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.
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...
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...
Li C, Liu K, Wei N, Hu S, Li X, Li C.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...
Liu L, Cao H, Ma H, Chen B, Liu W.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...
Yang X, Wen L, Wen M, Yao X, Meng J, Zeng Y, Ren W.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...
Gmel AI, Pirani A, McInnis L, Neuditschko M.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...
Huang Q, Wen M, Wen L, Li Q, Zeng Y, Wang J, Meng J, Ren W, Yao X.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...
