Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types

Szmatoła, Tomasz; Gurgul, Artur; Jasielczuk, Igor; Ocłoń, Ewa; Ropka‐Molik, Katarzyna; Stefaniuk‐Szmukier, Monika; Polak, Grażyna; Tomczyk-Wrona, Iwona; Bugno‐Poniewierska, Monika

doi:10.3390/ani12233293

Cited by 9 publications

(5 citation statements)

References 75 publications

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“…In our study, the ROH islet, including the QDPR and FAM184B genes, was found in the Soviet Heavy Draft horse breed, while in the work of Szmatoła et al, it was observed only in draft horses [33]. A homozygous region comprising the FGF5 gene, which are mutations that are associated with coat length in donkeys, has been found in American Standardbred horses [34] and is associated with the disease degenerative suspensory ligament desmitis [35].…”

Section: Discussionsupporting

confidence: 43%

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The Genetic Diversity of Stallions of Different Breeds in Russia

Дементьева

Nikitkina

Shcherbakov

et al. 2023

Genes

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The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heterozygous and homozygous ROH regions, evaluated inbreeding using FROH analysis, and generated a population structure using Admixture 1.3 software. Our findings indicate that the Arabian breed is an ancestor of many horse breeds. The study of the full-genome architectonics of breeds is of great practical importance for preserving the genetic characteristics of breeds and managing breeding. Studies were carried out to determine homozygous regions in individual breeds and search for candidate genes in these regions. Fifty-six candidate genes for the influence of selection pressure were identified. Our research reveals genetic diversity consistent with breeding directions and the breeds’ history of origin.

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Section: Discussionsupporting

confidence: 43%

“…A gene belonging to the ZNF gene family, which plays a key role in the regulation of muscle growth and differentiation, was also found in ECA11. The discovered gene may be associated with selection pressure for strength, endurance, and a high percentage of muscle tissue, especially in draft breeds [33].…”

Section: Discussionmentioning

confidence: 99%

The Genetic Diversity of Stallions of Different Breeds in Russia

Дементьева

Nikitkina

Shcherbakov

et al. 2023

Genes

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“…Numerous studies have demonstrated that same overlapping ROH segments between multiple individuals, so-called ROH islands, also highlight genetic regions that have been under selection, in cattle [ 7 , 8 ], sheep [ 9 – 11 ], and honeybees [ 12 ]. In horses, based on different genotyping platforms and ROH settings, numerous breed-specific ROH islands have already been identified that include genes associated with behaviour [ 13 , 14 ], coat colour [ 14 – 18 ], coat quality [ 19 ], fertility [ 13 , 18 – 22 ], size [ 15 , 22 ], skeletal development [ 18 , 19 , 23 ], muscle growth [ 24 ], geographical adaptations [ 14 , 25 ], and gait quality [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed

Gmel,

Mikko,

Ricard

et al. 2024

Genet Sel Evol

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Background The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity. Results To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. Conclusions The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.

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“…Horses have been selected based on conformation traits for centuries, resulting in diverse breeds with specific use (heavy type draught horses, light type sport horses, small ponies, etc.) 1 – 3 . Some traits, such as the concave (dished) head shape in the Arabian horse, are breed-specific and essentially aesthetic.…”

Section: Introductionmentioning

confidence: 99%

New genomic insights into the conformation of Lipizzan horses

Gmel

Brem

Neuditschko

2023

Sci Rep

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Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses. Based on this data, we identified significant quantitative trait loci (QTL) associated with cresty neck on equine chromosome (ECA)16 within the MAGI1 gene, and with type, hereby differentiating heavy from light horses on ECA5 within the POU2F1 gene. Both genes were previously described to affect growth, muscling and fatty deposits in sheep, cattle and pigs. Furthermore, we pin-pointed another suggestive QTL on ECA21, near the PTGER4 gene, associated with human ankylosing spondylitis, for shape differences in the back and pelvis (roach back vs sway back). Further differences in the shape of the back and abdomen were suggestively associated with the RYR1 gene, involved in core muscle weakness in humans. Therefore, we demonstrated that horse shape space data enhance the genomic investigations of horse conformation.

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Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types

Cited by 9 publications

References 75 publications

The Genetic Diversity of Stallions of Different Breeds in Russia

The Genetic Diversity of Stallions of Different Breeds in Russia

Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed

New genomic insights into the conformation of Lipizzan horses

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