sub-lineages. Only six in 10 of the Thoroughbreds sampled shared mitochondrial haplotype with other members of their maternal lineage, despite having a common maternal ancestor according to pedigree records. However, nine in 10 Thoroughbreds from the 103 sub-lineages sampled shared mtDNA with horses of their maternal pedigree sub-lineage. Thus, Thoroughbred maternal sub-lineage pedigree represents a more accurate breeding record than previously thought. Errors in pedigrees must have occurred largely, though, not exclusively, at sub-lineage foundation events, probably due to incomplete understanding of modes of inheritance in the past, where maternal sub-lineages were founded from individuals, related, but not by female descent.
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Affiliation(s)
- M A Bower
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
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Moridi M, Masoudi AA, Vaez Torshizi R, Hill EW. Mitochondrial DNA D-loop sequence variation in maternal lineages of Iranian native horses. Anim Genet 2012; 44:209-13. [DOI: 10.1111/j.1365-2052.2012.02389.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2012] [Indexed: 11/29/2022]
Affiliation(s)
- M. Moridi
- Department of Animal Science; Faculty of Agriculture; Tarbiat Modares University; Tehran Iran
| | - A. A. Masoudi
- Department of Animal Science; Faculty of Agriculture; Tarbiat Modares University; Tehran Iran
| | - R. Vaez Torshizi
- Department of Animal Science; Faculty of Agriculture; Tarbiat Modares University; Tehran Iran
| | - E. W. Hill
- Animal Genomics Laboratory; School of Agriculture; Food Science and Veterinary Medicine; College of Life Sciences; University College Dublin; Belfield Dublin Ireland
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Warmuth V, Manica A, Eriksson A, Barker G, Bower M. Autosomal genetic diversity in non-breed horses from eastern Eurasia provides insights into historical population movements. Anim Genet 2012; 44:53-61. [PMID: 22607477 DOI: 10.1111/j.1365-2052.2012.02371.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2012] [Indexed: 12/22/2022]
Abstract
Many events in the history of eastern Eurasia, including the process of domestication itself, the initial spread of domestic horses and subsequent movements, are believed to have affected the genetic structure of domestic horse populations in this area. We investigated levels of within- and between-population genetic diversity in 'non-breed horses' (working horses sampled in remote areas) from 17 locations in Asia and parts of Eastern Europe, using 26 autosomal microsatellite loci. Non-breed horses have not been subject to the same intensity of artificial selection and closed breeding as have most breed animals and are thus expected to better reflect the population history of domestic horses. Despite geographic distances of between 300 and 7000 km between sampling locations, pairwise F (ST) was very low (range: <0.001 to -0.033), suggesting historically high levels of gene flow. Our analyses of non-breed horses revealed a pattern of isolation by distance and a significant decline in genetic diversity (expected heterozygosity and allelic richness) from east to west, consistent with a westward expansion of horses out of East Asia. Although the timing of this putative expansion is unclear, our results highlight the benefit of studying animals that do not belong to particular breeds when investigating aspects of a population's history.
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Affiliation(s)
- Vera Warmuth
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
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Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol Biol 2011; 11:328. [PMID: 22082251 PMCID: PMC3247663 DOI: 10.1186/1471-2148-11-328] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 11/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. RESULTS In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago. CONCLUSIONS Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.
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Affiliation(s)
- Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
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Koban E, Denizci M, Aslan O, Aktoprakligil D, Aksu S, Bower M, Balcioglu BK, Ozdemir Bahadir A, Bilgin R, Erdag B, Bagis H, Arat S. High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia. Anim Genet 2011; 43:401-9. [PMID: 22497212 DOI: 10.1111/j.1365-2052.2011.02285.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia's role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.
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Affiliation(s)
- E Koban
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Kocaeli, Turkey
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Voronkova VN, Tsedev T, Sulimova GE. Comparative analysis of the informativeness of ISSR markers for estimating genetic diversity of horse breeds. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411080175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A. Origin and history of mitochondrial DNA lineages in domestic horses. PLoS One 2010; 5:e15311. [PMID: 21187961 PMCID: PMC3004868 DOI: 10.1371/journal.pone.0015311] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/08/2010] [Indexed: 11/18/2022] Open
Abstract
Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.
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Affiliation(s)
- Michael Cieslak
- Leibniz Institute for Zoo and Wildlife Research, Evolutionary Genetics, Berlin, Germany
| | - Melanie Pruvost
- Leibniz Institute for Zoo and Wildlife Research, Evolutionary Genetics, Berlin, Germany
- German Archaeological Institute, Berlin, Germany
- * E-mail: (AL); (MP)
| | | | - Michael Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, The University of York, Heslington, York, United Kingdom
| | - Arturo Morales
- Laboratory of Archaeozoology, Universidad Autonoma Madrid, Madrid, Spain
| | - Monika Reissmann
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - Arne Ludwig
- Leibniz Institute for Zoo and Wildlife Research, Evolutionary Genetics, Berlin, Germany
- * E-mail: (AL); (MP)
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Abstract
International interest in the prehistory and archaeology of the Eurasian steppes and Mongolia has increased dramatically since the collapse of the Soviet Union in 1991. This article surveys important new evidence and interpretations that have emerged from several collaborative projects in the past two decades. A particular emphasis is placed on issues that are crucial to regional studies in the steppe ecological zone; however, it also is suggested that steppe prehistory must come to play a more significant role in developing more comprehensive understandings of world prehistory. Key developments connected with the steppe include the diffusion of anatomically modern humans, horse domestication, spoke-wheeled chariot and cavalry warfare, early metal production and trade, Indo-European languages, and the rise of nomadic states and empires. In addition to these important issues, thoughts are offered on some of the current challenges that face archaeological scholarship in this region of the world.
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Affiliation(s)
- Bryan Hanks
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, Barrett E, Cassidy R, Nisbet RER, Hill EW, Howe CJ, Binns M. The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biol Lett 2010; 7:316-20. [PMID: 20926431 PMCID: PMC3061175 DOI: 10.1098/rsbl.2010.0800] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The paternal origins of Thoroughbred racehorses trace back to a handful of Middle Eastern stallions, imported to the British Isles during the seventeenth century. Yet, few details of the foundation mares were recorded, in many cases not even their names (several different maternal lineages trace back to ‘A Royal Mare’). This has fuelled intense speculation over their origins. We examined mitochondrial DNA from 1929 horses to determine the origin of Thoroughbred foundation mares. There is no evidence to support exclusive Arab maternal origins as some historical records have suggested, or a significant importation of Oriental mares (the term used in historic records to refer to Middle East and western Asian breeds including Arab, Akhal-Teke, Barb and Caspian). Instead, we show that Thoroughbred foundation mares had a cosmopolitan European heritage with a far greater contribution from British and Irish Native mares than previously recognized.
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Affiliation(s)
- M A Bower
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
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Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, Zhang YS, Zhang CM, Chen H. Multiple maternal origins of native modern and ancient horse populations in China. Anim Genet 2009; 40:933-44. [PMID: 19744143 DOI: 10.1111/j.1365-2052.2009.01950.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C Z Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
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Priskin K, Szabó K, Tömöry G, Bogácsi-Szabó E, Csányi B, Eördögh R, Downes CS, Raskó I. Mitochondrial sequence variation in ancient horses from the Carpathian Basin and possible modern relatives. Genetica 2009; 138:211-8. [PMID: 19789983 DOI: 10.1007/s10709-009-9411-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
Movements of human populations leave their traces in the genetic makeup of the areas affected; the same applies to the horses that move with their owners This study is concerned with the mitochondrial control region genotypes of 31 archaeological horse remains, excavated from pre-conquest Avar and post-conquest Hungarian burial sites in the Carpathian Basin dating from the sixth to the tenth century. To investigate relationships to other ancient and recent breeds, modern Hucul and Akhal Teke samples were also collected, and mtDNA control region (CR) sequences from 76 breeds representing 921 individual specimens were combined with our sequence data. Phylogenetic relationships among horse mtDNA CR haplotypes were estimated using both genetic distance and the non-dichotomous network method. Both methods indicated a separation between horses of the Avars and the Hungarians. Our results show that the ethnic changes induced by the Hungarian Conquest were accompanied by a corresponding change in the stables of the Carpathian Basin.
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Affiliation(s)
- K Priskin
- Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.
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43
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Kavar T, Dovč P. Domestication of the horse: Genetic relationships between domestic and wild horses. Livest Sci 2008. [DOI: 10.1016/j.livsci.2008.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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