Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse

Kang, Zhensheng; Shi, Jing; Lu, Guanting; Zhang, Yong; Zhang, Quanwei; Li, Zhe; Wang, Jianfu; ShuRu, Cheng

doi:10.5713/ab.23.0044

Cited by 2 publications

(4 citation statements)

References 30 publications

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“…Other authors have studied the origin of Akhal-Teke horses [24]. The data obtained on ADMIXTURE and PCA of Syrian Arabian horses and Akhal-Teke horses are fully consistent with our data, and confirm the origin of the Akhal-Teke breed from eastern horses.…”

Section: Discussionsupporting

confidence: 90%

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The Genetic Diversity of Horse Native Breeds in Russia

Atroshchenko,

Dementieva,

Shcherbakov

et al. 2023

Genes

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Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k ® array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.

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Section: Discussionsupporting

confidence: 90%

“…ADMIXTURE and PCA results revealed differences between individuals in riding horses (particularly Kabardin and Don breeds), which may be the result of introgression from other breeds. Other studies emphasize that the loss of local breeds' genetic uniqueness is due to the improvement of their sports performance by purebreds [8,24,25].…”

Section: Discussionmentioning

confidence: 99%

The Genetic Diversity of Horse Native Breeds in Russia

Atroshchenko,

Dementieva,

Shcherbakov

et al. 2023

Genes

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“…Akhal-Teke Originated in Turkmenistan, known for ancient lineage whose origin is of much debate (Kang 2023).…”

Section: Agriculturementioning

confidence: 99%

“…We selected 8 varieties of contemporary horses and three Asian landraces (Mongolia, Tibet, and Korea). Of these, several are subjected to high levels of contemporary anthropogenic selective pressure for racing and dressage (Bower 2012, Reviriaud 2002, Rodrigues 2021, Savelkouls 2015, Cosgrove 2020, Kang 2023, Esdaile 2022. Others, such as pastoral horses from Mongolia and Tibet, may have much lower levels of human intervention in their breeding.…”

Section: Horse Case Studymentioning

confidence: 99%

TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

Burke,

Chuong,

Taylor

et al. 2023

Preprint

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Transposable elements (TEs) replicate within genomes and are an active source of genetic variability in many species. Their role in immunity and domestication underscores their biological significance. However, analyzing TEs, especially within lesser-studied and wild populations, poses considerable challenges. To address this, we introduce TEPEAK, a simple and efficient approach to identify and characterize TEs in populations without any prior sequence or loci information. In addition to processing user-submitted genomes, TEPEAK integrates with the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) to increase cohort sizes or incorporate proximate species. Our application of TEPEAK to 256 horse genomes spanning 11 groups reaffirmed established genetic histories and highlighted disruptions in crucial genes. Some identified TEs were also detectable in species closely related to horses. TEPEAK paves the way for comprehensive genetic variation analysis in traditionally understudied populations by simplifying TE studies. TEPEAK is open-source and freely available at https://github.com/mrburke00/TEPEAK.

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Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse

Cited by 2 publications

References 30 publications

The Genetic Diversity of Horse Native Breeds in Russia

The Genetic Diversity of Horse Native Breeds in Russia

TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

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