The genomic history and global expansion of domestic donkeys.

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus).

Over 40 identified genetic variants contribute to white spotting in the horse. White markings and spotting are under selection for their impact on the economic value of an equine, yet many phenotypes have an unknown genetic basis. Previous studies also demonstrate an interaction between MC1R and ASIP pigmentation loci and white spotting associated with KIT and MITF. We investigated two stallions presenting with a white spotting phenotype of unknown cause. Exon sequencing of the KIT and MITF candidate genes identified a missense variant in KIT (rs1140732842, NC_009146.3:g.79566881T>C, p.T391A) predicted by SIFT and PROVEAN as not tolerated/deleterious. Three independent observers generated an Average Grade of White (AGW) phenotype score for 147 individuals based on photographs. The KIT variant demonstrates a significant QTL association to AGW (p = 3.3 × 10−12). Association with the MC1R Extension locus demonstrated that, although not in LD, MC1R e/e (chestnut) individuals had higher AGW scores than MC1R E/- individuals (p = 3.09 × 10−17). We also report complete linkage of the previously reported KIT W19 allele to this missense variant. We propose to term this variant W34, following the standardized nomenclature for white spotting variants within the equine KIT gene, and report its epistatic interaction with MC1R.

Demystifying the Genetic Origins of the Mangalarga Horse Through the Influential Stallion Turbante J.O.

Pedigrees and horse written ancestry contain numerous inconsistencies and divergence between farm histories, owner accounts and registration records. In particular, the origins of the Brazilian Mangalarga, or "Mangalarga Paulista'' horse breed is controversial, and the breed's popular history claims that one of its most famous individuals, Turbante J.O., may have been sired by an unknown Hanoverian stallion. Turbante J.O. sired over 1678 offspring and is present in about 71% of the male pedigrees. We genotyped Turbante J.O. and 29 registered Mangalarga individuals using a commercially available ancestry service and compared genomic to pedigree-based estimates. DNA was extracted for this sire from frozen semen samples. Other breed-average genomic ancestries for the Arabian, Thoroughbred, Saddlebred, and Hanoverian were utilized for comparison. Pedigree-based inbreeding coefficient (Fped) of Turbante J.O. and the 17 other Mangalargas were analyzed, and while Turbante J.O.'s Fped is estimated to be 18.5%, the genomic-based inbreeding coefficient is 33%. Pedigree-based co-ancestry coefficients estimate that about 3% of his ancestry should reflect Thoroughbred and Arabian heritage, however, the genomic analysis of Turbante J.O. identified 100% Iberian ancestry, and 99% in common with other Mangalarga individuals followed by other autochthonous Brazilian breeds, with no evidence of Hanoverian parentage. We demonstrate higher pedigree-estimated inbreeding coefficient errors than previously reported, perhaps a result of the pedigree depth, and the ability of genomic ancestral analysis to answer questions that pedigree analyses cannot. Due to the genomic relatedness, these results may provide more detailed guidelines in maintaining genetic diversity in this breed through selective outbreeding.

Ion Channel and Ubiquitin Differential Expression during Erythromycin-Induced Anhidrosis in Foals.

Macrolide drugs are the treatment of choice for Rhodococcus equi infections, despite severe side-effects temporary anhidrosis as a. To better understand the molecular biology leading to macrolide induced anhidrosis, we performed skin biopsies and Quantitative Intradermal Terbutaline Sweat Tests (QITSTs) in six healthy pony-cross foals for three different timepoints during erythromycin administration-pre-treatment (baseline), during anhidrosis and post-recovery. RNA sequencing of biopsies followed by differential gene expression analysis compared both pre and post normal sweating timepoints to the erythromycin induced anhidrosis episode. After Bonferroni correction for multiple testing, 132 gene transcripts were significantly differentially expressed during the anhidrotic timepoint. Gene ontology analysis of the full differentially expressed gene set identified over-represented biological functions for ubiquitination and ion-channel function, both biologically relevant to sweat production. These same mechanisms were previously implicated in heritable equine idiopathic anhidrosis and sweat gland function and their involvement in macrolide-induced temporary anhidrosis warrants further investigation.

Attack of the dark clones the genetics of reproductive and color traits of South African honey bees (Apis mellifera spp.).

The traits of two subspecies of western honey bees, Apis mellifera scutellata and A.m. capensis, endemic to the Republic of South Africa (RSA), are of biological and commercial relevance. Nevertheless, the genetic basis of important phenotypes found in these subspecies remains poorly understood. We performed a genome wide association study on three traits of biological relevance in 234 A.m. capensis, 73 A.m. scutellata and 158 hybrid individuals. Thirteen markers were significantly associated to at least one trait (P ≤ 4.28 × 10-6): one for ovariole number, four for scutellar plate and eight for tergite color. We discovered two possible causative variants associated to the respective phenotypes: a deletion in GB46429 or Ebony (NC_007070.3:g.14101325G>del) (R69Efs*85) and a nonsense on GB54634 (NC_007076.3:g.4492792A>G;p.Tyr128*) causing a premature stop, substantially shortening the predicted protein. The mutant genotypes are significantly associated to phenotypes in A.m. capensis. Loss-of-function of Ebony can cause accumulation of circulating dopamine, and increased dopamine levels correlate to ovary development in queenless workers and pheromone production. Allelic association (P = 1.824 x 10-5) of NC_007076.3:g.4492792A>G;p.Tyr128* to ovariole number warrants further investigation into function and expression of the GB54634 gene. Our results highlight genetic components of relevant production/conservation behavioral phenotypes in honey bees.

Hereditary Equine Regional Dermal Asthenia homozygote adult working horse with mild signs - A Case Report.

Hereditary Equine Regional Dermal Asthenia (HERDA) is an autosomal recessive condition present in the American Quarter Horse and other related breeds. Resulting from a mutation in the peptidyl-prolyl cis-trans isomerase B (PPIB) gene, HERDA is homologous to Ehlers-Danlos syndrome in humans. Characterized by fragile, hyperelastic, skin, HERDA affected horses often present first with slow-healing wounds usually on the dorsum, and resulting in atrophic scars, seromas, and ulcers. As there is no treatment for the condition affected horses are typically reported to be unrideable, and if persistent wounds are sufficiently severe, may require euthanasia. This case report describes clinical presentation and genetic diagnostics of HERDA in an 8-year-old horse with notably mild clinical signs, previously undiagnosed. On recommendation from the referring veterinarian, the horse owners pursued genetic diagnostics for HERDA following development of painful dorsal skin lesions under the saddle area during a riding clinic. The individual was confirmed homozygous for HERDA c.115G>A missense mutation in the PPIB gene by commercial testing service (Etalon Diagnostics Inc.). Further objective studies on the severity and clinical presentation of HERDA are necessary to evaluate complex elements of this disease. Furthermore, mildly affected individuals may be underdiagnosed as a result of not demonstrating the clinical signs that commonly encourage genetic testing.

Two Variants of KIT Causing White Patterning in Stock-Type Horses.

Over 30 polymorphisms in the KIT Proto-Oncogene Receptor Tyrosine Kinase (KIT) gene have been implicated in white spotting patterns ranging from small areas to full dermal depigmentation in the horse. We performed a candidate-gene exon sequencing approach on KIT and MITF, 2 known causatives of white spotting patterns, within 2 families of horses of unknown white spotting. Family 1 (Fam1, N = 5) consisted of a Quarter Horse stallion and 4 offspring with white spotting pattern ranging from legs, lower ventral, and head regions with jagged borders, to almost complete white. The second family (Fam2, N = 7) consisted of 6 half-sibling American Paint Horse/Quarter Horse and their dam, demonstrating unpigmented limbs with belly spots and an extensive white patterning on the face. This approach resulted in 2 variants significantly associated with familial phenotypes, where Fam1 variant is an indel leading to a frameshift mutation, and Fam2 a non-synonymous SNP. We validated the variants within an unrelated population of horses (Fam2 variant, P = 0.00271944) as well as for protein functional impact with ExPASy, Protter, Phyre2, SMART, PROVEAN, SIFT, and I-TASSER, confirming the reported associations. Fam1 associated variant, deemed W31, alters the protein sequence, leading to an early stop codon truncating the normal amino acid sequence from 972 to just 115 amino acids. Fam2 associated variant, deemed W32, may have a subtle impact on receptor function or could be in linkage with a non-coding or regulatory change creating the mild spotting pattern observed in this family.

Genomic Association of Chronic Idiopathic Anhidrosis to a Potassium Channel Subunit in a Large Animal Model.

Similar to humans, the horse relies predominantly on the evaporation of sweat from the skin surface to dissipate excess body heat. Loss of the sweat response or anhidrosis can result in life-threatening hyperthermia. Anhidrosis occurs more frequently in some breeds as well as occurs at an increased frequency among individuals with a family history, suggesting a heritable component to the pathology. Given the natural occurrence and indications of genetic components in the etiology, we utilized genomics to better understand the molecular mechanisms involved in sweat response. We performed a case-control (n = 200) GWAS targeting cases of chronic idiopathic anhidrosis in a controlled genetic background to discover the contributing regions and interrogated gene function for roles in the sweating mechanism. A region containing the KCNE4 gene, which encodes the ß-subunit of a potassium channel protein with a possible function in sweat gland outflow, was associated (P = 1.13 × 10-07) with chronic idiopathic anhidrosis through GWAS. A candidate mutation (NC_009149.3:g.11813731A > G, rs68643109) disrupting the KCNE4 protein structure could explain the disease but requires further investigation in larger populations. We show the potential role of ion channels and cellular damage in sweat response, correlating anhidrosis as a possible effect of congenital channelopathy.

Metabogenomics reveals four candidate regions involved in the pathophysiology of Equine Metabolic Syndrome.

An analogous condition to human metabolic syndrome, Equine Metabolic Syndrome (EMS) is defined by several clinical signs including obesity, hyperinsulinemia, and peripheral insulin dysregulation (ID). Affected horses may also exhibit hypertension, hyperlipemia and systemic inflammation. Measures of ID typically comprise the gold-standard for diagnosis in veterinary care. Yet, the dynamic nature of insulin homeostasis and complex procedures of typical assays make accurate quantification of ID and EMS challenging. This work aimed to investigate new strategies for identification of biochemical markers and correlated genes in EMS. To quantify EMS risk within this population, we utilized a composite score derived from nine common diagnostic variables. We applied a global liquid chromatography/mass spectroscopy approach (HPLC/MS) to whole plasma collected from 49 Arabian horses, resulting in 3392 high-confidence features and identification of putative metabolites in public databases. We performed a genome wide association analysis with genotypes from the 670k Affymetrix Equine SNP array utilizing EMS-correlated metabolites as phenotypes. We discovered four metabolite features significantly correlated with EMS score (P < 1.474 × 10-5). GWAs for these features results (P = 6.787 × 10-7, Bonferroni) identified four unique candidate regions (r2 > 0.4) containing 63 genes. Significant genomic markers capture 43.52% of the variation in the original EMS score phenotype. The identified genomic loci provide insight into the pathways controlling variation in EMS and the origin of genetic predisposition to the condition. Rapid, feasible and accurate diagnostic tools derived from metabogenomics can be translated into measurable benefits in the timeline and quality of preventative management practices to preserve health in horses.