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Equine Genetics, Evolution, and Breeds
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Equine Genetics, Evolution, and Breeds

A Special Issue of Animals (ISSN 2076-2615) belonging to the section "Equids".

Deadline for manuscript submissions: closed (31 August 2026) | Viewed by 6603

Editor

Dr. Laura Patterson Rosa

E-Mail Website
Guest Editor
Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Long Island University, New York, NY, USA
Interests: equine medicine and genomics; equine health; adaptation; population genetics

Special Issue Information

Dear Colleagues,

The genetic study of equine evolution and breeds offers essential insights into their long-standing relationship with humans, and the impact it has had on equine health, performance, and environmental adaptation traits. Furthermore, it carries the potential to illuminate evolutionary pathways and genomic foundations of breed and lineage-specific characteristics, supporting advances in selective breeding and the preservation of genetic diversity. This Special Issue invites submissions of original research and review articles exploring equine genetics across the domains of breed/population genetics and evolutionary adaptations. Manuscripts examining genetic contributions to physiological and behavioral traits, along with those addressing the conservation of rare and heritage breeds, are particularly welcome.

The areas of interest for this Special Issue include the following: genetic diversity and population structure across horse breeds, evolutionary adaptations in wild/feral and domesticated equine populations, conservation genetics and the management of rare or endangered breeds, the identification of genetic variants of disease, applications of genetic research for sustainable breed/population conservation.

Dr. Laura Patterson Rosa
Guest Editor

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Keywords

  • horses
  • genomics
  • conservation
  • population
  • adaptation

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Published Papers (5 papers)

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Research

22 pages, 15223 KB  
Article
Genomics in Equine MEED: Whole-Genome Sequencing and Target Mutation Identification
by Kayden Tanner, Marshall Mays, Thu Annelise Nguyen and Tomas Lugo
Animals 2026, 16(10), 1560; https://doi.org/10.3390/ani16101560 - 21 May 2026
Viewed by 1253
Abstract
Multisystemic eosinophilic epitheliotropic disease (MEED) is a rare and severe equine disorder characterized by chronic eosinophilic inflammation, epithelial disruption, and multi-organ involvement, with an undefined genetic basis. We performed the high-depth (~40×) whole-genome sequencing of an affected horse and compared it to 40 [...] Read more.
Multisystemic eosinophilic epitheliotropic disease (MEED) is a rare and severe equine disorder characterized by chronic eosinophilic inflammation, epithelial disruption, and multi-organ involvement, with an undefined genetic basis. We performed the high-depth (~40×) whole-genome sequencing of an affected horse and compared it to 40 control genomes. Over 6.3 million variants were identified, with moderate- and high-impact variants enriched in low-frequency categories, including rare and private variants absent from the controls. The affected horse was dominated by missense mutations, with relatively few high-impact variants, consistent with the distributed protein-altering effects rather than a single highly penetrant mutation. Gene prioritization and pathway analyses highlighted the disruption of cytoskeletal organization, microtubule dynamics, epithelial integrity, and immune regulation. The network analysis further revealed the interconnected structural and inflammatory pathways, suggesting a link between an impaired epithelial barrier function and immune homeostasis. Together, these findings provide the first population genomic insight into MEED and support a model in which cumulative mutations contribute to the epithelial instability and persistent inflammation characteristic of the disease. Full article
(This article belongs to the Special Issue Equine Genetics, Evolution, and Breeds)
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19 pages, 7551 KB  
Article
Unraveling the Molecular Mechanism of Bider Marking Formation in Dun Mongolian Horses Through Transcriptome Sequencing
by Tana An and Manglai Dugarjaviin
Animals 2026, 16(8), 1145; https://doi.org/10.3390/ani16081145 - 9 Apr 2026
Viewed by 1168
Abstract
(1) Background: The “Bider” marking refers to the symmetrical black stripes distributed on the shoulder blades of Dun Mongolian horses, representing an ancestral trait of significant genetic value. However, the molecular mechanisms underlying its formation remain unclear. This study aims to elucidate the [...] Read more.
(1) Background: The “Bider” marking refers to the symmetrical black stripes distributed on the shoulder blades of Dun Mongolian horses, representing an ancestral trait of significant genetic value. However, the molecular mechanisms underlying its formation remain unclear. This study aims to elucidate the molecular basis of these markings by comparing transcriptomic differences in skin tissues from variously pigmented areas of Mongolian horses’ “Bider” patterns. (2) Methods: Using three Dun Mongolian horses as subjects, skin tissue samples were collected from their shoulders (dark-marked and light-marked areas), dorsal midline, and croup regions for transcriptome sequencing. Differentially expressed genes were identified based on sequencing data, followed by Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Key findings were validated through quantitative reverse transcription polymerase chain reaction (qRT-PCR). (3) Results: The sequencing yielded approximately 893 million high-quality clean reads, with an overall alignment rate exceeding 96%. A total of 140 to 775 differentially expressed genes were identified. GO enrichment analysis revealed that these genes were significantly enriched in biological processes related to pigment metabolism, skin and hair follicle development, signal transduction (including calcium and cyclic guanosine monophosphate (cGMP) signaling), and immune regulation. KEGG analysis further indicated that multiple pathways closely associated with pigment regulation, including the calcium signaling pathway, tyrosine metabolism, cyclic adenosine monophosphate (cAMP) signaling pathway, and melanoma pathway, were significantly enriched across different tissue comparison groups, suggesting their potential key roles in coat color phenotype formation. The reliability of the sequencing data was corroborated by the results of qRT-PCR validation. (4) Conclusions: This study conducted a transcriptome analysis of skin samples from various pigmented regions of the Dun Mongolian horse’s Bider marking, revealing that the formation of this marking is associated with the differential expression of numerous genes and is co-regulated by multiple pigment-related signaling pathways. Full article
(This article belongs to the Special Issue Equine Genetics, Evolution, and Breeds)
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15 pages, 6190 KB  
Article
Differential Expression of MITF, WNT3A, SLC7A11, and EDN3 in the Shoulder ‘Bider Marking’ of Dun Mongolian Horses
by Tana An and Manglai Dugarjaviin
Animals 2026, 16(6), 967; https://doi.org/10.3390/ani16060967 - 19 Mar 2026
Cited by 1 | Viewed by 628
Abstract
(1) Background: The “Bider marking” on the shoulder of the Dun Mongolian horse represents a unique pigmentation pattern, the molecular formation mechanism of which remains incompletely understood. This study investigates the differential expression and protein localization of pigment-related genes—specifically the core transcription factor [...] Read more.
(1) Background: The “Bider marking” on the shoulder of the Dun Mongolian horse represents a unique pigmentation pattern, the molecular formation mechanism of which remains incompletely understood. This study investigates the differential expression and protein localization of pigment-related genes—specifically the core transcription factor MITF, as well as EDN3, SLC7A11, and WNT3A—in the skin. The analysis focuses on three distinct regions: the dark-colored area of the ‘Bider marking’ shoulder (BIDC), the light-colored area of the ‘Bider marking’ shoulder (BILC), and the non-Bider-marked shoulder area (NBIS). The aim is to clarify their correlation with the formation of this distinctive pigmentation pattern. (2) Methods: Skin tissue samples from both the “Bider marking” and non-Bider-marked shoulder regions were collected (n ≥ 3). The mRNA expression levels were quantified using RT-qPCR, protein levels were analyzed through Western blotting, and protein localization was assessed via immunohistochemistry and immunofluorescence. (3) Results: Compared to the NBIS group, both the BIDC and BILC groups exhibited significantly elevated protein expression of MITF and WNT3A. Further immunofluorescence showed that the distribution of MITF protein exhibits regional specificity in the epidermis and hair follicles. In the BIDC region, the protein is localized specifically to the stratum corneum of the epidermis, the dermal papilla, and the outer root sheath of hair follicles. In contrast, the mRNA and protein expression levels of SLC7A11 and EDN3 did not display consistent patterns among the three groups, and no specific differences were observed in tissue localization. (4) Conclusions: The findings show that the specific pigmentation in dark “Bider marking” regions is closely linked to the upregulated protein levels and unique spatial patterns of MITF and WNT3A; SLC7A11 and EDN3 may not be primary regulators of this trait. Full article
(This article belongs to the Special Issue Equine Genetics, Evolution, and Breeds)
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22 pages, 8429 KB  
Article
The Impact of MEI1 Alternative Splicing Events on Spermatogenesis in Mongolian Horses
by Dailing Song, Guoqing Wang, Terigele Baterin, Yajuan Weng, Manglai Dugarjaviin and Bei Li
Animals 2025, 15(23), 3435; https://doi.org/10.3390/ani15233435 - 28 Nov 2025
Viewed by 976
Abstract
Background: Normal spermatogenesis in Mongolian horses depends on the mitotic division of spermatogonia, two successive meiotic divisions, and the morphological transformation of spermatids into mature spermatozoa. The MEI1 gene is involved in the meiosis cycle and is required for normal chromosome association during [...] Read more.
Background: Normal spermatogenesis in Mongolian horses depends on the mitotic division of spermatogonia, two successive meiotic divisions, and the morphological transformation of spermatids into mature spermatozoa. The MEI1 gene is involved in the meiosis cycle and is required for normal chromosome association during meiosis. Previous studies have shown that alternative splicing of MEI1 may promote spermatogenesis in Mongolian horses. In this paper, the regulatory effects of different MEI1 alternative splicing events on Mongolian horse spermatogenesis are investigated. Results: In this study, two overexpressed lentiviral vectors with mutually exclusive exon (MXE) and skipped exon (SE) events of MEI1 were constructed and successfully used to infect Sertoli cells. After 72 h of viral infection, the expression of MEI1 was higher in the SE event than in the MXE event (p < 0.001), as shown by fluorescence quantification; transcriptomics and metabolomics were then used to screen and annotate the differential genes and metabolites, and 193 differentially expressed genes (comprising 109 genes, such as MEI1, and 84 genes with upregulated and downregulated expression, respectively) and 11,360 differentially expressed metabolites (comprising 7494 and 3866 metabolites with upregulated and downregulated expression, respectively) were screened. Differential genes and metabolites were mainly enriched in several metabolic pathways related to spermatogenesis. Differential genes such as IL31RA, ATP2B3, and CASQ2 were highly expressed in SE events, while IL11, PRLR, and CCR7 were highly expressed in MXE events. Metabolites such as folic acid and spermine were highly expressed during SE events, while citric acid and glutathione were highly expressed during MXE events. This suggests that both MXE and SE events of the MEI1 gene can promote the activity of the spermatogenesis signaling pathway. Conclusions: The MXE and SE splicing events of the MEI1 gene may influence spermatogenesis by regulating the expression of spermatogenesis-related genes and metabolites. These findings provide a theoretical foundation for further investigations into the regulatory mechanisms of different alternative splicing events in Mongolian horse spermatogenesis. Full article
(This article belongs to the Special Issue Equine Genetics, Evolution, and Breeds)
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20 pages, 6552 KB  
Article
Pilot Study on the Profiling and Functional Analysis of mRNA, miRNA, and lncRNA in the Skeletal Muscle of Mongolian Horses, Xilingol Horses, and Grassland-Thoroughbreds
by Wenqi Ding, Wendian Gong, Tugeqin Bou, Lin Shi, Yanan Lin, Huize Wu, Manglai Dugarjaviin and Dongyi Bai
Animals 2025, 15(8), 1123; https://doi.org/10.3390/ani15081123 - 13 Apr 2025
Cited by 3 | Viewed by 1545
Abstract
Muscle fibers, as the fundamental units of muscle tissue, play a crucial role in determining skeletal muscle function through their growth, development, and composition. To investigate changes in muscle fiber types and their regulatory mechanisms in Mongolian horses (MG), Xilingol horses (XL), and [...] Read more.
Muscle fibers, as the fundamental units of muscle tissue, play a crucial role in determining skeletal muscle function through their growth, development, and composition. To investigate changes in muscle fiber types and their regulatory mechanisms in Mongolian horses (MG), Xilingol horses (XL), and Grassland-Thoroughbreds (CY), we conducted histological and bioinformatic analyses on the gluteus medius muscle of these three horse breeds. Immunofluorescence analysis revealed that Grassland-Thoroughbreds had the highest proportion of fast-twitch muscle fibers at 78.63%, while Mongolian horses had the lowest proportion at 57.54%. Whole-transcriptome analysis identified 105 differentially expressed genes (DEGs) in the CY vs. MG comparison and 104 DEGs in the CY vs. XL comparison. Time-series expression profiling grouped the DEGs into eight gene sets, with three sets showing significantly up-regulated or down-regulated expression patterns (p < 0.05). Additionally, 280 differentially expressed long non-coding RNAs (DELs) were identified in CY vs. MG, and 213 DELs were identified in CY vs. XL. A total of 32 differentially expressed microRNAs (DEMIRs) were identified in CY vs. MG, while 44 DEMIRs were found in CY vs. XL. Functional enrichment analysis indicated that the DEGs were significantly enriched in essential biological processes, such as actin filament organization, muscle contraction, and protein phosphorylation. KEGG pathway analysis showed their involvement in key signaling pathways, including the mTOR signaling pathway, FoxO signaling pathway, and HIF-1 signaling pathway. Furthermore, functional variation-based analyses revealed associations between non-coding RNAs and mRNAs, with some non-coding RNAs targeting genes potentially related to muscle function regulation. These findings provide valuable insights into the molecular basis for the environmental adaptability, athletic performance, and muscle characteristics in horses, offering new perspectives for the breeding of Grassland-Thoroughbreds. Full article
(This article belongs to the Special Issue Equine Genetics, Evolution, and Breeds)
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