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Topic:Bioinformatics
Bioinformatics in horses involves the application of computational tools and techniques to analyze and interpret biological data related to equine species. This interdisciplinary field integrates biology, computer science, and information technology to study genetic, genomic, and proteomic information in horses. Bioinformatics can be used to investigate genetic variations, understand disease mechanisms, and assist in the development of targeted therapies and breeding programs. Key areas of focus include genome sequencing, gene expression analysis, and the identification of genetic markers associated with specific traits or conditions. This page compiles peer-reviewed research studies and scholarly articles that explore the application and impact of bioinformatics on equine genetics, health, and breeding.
Comparative genomics of Standardbred horses reveals candidate regions under selection for harness racing performance. Harness racing performance in horses is a complex polygenic trait influenced by genetic background, breeding history, training, and environment. Understanding genomic patterns shaped by long-term artificial selection provides insights into performance-related traits and breed-specific genomic variation. Objective: This study aimed to characterize genomic differentiation, population structure, and candidate genomic regions potentially influenced by historical selection in Standardbred horses using comparative whole-genome sequencing involving diverse horse breeds. Methods: Whole-genome sequenci...
Comparative genomic analysis of oxytocin and oxytocin receptor genes in the family Equidae. The oxytocin (OXT) - oxytocin receptor (OXTR) system regulates diverse biological processes including social behavior, stress responses, and processes related to domestication. While OXT is highly conserved, OXTR shows greater variability, which may contribute to species-specific adaptations. Methods: Comparative genomic analyses of OXT and OXTR coding sequences were performed across equid species using available genome assemblies and newly generated sequences obtained by next-generation sequencing. Phylogenetic relationships were inferred using maximum likelihood methods. Selection was assess...
Characterization of Lipizzan Horse Population From Lipica Stud Using Molecular and Pedigree Data. In this study, we analysed genetic diversity, population structure and inbreeding in the Lipica Stud Farm population by integrating pedigree records, microsatellite (STR) and genome-wide SNP data generated using the GGP Equine 70K BeadChip. The dataset comprised 233 horses from the Lipica Stud Farm, which served as the reference population for comparisons of diversity estimates based on pedigree-, STR- and SNP data. The STR data were originally generated for routine parentage verification and were included here to compare inbreeding estimates based on pedigree, STR and genome-wide SNP data. Pe...
Genome-Wide Identification and Characterization of the Wnt Gene Family in Donkey (Equus asinus): Phylogenetic Analysis and Expression Profiling. The gene family encodes highly conserved signaling molecules involved in vertebrate development, tissue homeostasis, and cell fate regulation. However, the evolutionary characteristics and potential biological functions of genes in the domestic donkey () remain poorly understood. In this study, we performed the first genome-wide identification and comprehensive characterization of the donkey gene family. A total of 19 genes were identified, consistent with the conserved repertoire reported in other mammalian species. Phylogenetic and synteny analyses revealed strong evolutionary conservat...
Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution. We present telomere-to-telomere genome assemblies of a Thoroughbred horse and a donkey derived from their mule offspring. Now adopted and annotated by NCBI as reference genomes, these assemblies resolve previously inaccessible regions, including satellite arrays, duplications, and telomeres. Equids are known to exhibit an uncoupling between satellite DNA and centromeric function. The completeness of these assemblies enabled annotation of both satellite-based and satellite-free centromeres, as well as non-centromeric satellite loci, revealing notable centromeric plasticity. They also allowed de...
Demographic change and selection patterns in thoroughbred racing horses over the 20th century. The Thoroughbred horse is a legacy of centuries of selective breeding for speed, emerging from the admixture of British mares and imported Oriental stallions. While previous work explored its genetic diversity, inbreeding, and selection signatures, the breed demographic and selection dynamics during the 20-century remain poorly understood. Here, we sequenced the genome of Phar Lap, a late-1920s/early-1930s racing champion, and analyzed the largest time-series of Thoroughbred whole-genome sequences, within a global panel of 850 horse genomes. Demographic modeling reveals a marked decline in gen...
Sequencing and Differential Analysis of miRNA in the Ovaries of Kazakh Horses During Estrus and Anestrus States. To reveal the regulatory role of miRNA in the estrous cycle transition of Kazakh horse ovaries and improve their reproductive efficiency, this study took the ovaries of Kazakh horses in the estrus period (DY group) and the quiescent period (DB group) as research objects. Small RNA sequencing and bioinformatics analysis were used to systematically analyze the expression characteristics and functional pathways of miRNA under the two physiological states. A total of 161 million high-quality miRNA tags were obtained through sequencing. Principal component analysis showed that the intra-group repea...
Genomic diversity and historical legacy of Baroque horses: a living cultural heritage. Baroque horses represent a distinctive group of breeds that emerged mainly between the 16th and 18th centuries, shaped by the demands of European royalty and their courts. Although recognised as separate breeds, they share common ancestry, breeding goals, and historical gene flow. This study aimed to evaluate their genomic diversity, population structure, and admixture patterns. We analysed 1 160 individuals from eight breeds - Lipizzan, Old Kladruby Horse, Pura Raza Española, Lusitano, Friesian, Criollo, Peruvian Paso, and Puerto Rican Paso Fino - using 34 026 single-nucleotide polymorphis...
Genome-Wide Characterization of the TGF-β Gene Family in Donkey (Equus asinus) Reveals Lineage-Specific Gene Duplications and Deleterious Mutations. The transforming growth factor-beta (TGF-β) superfamily regulates diverse biological processes, including proliferation, differentiation, apoptosis, tissue remodeling, and reproductive signaling across metazoans. Here, we performed a genome-wide characterization of the TGF-β gene family in donkey (, ASM1607732v2) using comparative genomics and bioinformatics analyses, with horse (, EquCab3.0) as a reference to investigate evolutionary conservation and functional divergence. Genome assemblies and proteomes were retrieved from NCBI, and TGF-β genes were identified using BLASTp and HMMER searc...
Cell-Type Deconvolution of Equine BALF RNA-Seq: A Critical Comparison with Matched Single-Cell Data. Bulk RNA sequencing (RNA-seq) averages signals across heterogeneous cell populations. Computational deconvolution methods aim to infer cell type composition and cell type-specific gene expression from bulk data, but their performance in equine samples has not been evaluated. In this study, we assessed the ability of computational deconvolution to recover cellular composition and differential expression signals in bronchoalveolar lavage fluid (BALF) from horses with severe equine asthma (SEA) and controls (CTL). Cryopreserved BALF samples from six SEA and five CTL horses previously analyzed b...
Matched embryo-endometrium RNA-seq reveals coordinated but asymmetric transcriptomic reprogramming at the onset of early equine pregnancy. Maternal recognition of pregnancy (MRP) in the mare requires coordinated adaptations of both the conceptus and the endometrium during the peri-recognition interval; however, integrated transcriptomic analyses of both compartments within the same biological window remain limited. Here, we analyzed conceptus RNA-seq data across embryonic age (Days 8 and 12 post ovulation) and endometrial RNA-seq data across pregnancy status (pregnant versus non-pregnant mares sampled between Days 8 and 12 post ovulation). In pregnant mares, conceptus recovery and endometrial biopsy collection were performed with...
Cytogenetic, genomic, and reproductive characterization of four pura Raza Española mares carrying a 64, X, del(X),t(X; Y) complex karyotype. Chromosomal abnormalities involving the sex chromosomes constitute critical genetic factors influencing fertility in horses. Nevertheless, a substantial proportion of individuals carrying sex chromosomal abnormalities exhibit normal reproductive phenotypes, which complicates their identification until adulthood. Here, we present four mares carrying a complex deletion/translocation rearrangement with the karyotype formula 64, X, del(X)(p∼25),t(X; Y)(p∼25; q∼15). The cases analyzed belong to three unrelated families of Pura Raza Española (PRE), all presenting the same chromosomal abnormal...
Research Trends and Emerging Frontiers in Racehorse Genetics: A Bibliometric Analysis. The global horse racing industry relies heavily on elite breeding. Therefore, a molecular understanding of athletic traits is crucial for the industry's advancement. This study utilized Bibliometrix, VOSviewer, and CiteSpace to conduct a comprehensive bibliometric analysis of 869 publications in the Web of Science Core Collection (2011-2025), decoding the academic landscape and evolutionary trajectory of equine genetics. The results indicate a significant upward trend in academic output since 2019, with the United States, South Korea, and the United Kingdom emerging as the primary contributors...
Whole Genome Data Uncover the Complex Origins of Polish Konik Horses. Polish Konik is a native horse breed from Poland often regarded as living descendants of the extinct Tarpan, which has been crucial to the breed's conservation status and cultural importance. To evaluate Polish Konik origins, we sequenced 12 whole genomes and compared them with 148 horse genomes, including those of modern breeds, ancient Polish horses, Przewalski horses, and the Tarpan. The ADMIXTURE results showed that Polish Konik is dominated by a single ancestral component, which is also common among ancient Polish samples and several primitive breeds. The PCA places Polish Konik in a comp...
Genomics in Equine MEED: Whole-Genome Sequencing and Target Mutation Identification. 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 rela...
Identification of gene conversion events in horse IGHV suggests preferential hotspots for diversification. The humoral immune response relies on a diverse antibody repertoire, which is expanded through processes such as somatic hypermutation, class-switch recombination and gene conversion. These processes are primarily mediated by activation-induced cytidine deaminase (AID). Gene conversion generates diversity in immunoglobulin heavy and light chains (IGHVs) in species such as chickens and rabbits, though it has not been widely studied. Since 80% of the equine IGHV repertoire originates from only three functional gene segments, we examined gene conversion events in horses to assess their role in an...
Telomere-to-telomere Genome Assembly of Equus kiang (Tibetan wild donkey). The Tibetan wild donkey (Equus kiang) is an endemic equid species inhabiting the Qinghai-Tibet Plateau, exhibiting remarkable chromosomal diversity within the Equus genus. Here we present a chromosome-level, telomere-to-telomere genome assembly for E. kiang generated using Illumina short reads, PacBio HiFi long reads, and Hi-C sequencing data. The final assembly spans 4.02 Gb and comprises 27 pseudochromosomes. Specifically, 8 chromosomes are gapless, 8 chromosomes have one gap, 7 chromosomes have 2-4 gaps, and the remaining 4 chromosomes have five or more gaps. Benchmarking Universal Single...
miRNA Sequencing and Differential Analysis of Testis in 1-Year-Old and 2-Year-Old Kazakh Horses. The represents a significant genetic resource within China's population, characterized by notable resilience and an ability to thrive on coarse forage. Nevertheless, a decline in its numbers has been observed recently, making the improvement of its reproductive performance crucial for the preservation of this breed and the advancement of the related industry. In this study, testicular tissues from 1-year-old (pre-pubertal) and 2-year-old (post-pubertal) were analyzed. miRNA sequencing was conducted on tissues from these age groups, followed by bioinformatics analyses to elucidate the functi...
Comparative analysis of mRNA and circRNA expression profiles and interaction networks in testicular tissues of Mongolian horses before and after sexual maturity. Mongolian horses, celebrated for their resilience and adaptability, undergo marked physiological transformations during sexual maturation. This study employed whole-transcriptome sequencing to conduct a comparative analysis of mRNA and circular RNA (circRNA) expression profiles, along with their interactive regulatory networks, in testicular tissues of Mongolian horses pre- and post-sexual maturity. Histological examinations using hematoxylin-eosin (H.E.) and 4’,6-diamidino-2-phenylindole (DAPI) staining revealed distinct morphological differences between sexually immature and mature testicu...
Genomic diversity and structure in arabian horses revealed by whole-genome sequencing: establishment of an allele frequency database of common genetic variation. BACKGROUND: The Arabian horse is a culturally and historically influential breed that has contributed to the development of many modern horse populations. However, genomic resources for this breed remain limited, particularly population-level allele frequency datasets that support studies of genetic diversity, selection, and disease. The aim of this study was to generate a comprehensive allele frequency database for Arabian horses using representative sampling and high-coverage whole-genome sequencing. RESULTS: We generated the first publicly available allele frequency database for the Arabian...
Genetic diversity in the Criollo Argentino horse from SNP array data. The Criollo Argentino horse is a national symbol and a heritage breed that represents both cultural identity and a key component of traditional production systems in Argentina. This study aimed to assess the genetic differentiation of the Criollo Argentino relative to other horse breeds and to infer potential factors shaping its diversity through the genomic analysis of 24 representative animals. Samples were genotyped using a medium-density SNP array containing 65,157 markers, and genetic diversity analyses were conducted across autosomal SNP sets filtered under different criteria. Contempora...
Unraveling the Molecular Mechanism of Bider Marking Formation in Dun Mongolian Horses Through Transcriptome Sequencing. (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 li...
Multi-omics profiling of the testes in Kazakh horses across sexual maturation. Equus caballus is a species of considerable economic and cultural significance. However, the regulatory networks involved in equine sexual maturation remain unclear and eventually limit its reproduction and utilization. In this study, testicular tissues from eight Kazakh horses at two developmental stages (2 years, representing pre-maturation, and 3 years, representing post-maturation) were analyzed using whole transcriptome sequencing, data-independent acquisition (DIA) proteomics, and untargeted metabolomics. An integrated regulatory network was constructed encompassing ceRNA, mRNA, prot...
miRNA Sequencing and Differential Analysis of Testes from 1-Year-Old and 3-Year-Old Kazakh Horses. This study aims to elucidate the miRNA regulatory mechanisms during the developmental process of Kazakh horse testes at 1 and 3 years of age. Through miRNA sequencing and bioinformatics analysis of testicular tissues from 1-year-old and 3-year-old horses, a developmentally stage-specific miRNA expression profile was constructed. A total of 1640 miRNAs were identified, among which 437 (380 up-regulated and 57 down-regulated) exhibited significant differential expression between the two age groups, including eca-miR-16, eca-miR-17, eca-miR-103, and eca-miR-199a-5p. Functional enrichment analysis...
An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array. Single nucleotide polymorphism (SNP) arrays are commonly used in livestock genetics to investigate complex traits including genome-wide associations and fine mapping, genomic prediction and genetic diversity analyses. In a European equine diversity study, we analysed the AxiomTM Equine 670K SNP genotype data from 2,768 equids representing 20 horse breeds and one donkey breed. Using a strict detection setting to identify genome-wide runs of homozygosity (ROH), 169 purebred horses displayed fewer ROH segments than F1 crosses. Under medium and relaxed settings, ROH counts increased, while some ho...
H3K4me3 CUT&Tag and Transcriptome Analysis Reveal the Epigenetic Regulatory Landscape in Mammary Gland Tissues of Yili Horses at Different Lactation Stages. H3K4me3, a well-established histone modification associated with active promoters, plays a critical role in orchestrating gene expression programs that govern mammary gland development and lactation. In this study, we present the first comprehensive epigenomic profiling of H3K4me3 modifications during mammary gland development in Yili horses using Cleavage Under Targets and Tagmentation (CUT&Tag) and RNA sequencing. Mammary gland tissues were collected from two developmental stages-early lactation and peak lactation. A total of 393 differentially expressed genes (DEGs) were identified betw...
Computational modelling of the equine arteritis virus GP5/M Dimer: Implications for immune evasion and virulence. Equine arteritis virus (EAV) is a positive-stranded RNA virus of the Arteriviridae family. Its GP5/M dimer, the principal component of the viral envelope, mediates virus budding and serves as a key target for neutralizing antibodies. Using AlphaFold3, we predicted the 3D structure of the EAV GP5/M dimer and compared it to its homolog in porcine reproductive and respiratory syndrome virus (PRRSV). Both complexes share a conserved architecture comprising a short ectodomain, three helical transmembrane regions, and a β-sheet-rich endodomain. EAV GP5 features a longer ectodomain with four α-heli...
Metatranscriptomics reveals the horse gut RNA virome and a viral sharing network with human and domestic animals. RNA viruses, a unique class of life forms, are widely distributed in nature and pose potential health risks. Monitoring the gut RNA virome in livestock is a crucial component of global health surveillance. As important companion animals, horses play a vital role in transportation and make significant contributions to various cultural and economic activities. Nevertheless, the characteristics of horse gut RNA viruses remain largely uncharted. Unassigned: In this study, we used metatranscriptome sequencing and bioinformatics methods to characterize viruses within the gut contents of 16 horses sp...
Sequencing and Analysis of mtDNA Genomes from the Teeth of Early Medieval Horses in Poland. This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland. Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens. Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G...
