Advances in Equine Genetics and Breeding

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 5618

Special Issue Editors


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

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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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

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 (4 papers)

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Research

20 pages, 3273 KiB  
Article
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
Viewed by 269
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 [...] Read more.
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)
19 pages, 5979 KiB  
Article
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
Viewed by 617
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 [...] Read more.
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  
Article
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
Viewed by 2200
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 [...] Read more.
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  
Article
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 1921
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. [...] Read more.
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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