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.
Breckenridge WC, Kuksis A.The triglyceride compositions of the milk fats of man, dog, guinea pig, cow, sheep, goat, and horse were compared by gas-liquid chromatography of the intact triglycerides and of the butyl esters of the component fatty acids. The milk fats of man, dog, and guinea pig, which were largely made up of long-chain fatty acids, showed a common pattern with major contributions made by the glycerides with 48-54 acyl carbon atoms. The milk fats of cow, sheep, and goat, which were rich in short-chain acids, showed significant proportions of triglycerides with 28-54 acyl carbon atoms. Horse milk, which con...
RANDALL CC, LAWSON LA.The research article discusses the successful adaptation of the Equine Abortion Virus (EAV) to L-M 929 cells, the impact on infected cultures, and possible reasons for earlier unsuccessful attempts. It […]
The goal of this research was to evaluate the ability of the genotyping information available in the Brazilian Criollo Horse Stud Book to describe the genetic variability of the breed and the exclusion probability determined in comparative tests. Altogether, two softwares were used in the analyses of the available genotypes: Cervus 3.0.3 and Genepop 4.0. Eight microsatellite markers totaled 109 alleles, with an average of 13.6 +/- 0.6 alleles per locus. Large differences between expected and observed heterozygosity were ubiquitous (0.821 +/- 0.07 and 0.470 +/- 0.17, respectively). Although the...
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 o...
Toft K, Honoré ML, Ripley NE, Nielsen MK, Fromm B, Mardahl M, Nielsen LN, Nejsum P, Thamsborg SM, Cirera S, Pihl TH.The equine bloodworm, Strongylus vulgaris, is a highly pathogenic parasite causing potentially fatal vascular and intestinal damage. Parasites express and release microRNAs (miRNAs) for internal regulation and to modulate host immunity. The complete set of miRNAs expressed by S. vulgaris (the S. vulgaris miRNAome) remains unannotated and the aim of this study was to annotate the miRNAome of L4 and L5 stages of S. vulgaris, and to examine differences in miRNA abundance between larval stages and sexes. Furthermore, we aimed to determine if miRNAs were detectable in excretory/secretory products (...
Smith MZ, York M, Townsend KS, Martin LM, Gull T, Coghill LM, Ericsson AC, Johnson PJ.Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated. Objective: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses. Methods: Experimental prospective cohort study using a single horse group. Methods: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for ...
Chakraborty A, Dutta P, Amrit R, Dey P, Osborne WJ.Endosymbiotic bacteria are known to synthesize bioactive compounds which have biotechnological potentials that enhance immune responses by stimulating the production of immune cells. Horse milk is widely known to have nutraceutical and antimicrobial activities; however, there are no scientific reports on its inhibitory effects. VITAPRJS1, isolated from horse milk, showed non-hemolytic properties and was significantly tolerant to bile salt and NaCl. The isolate also exhibited potent antibacterial activity against pathogenic bacterial strains such as Escherichia coli, Pseudomonas aeruginosa, Sta...
Faulk C.Sequencing a genome by students has now become practical as we demonstrated with our recent publication of the Przewalski's horse (Equus ferus przewalskii) genome. In this review, I describe my experience teaching genome assembly in the classroom. In my course, students sequenced, assembled, and published a high-quality genome for Przewalski's horse using Oxford Nanopore long-read sequencing with only $4000 of materials. Along with the genome, we assembled the mitochondrial genome, sequence variants, predicted gene annotations, and DNA methylation levels. Our genome statistics far exceeded the...
Frontiers in geneticsFebruary 27, 2025
Volume 16 1534461 doi: 10.3389/fgene.2025.1534461
Barber AM, Kingsley NB, Peng S, Giulotto E, Bellone RR, Finno CJ, Kalbfleisch T, Petersen JL.The Functional Annotation of Animal Genomes (FAANG) consortium aims to annotate animal genomes across species, and work in the horse has substantially contributed to that goal. As part of this initiative, chromatin immunoprecipitation with sequencing (ChIP-seq) was performed to identify histone modifications corresponding to enhancers (H3K4me1), promoters (H3K4me3), activators (H3K27ac), and repressors (H3K27me3) in eight tissues from two Thoroughbred stallions: adipose, parietal cortex, heart, lamina, liver, lung, skeletal muscle, and testis. The average genome coverage of peaks identified by...
Bianchi D, Santos RRD, Peleja PL, de Sousa ABB, da Silva Evangelista M, de Almeida Júnior JS, Barata LES, Moraes WP, Minervino AHH. (tropical horse tick) is a tick species commonly found parasitizing horses and other equids in the Amazon region, causing economic losses. Currently, tick control is based on chemical acaricides, usually in a power formulation for topical use. However, its indiscriminate use results in the emergence of resistant tick lineages. Several plant compounds have been tested for their acaricide activity. In the Amazon, several plants are used for oil extraction, resulting in the production of solid residue (waste) that may contain chemical molecules with biological activities. Thus, we aimed to test ...
de Carvalho CN, Cunha PP, Belo J, Muñiz F, Baucon A, Cachão M, Figueiredo S, Buylaert JP, Galán JM, Belaústegui Z, Cáceres LM, Zhang Y....Multiple sources of evidence for the systematic use of coastal ecosystems and resources by Neanderthals are known. Fossil hominin footprints offer direct portraits of individual or social group presence and locomotor behavior, and interspecific interactions, in the coastal ecospace. Here we describe the first two hominin tracksites found in the southwestern most region of Europe. At Monte Clérigo, dated to 78 ± 5 ka, trackways of three individuals demonstrate how Neanderthals navigated dune landscapes. These behaviors suggest route planning, with dune systems serving as advantageous set...
Zhang X, Liu Y, Ma W, Li L, Bai D, Dugarjaviin M.Mongolian horses are renowned for their remarkable endurance and ability to adapt to harsh environments. To delve deeper into the molecular mechanisms that underlie these traits, researchers conducted a comprehensive analysis of transcriptomic and proteomic changes in Mongolian horses at three distinct time points: before, immediately after, and 24 h following a 20 km run. The transcriptomic analysis uncovered significant variations in gene expression patterns across these time points. Specifically, 291 differentially expressed genes (DEGs) were identified when comparing pre-exercise to post-e...
Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, nati...
Pasicka E, Baca M, Popović D, Makowiecki D, Janeczek M.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...
Steensma MJ, Ducro BJ, Dibbits B, Doekes HP, van Schipstal JGC, Kalblfleisch T, Groenen MAM, Derks MFL.In horses, genetic diversity is predominantly observed between breeds, with little variation within breeds. The studbooks of the two largest horse populations in the Netherlands, the Dutch Warmblood horse and Friesian horse population, have ongoing conservation projects including collecting large-scale genotype and sequence data. The current reference genome, derived from a Thoroughbred horse can lead to bias in genetic analyses of other horse breeds. Therefore, the aim of this study was to create high-quality breed-specific reference genomes of Dutch Warmblood and Friesian horses. We performe...
Cullen JN, Cieslak J, Petersen JL, Bellone RR, Finno CJ, Kalbfleisch TS, Calloe K, Capomaccio S, Cappelli K, Coleman SJ, Distl O, Durward-Akhurst SA....MicroRNAs (miRNAs) are essential regulators of gene expression, yet few comprehensive databases exist for miRNA expression in non-model species, limiting our ability to characterize their roles in gene regulation, development, and disease. Similarly, isomiRs - length and sequence isoforms of canonical miRNAs with potentially altered regulatory targets and functions - have received even less attention in non-model species, including the horse, leaving a critical gap in our understanding of their biological significance. To address these challenges, we developed an open-source, containerized pip...
Maniego J, Swinburne J, Hincks P, Habershon-Butcher J, Given J, Ryder E.Gene editing and genome manipulation offer great promise for treating diseases in both humans and animals. There is a danger, however, that this technology could be used for other purposes such as performance enhancement. To detect such 'gene doping' events, we evaluated a targeted enrichment panel and next-generation sequencing to assess its reproducibility, sensitivity, and capability of variant detection on a wide variety of samples and biological matrices. The panel was verified against existing data for the myostatin gene, a PCR-based SNP panel, and whole genome sequencing in a subset of ...
da Silva GM, Navas C, Carvalho MB, Sampaio Y, Rocha MN, Gomes-Silva A, de Matos Guedes HL, Cunha L, Castilho LR, da Silva JL, Felicori LF.Horse immunoglobulins have been utilized for over a century in serotherapy to treat venomous animal bites and various other conditions. However, molecular-level information about these immunoglobulins remains limited, particularly regarding immunoglobulin lambda light chains (Igλ), which constitute over 90 % of circulating antibodies. Despite the sequencing of the equine genome, the International ImMunoGeneTics information system (IMGT) has not yet annotated Igλ in its database, restricting the analysis of the horse antibody repertoire. In this study, we analyzed the equine Igλ repertoire...
Moghbeli Damane M, Ayatollahi Mehrgardi A, Esmailizadeh A, Momen M.Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance. Generally, in the horse population, inbreeding is caused by geographically restricted areas and intensive natural or artificial selection. For this reason, assessing accurate inbreeding is essential for developing and implementing effective breeding strategies aimed at preserving genetic diversity and reducing the harmful consequences of inbreeding. One of the most accurate approaches for assessing genomic inbreeding and autozygosity is through the analysis of runs of homozygosity...
Frontiers in geneticsNovember 12, 2025
Volume 16 1439312 doi: 10.3389/fgene.2025.1439312
Tang C, Yang B, Dawulietihan G, Xue L, Liu S, Yalimaimaiti Y, Wang Q, Yang N, Sun X, Wang Y, Wumaier A, Khizat S, Assanbayev T, Kozhanov Z....Xinjiang is a region renowned for its rich diversity of native horse breeds, making it one of the most affluent equine genetic resource areas in China. While prized for their high adaptability and tolerance to roughage, the conservation of these native breeds faces challenges from the introduction of external breeds and industrial changes. Furthermore, the unknown population structure of Xinjiang horse breeds has hindered effective conservation efforts. Unassigned: This study presents the first comprehensive Single Nucleotide Polymorphism (SNP) analysis of seven Xinjiang native horse breeds. W...
Chessari G, Reich P, Criscione A, Falker-Gieske C, Mastrangelo S, Tumino S, Bordonaro S, Marletta D, Tetens J.Single nucleotide polymorphism (SNP) arrays are commonly used for studying the genomic structure and diversity of livestock breeds, but whole-genome sequencing (WGS) provides higher-resolution genomic data. Genotype imputation has become a standard practice for increasing the genomic resolution of association studies. This work aimed to extend imputation to biodiversity analyses, comparing SNP array data before and after imputation. A 40 k SNP dataset of 281 horses from 12 breeds (DS) was imputed to sequence-level using a reference panel of 327 sequenced individuals, generating approximately 9...
Saldaña CL, Justo S, Murga L, Vásquez HV, Maicelo JL, Arbizu CI, Bardales W.The complete mitochondrial genome of the Peruvian Paso Horse was assembled using PacBio HiFi long reads, resulting in a high-quality circular genome of 16,617 bp comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition and gene structure were consistent with other equine mitogenomes. Codon usage analysis revealed a bias toward CUA (Leu), AUA and AUC (Ile), suggesting translational optimization. Thirty-five heteroplasmic variants were identified, predominantly located in RNA genes (12 S rRNA and tRNA-Phe), with allele frequencies between 0.10 and 0.6...
Veit M, Matczuk AK.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...
El-Ghaly W, El Kamli T, Zaari Lambarki L, El Hamdani M, Lahkak FE, Benmoussa A, Balouch L, Bakkali F, Saffaj T, Jhilal F.The quality of quantitative results in bioanalysis requires not only a validated analytical method but also a rigorous estimation of measurement uncertainty. This study examines the challenges associated with the implementation of two distinct approaches in equine anti-doping control for the assessment of uncertainty associated with an ultra-high-performance liquid chromatography-high resolution mass spectrometry quantitative method for caffeine and lidocaine in horse urine. The bottom-up approach, based on the ISO Guide to the Expression of Uncertainty in Measurement (ISO GUM), was compared t...
Liu X, Liu A, Khan MZ, Zhu Q, Zheng Y, Chen W, Cai B, Yan Z, Peng Y, Wang C.The gene family plays an indispensable role in regulating embryonic development, cell differentiation, and morphogenesis. This study employed bioinformatics approaches for systematic analysis, ultimately identifying 33 gene family members from the donkey genome. Physicochemical property analysis revealed that the number of amino acids encoded ranged from 94 to 444, with 31 members classified as alkaline proteins. Their secondary structure was predominantly composed of random coils and alpha helices, and all members were localized to the nucleus. Conserved motif analysis further demonstrated ...
Van Buren SL, Petersen JL, Brown CT, Finno CJ.With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identifi...
