FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Mammalian genome : official journal of the International Mammalian Genome Society2024; 36(1); 118-128; doi: 10.1007/s00335-024-10089-6

Unraveling the maternal heritage: identifying the complex origins of indigenous Indian horse and pony breeds through mitochondrial genome analysis.

Abstract: This study explored the maternal genetic diversity of six indigenous Indian horse and pony breeds (Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari) using comprehensive mitochondrial genome (mitogenome) analysis. Blood samples from 53 horses across diverse agro-climatic zones of India were analyzed, revealing 36 distinct haplotypes, with a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices suggest significant maternal genetic diversity in Indian equines. A median-joining (MJ) network, based on the hypervariable region of the D-loop along with sequences of Indian equids retrieved from the NCBI, identified 55 haplotypes, including shared haplotypes across 2-5 breeds. Hierarchical AMOVA analysis revealed that 95.20% of genetic variation was within populations, while only 4.80% was among different groups, indicating minimal genetic structuring based on geographic distribution. Phylogenetic analysis of these mitogenomes, alongside global sequences, revealed significant genetic variability without clear geographic clustering, highlighting extensive gene flow and interbreeding across regions. Median-Joining network based on D-loop sequence revealed that Indian horses conform to seven of the 18 globally recognized haplogroups (A, B, G, J, L, M, and P), with haplogroup A being the most frequent. This research contributes to the broader understanding of equine genetic diversity, aligning with global patterns of extensive maternal haplotype diversity, and underscores the intricate genetic backgrounds resulting from historical breeding practices.
© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Get Full Text
Publication Date: 2024-12-04 PubMed ID: 39630294PubMed Central: 3289334DOI: 10.1007/s00335-024-10089-6Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research investigated the genetic diversity of six indigenous Indian horse and pony breeds through mitochondrial genome analysis. This genetic diversity of these breeds is substantial and does not exhibit strong geographical clustering, suggesting an extensive history of breeding across regions.

Research Method

  • The study used comprehensive mitochondrial genome analysis to explore the maternal genetic diversity of six indigenous Indian horse and pony breeds. These were Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari breeds.
  • Blood samples from 53 horses from various climatic regions of India were analyzed. The analysis revealed 36 distinct genetic variations known as haplotypes.

Major Findings

  • The genetic analysis showed a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices signify a significant level of maternal genetic diversity in Indian equine populations.
  • A technique called a median-joining (MJ) network was employed to get a better understanding of this genetic diversity. Along with NCBI retrieved sequences of Indian equids, the network identified 55 haplotypes, indicating shared genetics across 2 to 5 breeds.
  • The hierarchical AMOVA analysis results showed that 95.20% of genetic variation was within populations, while only 4.80% was among different groups. This implies a minimal influence of geographic distribution on genetic differentiation in these Indian equine breeds.
  • Phylogenetic analysis, which looks at the evolutionary relationships between species, of the mitochondrial genomes showed significant genetic variability without clear geographic clustering. This indicates that there has been high gene flow and interbreeding across different regions.
  • The median-joining network based on D-loop sequence revealed that Indian horses belong to seven of the 18 globally recognized haplogroups (A, B, G, J, L, M, and P), with haplogroup A being the most common. This data supports the view of globally extensive maternal haplotype diversity in horses.

Implications of the Research

  • The research provides insights into the extensive maternal genetic diversity in Indian equine populations. The detected genetic diversity is not necessarily due to geographical location but likely from extensive interbreeding throughout history, an insight that can be applied globally for equine genetic diversity.
  • This research also contributes to the understanding of the intricate genetic backgrounds resulting from historical breeding practices. It strengthens the argument for considering maternal genetic diversity when defining breeds for conservation purposes.

Cite This Article

APA
Ahlawat S, Sharma U, Niranjan SK, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK, Mehta SC. (2024). Unraveling the maternal heritage: identifying the complex origins of indigenous Indian horse and pony breeds through mitochondrial genome analysis. Mamm Genome, 36(1), 118-128. https://doi.org/10.1007/s00335-024-10089-6

Publication

Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
NlmUniqueID: 9100916
Country: United States
Language: English
Volume: 36
Issue: 1
Pages: 118-128

Researcher Affiliations

Ahlawat, Sonika
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India. sonika.ahlawat@gmail.com.
Sharma, Upasna
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Niranjan, S K
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Chhabra, Pooja
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Arora, Reena
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Sharma, Rekha
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Singh, Karan Veer
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Vijh, R K
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
Mehta, S C
  • Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner, India.

MeSH Terms

  • Animals
  • Horses / genetics
  • Horses / classification
  • Genome, Mitochondrial
  • Haplotypes
  • Phylogeny
  • India
  • Genetic Variation
  • Breeding
  • Female
  • Maternal Inheritance
  • DNA, Mitochondrial / genetics

Conflict of Interest Statement

Declarations. Competing interests: The authors declare no competing interests.

References

This article includes 49 references
  1. Achilli A, Olivieri A, Soares P, Lancioni H, Kashani BH, Perego UA. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.. Proc Natl Acad Sci 109(7):2449.
    pubmed: 22308342pmc: 3289334doi: 10.1073/pnas.1111637109google scholar: lookup
  2. Ahlawat S, Sharma U, Arora R, Sharma R, Chhabra P, Singh KV, Vijh RK. Mitogenomic phylogeny reveals the predominance of the nubian lineage of African wild ass in Indian donkeys.. Gene 880:147627.
    pubmed: 37429369doi: 10.1016/j.gene.2023.147627google scholar: lookup
  3. Ahlawat S, Niranjan SK, Arora R, Vijh RK, Kumar A, Sharma U, Raheja M, Popli K, Sadav S, Mehta SC. Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.. Funct Integr Genomics 24:195.
    pubmed: 39441226doi: 10.1007/s10142-024-01482-0google scholar: lookup
  4. Ahlawat S, Sharma U, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK. Maternal genetic diversity and phylogenetic analysis of Indian riverine and swamp buffaloes: insights from complete mitochondrial genomes.. Mamm Genome .
    doi: 10.1007/s00335-024-10048-1pubmed: 39738581google scholar: lookup
  5. Ayad LAK, Pissis SP. MARS: improving multiple circular sequence alignment using refined sequences.. BMC Genom 18(1):86.
    doi: 10.1186/s12864-016-3477-5google scholar: lookup
  6. Bandelt H, Forster P, Rohl A. Median joining networks for inferring intraspecific phylogenies.. Mol Biol Evol 16:37–48.
    pubmed: 10331250doi: 10.1093/oxfordjournals.molbev.a026036google scholar: lookup
  7. Behl R, Behl J, Gupta N, Gupta SC, Ahlawat SPS, Ragnekar M, Katoch S, Ahmed Z. Genetic closeness of Zanskari and Spiti ponies of India inferred through microsatellite markers.. J Equine Vet Sci 26:257–261.
    doi: 10.1016/j.jevs.2006.04.002google scholar: lookup
  8. Behl R, Behl J, Gupta N, Gupta SC. Genetic relationships of five Indian horse breeds using microsatellite markers.. Animal 4:483–488.
    doi: 10.1017/S1751731107694178google scholar: lookup
  9. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. MITOS: Improved de novo metazoan mitochondrial genome annotation.. Mol Phylogenet Evol 69(2):313–319.
    pubmed: 22982435doi: 10.1016/j.ympev.2012.08.023google scholar: lookup
  10. Cardinali I, Lancioni H, Giontella A, Capodiferro MR, Capomaccio S, Buttazzoni L. An overview of ten Italian horse breeds through mitochondrial DNA.. PLoS ONE 11:e0153004.
    pubmed: 27054850pmc: 4824442doi: 10.1371/journal.pone.0153004google scholar: lookup
  11. Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M, Prabhu A, Bucca S, Bugno-Poniewierska M, Wallner B, Malek J, Miller DC, Clark AG, Antczak DF, Brooks SA. Genome diversity and the origin of the arabian horse.. Sci Rep 10(1):9702.
    pubmed: 32546689pmc: 7298027doi: 10.1038/s41598-020-66232-1google scholar: lookup
  12. Czerneková V, Kott T, Majzlík I. Mitochondrial D-loop sequence variation among Hucul horse.. Czech J Anim Sci 58(10):437–442.
    doi: 10.17221/6992-CJASgoogle scholar: lookup
  13. Delsol N, Stucky BJ, Oswald JA, Reitz EJ, Emery KF, Guralnick R. Analysis of the earliest complete mtDNA genome of a Caribbean colonial horse (Equus caballus) from 16th-century Haiti.. PLoS ONE 17(7):e0270600.
    pubmed: 35895670pmc: 9328532doi: 10.1371/journal.pone.0270600google scholar: lookup
  14. Devi KM, Ghosh SK. Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop.. Mol Biol Rep 40:5861–5867.
    pubmed: 24068432doi: 10.1007/s11033-013-2692-2google scholar: lookup
  15. Diwedi J, Singh AW, Ahlawat S, Sharma R, Arora R, Sharma H, Raja KN, Verma NK, Tantia MS. Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats.. Gene 756:144910.
    pubmed: 32574758doi: 10.1016/j.gene.2020.144910google scholar: lookup
  16. Engel L, Becker D, Nissen T, Russ I, Thaller G, Krattenmacher N. Exploring the origin and relatedness of maternal lineages through analysis of mitochondrial DNA in the Holstein horse.. Front Genet 12:632500.
    pubmed: 34335677pmc: 8320364doi: 10.3389/fgene.2021.632500google scholar: lookup
  17. Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.. Mol EcolResour 10(3):564–567.
  18. Gáspárdy A, Wagenhoffer Z, Fürlinger D, Halmágyi M, Bodó I, Lancioni H, Maróti-Agóts. Matrilineal composition of the reconstructed stock of the Szekler horse breed.. Agriculture 13:456.
  19. Guo X, Pei J, Bao P, Zhou Y, Wu X, Liang C, Ding X, Yan P. Complete mitochondrial genome of Equus caballus (Datong horse).. Mitochondrial DNA Part B 4:1.
  20. Gupta AK, Chauhan M, Bhardwaj A, Gupta N, Gupta SC, Pal Y, Tandon SN, Vij RK. Comparative genetic diversity analysis among six Indian breeds and English Thoroughbred horses.. Livest Sci 163(5):1–11.
    doi: 10.1016/j.livsci.2014.01.028google scholar: lookup
  21. Gupta AK, Chauhan M, Bhardwaj A, Vijh RK. Assessment of demographic bottleneck in Indian horse and endangered pony breeds.. J Genet 94:e56–e62.
    pubmed: 26708456doi: 10.1007/s12041-015-0570-5google scholar: lookup
  22. Hristov P, Yordanov G, Ivanova A, Mitkov I, Sirakova D, Mehandzyiski I, Radoslavov G. Mitochondrial diversity in mountain horse population from the South-Eastern Europe.. Mitochondrial DNA DNA Mapp Seq Anal 28(6):787–792.
  23. Ianella P, Albuquerque MSM, Paiva SR, Egito AA, Almeida LD, Sereno FTPS, Carvalho LFR, Mariante AS, McManus CM. D-loop haplotype diversity in Brazilian horse breeds.. Genet Mol Biol 40(3):604–609.
    pubmed: 28863209pmc: 5596364doi: 10.1590/1678-4685-gmb-2016-0166google scholar: lookup
  24. Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C. Mitochondrial DNA and the origins of the domestic horse.. Proc Natl Acad Sci 99(16):10905.
    pubmed: 12130666pmc: 125071doi: 10.1073/pnas.152330099google scholar: lookup
  25. Ji JY, Li WX, Wang AT, Zhang Y. MitoFlex: an efficient, high-performance toolkit for animal mitogenome assembly, annotation and visualization.. Bioinform 37(18):3001–3003.
    doi: 10.1093/bioinformatics/btab111google scholar: lookup
  26. Khanshour AM, Cothran EG. Maternal phylogenetic relationships and genetic variation among arabian horse populations using whole mitochondrial DNA D-loop sequencing.. BMC Genet 14:83.
    pubmed: 24034565pmc: 3847362doi: 10.1186/1471-2156-14-83google scholar: lookup
  27. Khrabrova LA, Blohina NV, Bazaron BZ, Khamiruev TN. Variability of mitochondrial DNA D-loop sequences in Zabaikalskaya horse breed.. Vavilov J Genet Breed 25:486–491.
    doi: 10.18699/VJ21.055google scholar: lookup
  28. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms.. Mol Biol Evol 35(6):1547–1549.
    pubmed: 29722887pmc: 5967553doi: 10.1093/molbev/msy096google scholar: lookup
  29. Kvist L, Niskanen M. Modern northern domestic horses carry mitochondrial DNA similar to Przewalski’s horse.. J Mammal Evol 28:371–376.
    doi: 10.1007/s10914-020-09517-6google scholar: lookup
  30. Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L. The origins and spread of domestic horses from the western eurasian steppes.. Nature 1–7.
  31. 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 11:328.
    pubmed: 22082251pmc: 3247663doi: 10.1186/1471-2148-11-328google scholar: lookup
  32. Lira J, Linderholm A, Olaria C, Brandström Durling M, Gilbert MTP, Ellegren H. Ancient DNA reveals traces of Iberian neolithic and bronze age lineages in modern Iberian horses.. Mol Ecol 19(1):64–78.
    pubmed: 19943892doi: 10.1111/j.1365-294X.2009.04430.xgoogle scholar: lookup
  33. Luikart G, Gielly L, Excoffier L, Vigne JD, Bouvet J, Taberlet P. Multiple maternal origins and weak phylogeographic structure in domestic goats.. Proc Natl Acad Sci 98(10):5927–5932.
    pubmed: 11344314pmc: 33315doi: 10.1073/pnas.091591198google scholar: lookup
  34. McGahern A, Bower MAM, 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 37:494–497.
    pubmed: 16978180doi: 10.1111/j.1365-2052.2006.01495.xgoogle scholar: lookup
  35. Moridi M, Masoudi AA, Vaez Torshizi R, Hill EW. Mitochondrial DNA D-loop sequence variation in maternal lineages of Iranian native horses.. Anim Genet 44(2):209–213.
    pubmed: 22732008doi: 10.1111/j.1365-2052.2012.02389.xgoogle scholar: lookup
  36. Pal Y, Bhardwaj A, Legha RA, Talluri TR, Mehta SC, Tripathi BN. Phenotypic characterization of Kachchhi-Sindhi horses of India.. Indian J Anim Resear 10:4221.
  37. Pal Y, Legha RA, Bhardwaj A, Tripathi BN. Status and conservation of equine biodiversity in India.. Indian J Comp Microbiol Immunol Infect Dis 41(2):174–184.
  38. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space.. Syst Biol 61(3):539–542.
    pubmed: 22357727pmc: 3329765doi: 10.1093/sysbio/sys029google scholar: lookup
  39. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, RamosOnsins SE, Sánchez-Gracia A. DnaSP 6: DNA sequence polymorphism analysis of large datasets.. Mol Biol Evol 34:3299–3302.
    pubmed: 29029172doi: 10.1093/molbev/msx248google scholar: lookup
  40. Sai Satyanarayana D, Ahlawat S, Sharma R, Arora R, Sharma A, Tantia MS, Vijh RK. Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels.. Gene 820:146279.
    doi: 10.1016/j.gene.2022.146279google scholar: lookup
  41. Sambrook J, Russell DW. Molecular cloning: a Laboratory Manuel III.. .
  42. Sharma R, Kishore A, Mukesh M, Ahlawat S, Maitra A, Pandey AK, Tantia MS. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers.. BMC Genet 16:73–84.
    pubmed: 26123673pmc: 4485874doi: 10.1186/s12863-015-0221-0google scholar: lookup
  43. Sharma R, Ahlawat S, Sharma H, Sharma P, Panchal P, Arora R, Tantia MS. Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agroecological regions of India.. Sci Rep 10:20422.
    pubmed: 33235268pmc: 7687881doi: 10.1038/s41598-020-77480-6google scholar: lookup
  44. Sharma A, Ahlawat S, Sharma R, Arora R, Singh KV, Malik D, Banik S, Singh TR, Tantia MS. Tracing the genetic footprints: India’s role as a gateway for pig migration and domestication across continents.. Anim Biotechnol 34(9):5173–5179.
    pubmed: 37847106doi: 10.1080/10495398.2023.2268683google scholar: lookup
  45. Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia.. Saudi J Biol Sci 30:103741.
    pubmed: 37575470pmc: 10413190doi: 10.1016/j.sjbs.2023.103741google scholar: lookup
  46. Vilà C, Leonard JA, Götherström A, Marklund S, Sandberg K, Lidén K. Widespread origins of domestic horse lineages.. Science 291(5503):474–477.
    pubmed: 11161199doi: 10.1126/science.291.5503.474google scholar: lookup
  47. Wolfsberger WW, Ayala NM, Castro-Marquez SO, Irizarry-Negron VM, Potapchuk A, Shchubelka K, Potish L, Majeske AJ, Oliver LF, Lameiro AD, Martínez-Cruzado JC, Lindgren G, Oleksyk TK. Genetic diversity and selection in Puerto Rican horses.. Sci Rep 12(1):515.
    pubmed: 35017609pmc: 8752667doi: 10.1038/s41598-021-04537-5google scholar: lookup
  48. Yang L, Kong X, Yang S, Dong X, Yang J, Gou X. Haplotype diversity in mitochondrial DNA reveals the multiple origins of tibetan horse.. PLoS ONE 13(7):e0201564.
    pubmed: 30052677pmc: 6063445doi: 10.1371/journal.pone.0201564google scholar: lookup
  49. Yoon SH, Lee W, Ahn H, Caetano-Anolles K, Park K-D, Kim H. Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: phylogenomic and bayesian coalescent perspectives.. PLoS ONE 13(9):e0203917.
    pubmed: 30216366pmc: 6138400doi: 10.1371/journal.pone.0203917google scholar: lookup

Citations

This article has been cited 2 times.
  1. Saldaña CL, Justo S, Murga L, Vásquez HV, Maicelo JL, Arbizu CI, Bardales W. Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing. Sci Rep 2025 Dec 21;16(1):85.
    doi: 10.1038/s41598-025-29107-xpubmed: 41423464google scholar: lookup
  2. Sharma M, Singh A, Kumar V, Olla N, Arora R, Sharma R, Mohan NH, Ahlawat S. Advances in Equine Genomics: Decoding the Genetic Architecture of Morphology, Performance, Behavior, and Adaptation. Mol Biotechnol 2025 Dec 19;.
    doi: 10.1007/s12033-025-01544-zpubmed: 41417456google scholar: lookup
Subscribe to our newsletter
Join 99,727 horse owners like you who receive our email updates on horse health and nutrition.