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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Equids".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 14830

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Dr. Robin E. Everts

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Etalon Inc., Menlo Park, CA 94025,USA
Interests: horse genetics; disease; inheritance; pharmacogenetics

Dr. Samantha A. Brooks

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Guest Editor

Brooks Equine Genetic Lab., Department of Animal Science, Genetic Institute, University of Florida, Gainesville, FL, USA
Interests: equine genetics; genetic disorders; coat color; neurological conditions
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Dear Colleagues,

Advances in genetics enabled us to discern genes and mutations for various phenotypes in horses, including traits for health, performance or coat color. It also has provided avenues to measure actual inbreeding percentages and allows for tools to establish long-term health and conservation of different breeds. All this information can now be used to help breeders be more successful in creating the type of horse they dream of. In this issue, research on all aspects of horse genetics, breeding and reproduction, as well as other topics, will be considered as they guide breeders to this goal. These topics could include molecular genetics, biodiversity, life cycles, and functional gene and regulatory mechanisms in complex traits.

The aim of this Special Issue of Animals is to collate the latest advances and insights from the research fields of (comparative) genetics, regulatory mechanisms, and breeding methods of horse. We strive for this Special Issue to provide a better understanding of the genetic mechanisms underlying complex traits and provide new approaches to improve the breeding of horses. We welcome the submission of multiple article types, such as original research articles, reviews, methods, etc.

Dr. Robin E. Everts
Dr. Samantha A. Brooks
Guest Editors

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Published Papers (11 papers)

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18 pages, 7388 KiB

Open AccessFeature PaperArticle

A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in Equus caballus

by Rachele Antonacci, Francesco Giannico, Roberta Moschetti, Angela Pala, Anna Caputi Jambrenghi and Serafina Massari

Animals 2024, 14(19), 2817; https://doi.org/10.3390/ani14192817 - 29 Sep 2024

Viewed by 557

Abstract

In this paper, we report a comprehensive and consistent annotation of the locus encoding the β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly using bioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locus among the mammalian species studied to date, with a significantly higher number of genes related to extensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes, were identified. The general genomic organization resembles that of other mammals, with a V cluster of 135 TRBV genes located upstream of two in-tandem aligned TRBD-J-C clusters and an inverted TRBV gene at the 3′ end of the last TRBC gene. However, the horse b-chain repertoire would be affected by a high number of non-functional TRBV genes. Thus, we queried a transcriptomic dataset derived from splenic tissue of a healthy adult horse, using each TRBJ gene as a probe to analyze clonotypes encompassing the V(D)J junction. This analysis provided insights into the usage of the TRBV, TRBD, and TRBJ genes and the variability of the non-germline-encoded CDR3. Our results clearly demonstrated that the horse β-chain constitutes a complex level of variability, broadly like that described in other mammalian species. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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13 pages, 1419 KiB

Open AccessFeature PaperArticle

Exploring the Genetic Landscape of Vitiligo in the Pura Raza Español Horse: A Genomic Perspective

by Nora Laseca, Antonio Molina, Davinia Perdomo-González, Chiraz Ziadi, Pedro J. Azor and Mercedes Valera

Animals 2024, 14(16), 2420; https://doi.org/10.3390/ani14162420 - 21 Aug 2024

Viewed by 1019

Abstract

Vitiligo is a depigmentation autoimmune disorder characterized by the progressive loss of melanocytes leading to the appearance of patchy depigmentation of the skin. The presence of vitiligo in horses is greater in those with grey coats. The aim of this study was therefore to perform a genome-wide association study (GWAS) to identify genomic regions and putative candidate loci associated with vitiligo depigmentation and susceptibility in the Pura Raza Español population. For this purpose, we performed a wssGBLUP (weighted single step genomic best linear unbiased prediction) using data from a total of 2359 animals genotyped with Affymetrix Axiom™ Equine 670 K and 1346 with Equine GeneSeek Genomic Profiler™ (GGP) Array V5. A total of 60,136 SNPs (single nucleotide polymorphisms) present on the 32 chromosomes from the consensus dataset after quality control were employed for the analysis. Vitiligo-like depigmentation was phenotyped by visual inspection of the different affected areas (eyes, mouth, nostrils) and was classified into nine categories with three degrees of severity (absent, slight, and severe). We identified one significant genomic region for vitiligo around the eyes, eight significant genomic regions for vitiligo around the mouth, and seven significant genomic regions for vitiligo around the nostrils, which explained the highest percentage of variance. These significant genomic regions contained candidate genes related to melanocytes, skin, immune system, tumour suppression, metastasis, and cutaneous carcinoma. These findings enable us to implement selective breeding strategies to decrease the incidence of vitiligo and to elucidate the genetic architecture underlying vitiligo in horses as well as the molecular mechanisms involved in the disease’s development. However, further studies are needed to better understand this skin disorder in horses. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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18 pages, 3149 KiB

Open AccessArticle

Gene Expression Analysis before and after the Pelvic Flexure in the Epithelium of the Equine Hindgut

by Cameron D. Moss, Amber L. Wilson, Kailee J. Reed, Kaysie J. Jennings, Isabelle G. Z. Kunz, Gabriele A. Landolt, Jessica Metcalf, Terry E. Engle and Stephen J. Coleman

Animals 2024, 14(16), 2303; https://doi.org/10.3390/ani14162303 - 8 Aug 2024

Viewed by 1249

Abstract

Previous research demonstrated the distribution of distinct microbial communities in the equine hindgut surrounding the pelvic flexure. The current study evaluated gene expression in epithelial tissues surrounding the pelvic flexure to characterize patterns that might correlate with microbial distribution. Gene expression was determined by analyzing RNA sequence data from the pelvic flexure, the left and right ventral colon, and the left and right dorsal colon. An average of 18,330 genes were expressed across the five tissues sampled. Most of the genes showed some level of expression in all five tissues. Tissue-restricted patterns of expression were also observed. Genes with restricted expression in the left ventral and left dorsal colons have communication, signaling, and regulatory functions that correlate with their known physiology. In contrast, genes expressed exclusively in the pelvic flexure have diverse functions. The ontology of genes differentially expressed between the pelvic flexure and the surrounding tissues was associated with immune functions and signaling processes. Despite being non-significant, these enrichment trends were reinforced by the functions of statistically significant expression differences between tissues of the hindgut. These results provide insight into the physiology of the equine hindgut epithelium that might influence the microbiota and its distribution. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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19 pages, 8643 KiB

Open AccessArticle

Comparative Study on the Sperm Proteomes of Horses and Donkeys

by Hong Ren, Xin Wen, Qianqian He, Minna Yi, Manglai Dugarjaviin and Gerelchimeg Bou

Animals 2024, 14(15), 2237; https://doi.org/10.3390/ani14152237 - 31 Jul 2024

Viewed by 735

Abstract

The reproductive performance of horse sperm and donkey sperm has been reported to differ. Sperm proteins play a crucial role in sperm viability and fertility. Although differences between species are known, no prior study has investigated disparities in the sperm proteome between horses and donkeys. Therefore, this study characterized and compared the sperm proteomes of horses and donkeys using 4D-DIA mass spectrometry technology. We identified 3436 proteins in horse sperm and 3404 proteins in donkey sperm. Of these, 3363 proteins were expressed in both horse and donkey sperm, with 73 proteins being specifically expressed in horse sperm, and 41 in donkey sperm. According to data analysis, donkeys exhibited a greater percentage of motility and progressive movement in straight-line sperm than horses, as well as lower percentages of static and slow sperm than horses. Joint analysis of the results from the horse and donkey sperm proteomes and their CEROS II-read parameters demonstrated a possible association between sperm proteins and their sperm viability patterns. These findings suggest that there are discrepancies in the expression levels and protein compositions of horse and donkey sperm and that certain specific proteins may be responsible for the differences in performance between these two species. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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14 pages, 790 KiB

Open AccessArticle

Breeding Value Estimation Based on Morphological Evaluation of the Maremmano Horse Population through Factor Analysis

by Andrea Giontella, Maurizio Silvestrelli, Alessandro Cocciolone, Camillo Pieramati and Francesca Maria Sarti

Animals 2024, 14(15), 2232; https://doi.org/10.3390/ani14152232 - 31 Jul 2024

Viewed by 693

Abstract

Morphological scoring is a common evaluation method for domestic animals. The National Association of Maremmano Breeders (ANAM) has provided a dataset containing the records of 600 horses, four metric measurements (cm) and 24 traits with a continuous evaluation scale, each one with 15 classes. Moreover, a body condition score (BCS) with five classes is included. In this study, factor analysis was conducted to create a small number of informative factors (3) obtained from these traits, and a new BLUP-AM-MT index was established. The New Estimated Breeding Value (NEBV1) of each horse was computed by adding the genetic indexes of the three factors, with each one multiplied using a coefficient indicated by ANAM. The practical feasibility of the NEBV1 was evaluated through Spearman correlations between the rankings of the NEBV1 and the rankings of the BLUP-AM-MT, estimated through the four biometric measures and the morphological score (MS) assigned to each horse by the ANAM judges. The factorial analysis was used to estimate three factors: the “Trunk Dimension”, “Legs” and “Length”. As the explained variance was only 32%, the model was rotated, and the heritability of the three factors were 0.51, 0.05 and 0.41, respectively. After rotation, the estimated correlations between the new NEBV1 and the biometric measures were improved. These results should encourage breeders to adopt a breeding value index that takes into consideration the factors derived from all the variables observed in the morphological evaluation of the Maremmano. In this way, breeders can use it to select the best animals for breeding. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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16 pages, 2508 KiB

Open AccessFeature PaperArticle

Genetic Diversity and Population Structure of Dülmen Wild, Liebenthal and Polish Konik Horses in Comparison with Przewalski, Sorraia, German Draught and Riding Horses

by Silke Duderstadt and Ottmar Distl

Animals 2024, 14(15), 2221; https://doi.org/10.3390/ani14152221 - 31 Jul 2024

Cited by 1 | Viewed by 873

Abstract

The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of −0.035. Pairwise genetic distances (F_ST, Nei’s standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski’s horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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20 pages, 4378 KiB

Open AccessArticle

Comparative Analysis of mRNA and lncRNA Expression Profiles in Testicular Tissue of Sexually Immature and Sexually Mature Mongolian Horses

by Yuanyi Liu, Ming Du, Lei Zhang, Na Wang, Qianqian He, Jialong Cao, Bilig Zhao, Xinyu Li, Bei Li, Gerelchimeg Bou, Yiping Zhao and Manglai Dugarjaviin

Animals 2024, 14(12), 1717; https://doi.org/10.3390/ani14121717 - 7 Jun 2024

Cited by 1 | Viewed by 1017

Abstract

Testicular development and spermatogenesis are tightly regulated by both coding and non-coding genes, with mRNA and lncRNA playing crucial roles in post-transcriptional gene expression regulation. However, there are significant differences in regulatory mechanisms before and after sexual maturity. Nevertheless, the mRNAs and lncRNAs in the testes of Mongolian horses have not been systematically identified. In this study, we first identified the testicular tissues of sexually immature and sexually mature Mongolian horses at the tissue and protein levels, and comprehensively analyzed the expression profiles of mRNA and lncRNA in the testes of 1-year-old (12 months, n = 3) and 10-year-old (n = 3) Mongolian horses using RNA sequencing technology. Through gene expression analysis, we identified 16,582 mRNAs and 2128 unknown lncRNAs that are commonly expressed in both sexually immature and sexually mature Mongolian horses. Meanwhile, 9217 mRNAs (p < 0.05) and 2191 unknown lncRNAs (p < 0.05) were identified as differentially expressed between the two stages, which were further validated by real-time fluorescent quantitative PCR and analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The analysis results showed that genes in the sexually immature stage were mainly enriched in terms related to cellular infrastructure, while genes in the sexually mature stage were enriched in terms associated with hormones, metabolism, and spermatogenesis. In summary, the findings of this study provide valuable resources for a deeper understanding of the molecular mechanisms underlying testicular development and spermatogenesis in Mongolian horses and offer new perspectives for future related research. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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19 pages, 5979 KiB

Open AccessArticle

Single-Cell Transcriptome Sequencing Reveals Molecular Expression Differences and Marker Genes in Testes during the Sexual Maturation of Mongolian Horses

by Yuanyi Liu, Ming Du, Xinyu Li, Lei Zhang, Bilig Zhao, Na Wang and Manglai Dugarjaviin

Animals 2024, 14(9), 1258; https://doi.org/10.3390/ani14091258 - 23 Apr 2024

Cited by 2 | Viewed by 1123

Abstract

This study aimed to investigate differences in testicular tissue morphology, gene expression, and marker genes between sexually immature (1-year-old) and sexually mature (10-year-old) Mongolian horses. The purposes of our research were to provide insights into the reproductive physiology of male Mongolian horses and to identify potential markers for sexual maturity. The methods we applied included the transcriptomic profiling of testicular cells using single-cell sequencing techniques. Our results revealed significant differences in tissue morphology and gene expression patterns between the two age groups. Specifically, 25 cell clusters and 10 cell types were identified, including spermatogonial and somatic cells. Differential gene expression analysis highlighted distinct patterns related to cellular infrastructure in sexually immature horses and spermatogenesis in sexually mature horses. Marker genes specific to each stage were also identified, including APOA1, AMH, TAC3, INHA, SPARC, and SOX9 for the sexually immature stage, and PRM1, PRM2, LOC100051500, PRSS37, HMGB4, and H1-9 for the sexually mature stage. These findings contribute to a deeper understanding of testicular development and spermatogenesis in Mongolian horses and have potential applications in equine reproductive biology and breeding programs. In conclusion, this study provides valuable insights into the molecular mechanisms underlying sexual maturity in Mongolian horses. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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12 pages, 1472 KiB

Open AccessArticle

Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses

by Aiden McFadden, Micaela Vierra, Holly Robilliard, Katie Martin, Samantha A. Brooks, Robin E. Everts and Christa Lafayette

Animals 2024, 14(3), 517; https://doi.org/10.3390/ani14030517 - 5 Feb 2024

Cited by 2 | Viewed by 2865

Abstract

The influence of a horse’s appearance on health, sentimental and monetary value has driven the desire to understand the etiology of coat color. White markings on the coat define inclusion for multiple horse breeds, but they may disqualify a horse from registration in other breeds. In domesticated horses (Equus caballus), 35 KIT alleles are associated with or cause depigmentation and white spotting. It is a common misconception among the general public that a horse can possess only two KIT variants. To correct this misconception, we used BEAGLE 5.4-phased NGS data to identify 15 haplotypes possessing two or more KIT variants previously associated with depigmentation phenotypes. We sourced photos for 161 horses comprising 12 compound genotypes with three or more KIT variants and employed a standardized method to grade depigmentation, yielding average white scores for each unique compound genotype. We found that 7 of the 12 multi-variant haplotypes resulted in significantly more depigmentation relative to the single-variant haplotypes (ANOVA). It is clear horses can possess more than two KIT variants, and future work aims to document phenotypic variations for each compound genotype. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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23 pages, 4292 KiB

Open AccessArticle

A Functional Single-Nucleotide Polymorphism Upstream of the Collagen Type III Gene Is Associated with Catastrophic Fracture Risk in Thoroughbred Horses

by Esther Palomino Lago, Arabella Baird, Sarah C. Blott, Rhona E. McPhail, Amy C. Ross, Sian A. Durward-Akhurst and Deborah J. Guest

Animals 2024, 14(1), 116; https://doi.org/10.3390/ani14010116 - 28 Dec 2023

Viewed by 2474

Abstract

Fractures caused by bone overloading are a leading cause of euthanasia in Thoroughbred racehorses. The risk of fatal fracture has been shown to be influenced by both environmental and genetic factors but, to date, no specific genetic mechanisms underpinning fractures have been identified. In this study, we utilised a genome-wide polygenic risk score to establish an in vitro cell system to study bone gene regulation in horses at high and low genetic risk of fracture. Candidate gene expression analysis revealed differential expression of COL3A1 and STAT1 genes in osteoblasts derived from high- and low-risk horses. Whole-genome sequencing of two fracture cases and two control horses revealed a single-nucleotide polymorphism (SNP) upstream of COL3A1 that was confirmed in a larger cohort to be significantly associated with fractures. Bioinformatics tools predicted that this SNP may impact the binding of the transcription factor SOX11. Gene modulation demonstrated SOX11 is upstream of COL3A1, and the region binds to nuclear proteins. Furthermore, luciferase assays demonstrated that the region containing the SNP has promoter activity. However, the specific effect of the SNP depends on the broader genetic background of the cells and suggests other factors may also be involved in regulating COL3A1 expression. In conclusion, we have identified a novel SNP that is significantly associated with fracture risk and provide new insights into the regulation of the COL3A1 gene. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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8 pages, 211 KiB

Open AccessCommentary

Equus in Online Mendelian Inheritance in Animals (OMIA)

by Imke Tammen, Ernest Bailey, Marius Mather and Frank W. Nicholas

Animals 2024, 14(14), 2069; https://doi.org/10.3390/ani14142069 - 15 Jul 2024

Cited by 2 | Viewed by 737

Abstract

Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes information for Equus inherited traits/diseases (collectively called phenes). The database focuses on Mendelian traits and their likely causal variants (mutations). Some of these Mendelian traits are favored by humans, e.g., coat color, while others are diseases. Additions to OMIA are based on publications of peer-reviewed research. Maintaining up-to-date information in OMIA is a challenge, owing to the multiplicity of species, the increase in the number of relevant publications, and as reference genomes and methods of citation continue to evolve. This challenge has been successfully aided by contributions from scientists from around the world. In some cases, those scientists are faculty members who charge their students with curation as an educational activity. Recently, OMIA has introduced computerized lists of standardized names and synonyms (called ontologies) for breeds of Equus and other animals and for phene categories. These ontologies facilitate increased connectivity between OMIA and other online resources. OMIA is and will continue to be a major reference resource for Mendelian phenes in the genus Equus. Full article

(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)

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