Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing
- Published
- Accepted
- Subject Areas
- Biodiversity, Conservation Biology, Genetics, Veterinary Medicine, Zoology
- Keywords
- Equus caballus, genetic diversity, mtDNA, D-loop region, Hungarian Draft horse
- Copyright
- © 2017 Csizmár et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing. PeerJ Preprints 5:e3087v1 https://doi.org/10.7287/peerj.preprints.3087v1
Abstract
Background. Hungarian draft is a horse breed with a recent mixed ancestry. The interest in their conservation and characterization has increased over the last few years. It was developed in the 1920s by crossing local mares with draught horses imported from France and Belgium. 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 programme, in this present study a hypervariable region of the mithocrondial 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 were revealed. 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 populations, although they were higher within than among the total number of breeds (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 were no clear clustering on the median joining tree. The overall information given in this work led us to consider that the genetic scenario of this breed is more likely to be due to ‘ancestrally’ different genetic backrounds. This study could contribute to the development of a detailed breeding plan of Hungarian draft horse and help to formulate its genetic conservation plan, with the aim of increasing the population size, but avoiding inbreeding while, on the other hand, also facilitating genetic exchange among the populations.
Author Comment
In this work, we followed genetic diversity among Hungarian draft horse breed, through the use of mitochondrial DNA. Up-to-date, no other comprehensive/extensive study has been undertaken to evaluate the genetic diversity of Eastern European horse breed. In addition, we performed a comparative analysis between the Hungarian draft horse and that of 419 mtDNA from GenBank in order to reveal genetic relationships of the studied populations with other breeds worldwide. We consider current results to be of importance for the conservation efforts of the Draft horse breed found in Eastern-Central and Southern Europe.
We believe that these results are of interest for the readers of PeerJ journal, and correspond to the scope of the journal. We hereby state that this work is original and has not been published or accepted for publication elsewhere, and is not being under consideration for submission to another journal. The current submission has been approved by all authors, and all persons entitled to authorship have been so named. Looking forward to your decisions regarding the manuscript revision process, at your earliest convenience.
Supplemental Information
A maximum likelihood tree represents the phylogenetic relationship among 285 partial mtDNA D-loop sequences from members of the genus Equus including haplotypes of the Hungarian draft and reference sequence
The phylogenetic tree was based on the Tamura-Nei model of evolution with gamma distribution of rates and 1,000 bootstrap replicates (Tamura & Nei, 1993). Different colors represent different haplogroups differentiated by sequence motifs of the mtDNA clusters by [25]: A1 (light purple), A2 (dark blue), A5 (brown), A6 (light blue), B1 (yellow), B2 (turquoise), C1 (dark green), C2 (red), D2 (mustard yellow), D3 (dark purple), E (black), F1 (grey), F2 (light green), G (orange). The red square represents the reference sequence.
Median network of horse haplotypes
Included are those of the 285 Hungarian draft individuals analysed in this study, plus sequences of European breeds available in the Genbank nucleotide database. Sectors are proportional to the frequency of each haplotype. Horizontal bars represent the mutational steps. MH, Hungarian draft, our samples (number of samples: 285); Rin, Rhineland Heavy draft (25); Nori, Noriker (10); Tat, Turkoman Akhal Teke (19); Ital, Italian heavy draught (27); Bre, Breton (58); Arb, Arabian (10); Fin, Finn horse (2); PP, Polish primitiv (3); HC, Hucul (10); Zem, Zemaitukai heavy type (7); Shi, Shire (10); Vlad, Vladimir draught horse (21); Cly, Clydesdale (17); Irn, Iranian (14); Tra, Trakehner (4); Csp, Caspian Pony (5); Ph, Polish heavy (3); Mrn, Maremmano (15); Pos, Posavina (20); Akt, Akhal teke (16); Shet, Shetland pony (12); Pur, Pura Raza Espanola (17); Hhv, Croatian heavy draft (11); Mur, Murinsulaner (8); Fell, Fell (2); Ic, Icelandic Horse (2); Nf, Norwegian Fjord (2); Rom, Romanian draft horse (1); Per, Percheron (3); Lhd, Lithuanian heavy drought (3); Old, Oldenburg (1); And, Andalusian (2); Sil, Silesian (1); Ital, Italian (3); Sc, Scottish Highland (2); Be, Belgian (13); Tho, Thoroughbred horse (1); Aph, American Paint horse (1); Han, Hanovarian (3); Wiel, Wielkopolski (3); Syr, Syrian (5); Gia, Giara horse (2); His, Holstein (2); Prze, Przewalskii (3); Got, Gotland (3); Sf, Suffolk Punch (1); West, Westfalian (1); Chin, Chincoteague pony (1); Cle, Cleveland bay horse (11); Sad, Saddlebred (1); Ex, Exmoor pony (1).
Matrix of pairwase FST values
Significance level=0.05.
Polymorphic sites in the control region of the Hungarian draft horse population sequenced
Nucleotide positions 15531–15752 as compared to GenBank reference sequence X79547 [11]. Sequence identity is indicated by ‘.’, gaps by ‘-‘.