Analysis of the Pedigree and Ancestors of the Cutting Population of the Quarter Horse Breed

Rodrigues, Larissa Yahagi; Faria, Ricardo António da Silva; Silva, Josineudson Augusto Ii. de Vasconcelos

doi:10.1016/j.jevs.2021.103385

Cited by 3 publications

(4 citation statements)

References 30 publications

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“…Recently, many studies have been focused on the loss of biodiversity [ 23 , 24 , 25 ] or the increase in deleterious genotypes [ 26 ] caused by such inbreeding (as reviewed in [ 7 ]). In the last 200 years, the inbreeding practice led to the phenotypical expression at homozygous sites of deleterious variants [ 27 ], as highlighted when the coefficients are calculated in order to evaluate the genetic diversity among different horse breeds [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ,…”

Section: Introductionmentioning

confidence: 99%

Unlocking Horse Y Chromosome Diversity

Cardinali

Giontella

Tommasi

et al. 2022

Genes

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The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.

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Section: Introductionmentioning

confidence: 99%

Unlocking Horse Y Chromosome Diversity

Cardinali

Giontella

Tommasi

et al. 2022

Genes

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“…Due to technical innovations and motorization, military as well as agricultural usage also decreased. The genetic loss of the Furioso-North Star was almost equal to Lusitano [ 43 ] and Maremanno [ 35 ] horses, whereas the estimations for Gidran and Nonius were quite close to Old-Kladruber [ 8 ] and Quarter [ 7 , 40 ].…”

Section: Discussionmentioning

confidence: 99%

“…Several publications in the past few years have described the genetic variability of different breeds of horses based on pedigree analysis. There were studies about world breeds such as English Thoroughbred [ 3 ], Arabian [ 4 , 5 , 6 ], and Quarter Horse [ 7 ] breeds. Furthermore, local breeds such as Old Kladruber [ 8 ], Posavina [ 9 ], and Pura Raza Español [ 10 , 11 ] were analyzed as well.…”

Section: Introductionmentioning

confidence: 99%

Pedigree-Based Description of Three Traditional Hungarian Horse Breeds

Klein

Oláh

Mihok

et al. 2022

Animals

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The Mezőhegyes Stud was founded in 1784 where three different horse breeds were developed: the Furioso-North Star, the Gidran, and the Nonius. These breeds were based on the same mare population, but each breed had different utilization purposes. Our aim was to analyze the pedigree information of these three indigenous breeds. The genealogical information was traced back from the actual breeding population back to the founder animals, and the final database contained more than 47,000 horses. The reference populations were defined as the registered breeding animals in 2019. The complete generation equivalent was 16.45 for the Gidran breed, 15.18 for Furioso-North Star, and 12.64 for Nonius, respectively. Due to the utilization of English Thoroughbred during the breeding history, the average maximum generations were close to 36 generations for each breed. The average relatedness was approximately 4%. The average Wright’s inbreeding coefficient was the highest for the Nonius breed (5.59%). Kalinowski’s decomposition of inbreeding showed that inbreeding is originated mainly from the past; the current fixation of alleles was higher for the Nonius horse breed. There was a reasonable bottleneck effect for each breed. The estimated effective population sizes suggest that there is no problem with the maintaining of Mezőhegyes horse breeds.

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“…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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Analysis of the Pedigree and Ancestors of the Cutting Population of the Quarter Horse Breed

Cited by 3 publications

References 30 publications

Unlocking Horse Y Chromosome Diversity

Unlocking Horse Y Chromosome Diversity

Pedigree-Based Description of Three Traditional Hungarian Horse Breeds

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

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