Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences.
Abstract: There are large populations of indigenous horse () 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 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.
Publication Date: 2018-06-01 PubMed ID: 29868288PubMed Central: PMC5985762DOI: 10.7717/peerj.4896Google Scholar: Lookup
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Summary
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This study investigates the matrilineal genetic diversity and origins of domestic horses in East Asia, using mitochondrial DNA and hypervariable region sequences. The study reveals multiple origins of the maternal lineage of these horses, with some lineages likely originating from East Asia.
Methodology
- To explore the patterns of matrilineal inheritance in domestic horses, a phylogenetic study was conducted. This involved 31 domestic horse mitochondrial DNA genomes along with 317 others sourced from GenBank.
- The updated phylogeny was analyzed in conjunction with a total of 5,180 mitochondrial HVR-1 sequences derived from horses.
Results
- Eighteen diverse haplogroups (Aw-Rw) were revealed from the analysis of the complete mitochondrial genomes.
- Most of these haplogroups had a divergence time that predates the earliest domestication of wild horses approximately 5,800 years ago and transpired during the Upper Paleolithic era (35-10 KYA).
- Some haplogroups showcased geographic patterns. The Lw group had a significantly higher frequency in European horses compared to those from other regions, whereas haplogroups Jw, Rw, and some maternal lineages of Cw were more common in East Asian horses.
- The 5,180 horse mitochondrial HVR-1 sequences fell into nine major haplogroups (A-I).
- A corresponding relationship between the haplotypes of the HVR-1 and those of the whole mitochondrial DNA sequences was established.
- The HVR-1 sequence data suggests that Jw, Rw, and certain haplotypes of Cw may have East Asian origins, while Lw likely originated in Europe.
Conclusions
- This study supports the theory of multiple origin points for the maternal lineage of domestic horses.
- Some of the maternal lineages of these domestic horses are suggested to have originated in East Asia, contributing a fresh perspective to the origins and migration patterns of domestic horses.
Cite This Article
APA
Ma H, Wu Y, Xiang H, Yang Y, Wang M, Zhao C, Wu C.
(2018).
Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences.
PeerJ, 6, e4896.
https://doi.org/10.7717/peerj.4896 Publication
Researcher Affiliations
- 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.
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, China.
- 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.
- 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.
- 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.
Conflict of Interest Statement
The authors declare there are no competing interests.
References
This article includes 30 references
- Achilli A, Bonfiglio S, Olivieri A, Malusà A, Pala M, Hooshiar Kashani B, Perego UA, Ajmone-Marsan P, Liotta L, Semino O, Bandelt HJ, Ferretti L, Torroni A. The multifaceted origin of taurine cattle reflected by the mitochondrial genome.. PLoS One 2009 Jun 1;4(6):e5753.
- Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MC, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt HJ, Torroni A. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2449-54.
- Cai D, Tang Z. Ancient DNA provides new insights into the origin of the Chinese domestic horse. Journal of Archaeological Science 2009;36:835–842.
- 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 Dec 20;5(12):e15311.
- Clutton-brock J. A natural history of domesticated mammals. Praehistorische Zeitschrif 1990;65:73–76.
- Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing.. Nat Methods 2012 Jul 30;9(8):772.
- Ding ZL, Oskarsson M, Ardalan A, Angleby H, Dahlgren LG, Tepeli C, Kirkness E, Savolainen P, Zhang YP. Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA.. Heredity (Edinb) 2012 May;108(5):507-14.
- Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences.. Mol Biol Evol 2005 May;22(5):1185-92.
- Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees.. BMC Evol Biol 2007 Nov 8;7:214.
- Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7.. Mol Biol Evol 2012 Aug;29(8):1969-73.
- Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.. Syst Biol 2003 Oct;52(5):696-704.
- Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Weber J, Olek K. Mitochondrial DNA and the origins of the domestic horse.. Proc Natl Acad Sci U S A 2002 Aug 6;99(16):10905-10.
- 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 Dec;40(6):933-44.
- Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.. Bioinformatics 2009 Jun 1;25(11):1451-2.
- Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H. Limited number of patrilines in horse domestication.. Nat Genet 2004 Apr;36(4):335-6.
- Ling Y, Ma Y, Guan W, Cheng Y, Wang Y, Han J, Jin D, Mang L, Mahmut H. Identification of Y chromosome genetic variations in Chinese indigenous horse breeds.. J Hered 2010 Sep-Oct;101(5):639-43.
- Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M. Discovery of lost diversity of paternal horse lineages using ancient DNA.. Nat Commun 2011 Aug 23;2:450.
- 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 Nov 14;11:328.
- Macfadden BJ. Fossil horses: systematics, paleobiology, and evolution of the family equidae. Earth-Science Reviews 1995;39:129–130.
- McGahern A, Bower MA, Edwards CJ, Brophy PO, Sulimova G, Zakharov I, Vizuete-Forster M, Levine M, Li S, MacHugh DE, Hill EW. Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations.. Anim Genet 2006 Oct;37(5):494-7.
- Outram AK, Stear NA, Bendrey R, Olsen S, Kasparov A, Zaibert V, Thorpe N, Evershed RP. The earliest horse harnessing and milking.. Science 2009 Mar 6;323(5919):1332-5.
- Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.. Mol Ecol Resour 2015 Sep;15(5):1238-42.
- Shi NN, Fan L, Yao YG, Peng MS, Zhang YP. Mitochondrial genomes of domestic animals need scrutiny.. Mol Ecol 2014 Nov;23(22):5393-7.
- Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P. Are cattle, sheep, and goats endangered species?. Mol Ecol 2008 Jan;17(1):275-84.
- Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ. Harvesting the fruit of the human mtDNA tree.. Trends Genet 2006 Jun;22(6):339-45.
- Vilà C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages.. Science 2001 Jan 19;291(5503):474-7.
- Wallner B, Piumi F, Brem G, Müller M, Achmann R. Isolation of Y chromosome-specific microsatellites in the horse and cross-species amplification in the genus Equus.. J Hered 2004 Mar-Apr;95(2):158-64.
- Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds.. PLoS One 2013;8(4):e60015.
- Xu X, Arnason U. The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region.. Gene 1994 Oct 21;148(2):357-62.
- Yang Y, Zhu Q, Liu S, Zhao C, Wu C. The origin of Chinese domestic horses revealed with novel mtDNA variants.. Anim Sci J 2017 Jan;88(1):19-26.
Citations
This article has been cited 3 times.- Kang Z, Shi J, Liu T, Zhang Y, Zhang Q, Liu Z, Wang J, Cheng S. Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse.. Anim Biosci 2023 Oct;36(10):1499-1507.
- Hong JH, Oh CS, Kim S, Kang IU, Shin DH. Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area.. Anim Biosci 2022 Aug;35(8):1141-1150.
- Ma H, Wang S, Zeng G, Guo J, Guo M, Dong X, Hua G, Liu Y, Wang M, Ling Y, Ding X, Zhao C, Wu C. The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data.. Genes (Basel) 2019 Mar 21;10(3).
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