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Congenital stationary night blindness (CSNB) is an ocular disorder characterized by nyctalopia. An autosomal recessive missense mutation in glutamate metabotropic receptor 6 (GRM6 c.533C>T, p.(Thr178Met)), called CSNB2, was previously identified in one Tennessee Walking Horse and predicted to reduce binding affinity of the neurotransmitter glutamate, impacting the retinal rod ON‐bipolar cell signaling pathway. Thus, the first aim was to identify the allele frequency (AF) of CSNB2 in breeds with reported cases of CSNB and breeds closely related to the Tennessee Walking Horse. The second aim was to perform ocular examinations in multiple breeds to confirm the link between genotype and CSNB phenotype. In evaluating 3518 horses from 14 breeds, the CSNB2 allele was identified in nine previously unreported breeds. The estimated AF was highest in pacing Standardbreds (0.17) and lowest in American Quarter Horses (0.0010). Complete ophthalmic examinations and electroretinograms (ERG) were performed on 19 horses from three breeds, including one CSNB2 homozygote from each breed. All three CSNB2/CSNB2 horses had an electronegative ERG waveform under scotopic light conditions consistent with CSNB. The remaining 16 horses (seven CSNB2/N and nine N/N) had normal scotopic ERG results. All horses had normal photopic ERGs. This study provides additional evidence that GRM6 c.533C>T homozygosity is likely causal to CSNB in Tennessee Walking Horses, Standardbreds, and Missouri Fox Trotting Horses. Genetic testing is recommended for breeds with the CSNB2 allele to limit the production of affected horses. This study represents the largest across‐breed identification of CSNB in the horse and suggests that this disorder is likely underdiagnosed. [ABSTRACT FROM AUTHOR]

Background: Genetic testing is required for the registration of foals of most equine breeds. Objectives: To describe two clinical cases of marked delayed embryonic development or delayed fertilisation in pregnancies generated by embryo transfer. Study design: Case report. Methods: Donor mares were inseminated with semen from one stallion during one oestrous cycle and semen from a different stallion on the subsequent oestrous cycle. Embryo(s) were collected 8 days after ovulation during the second oestrous cycle and transferred into synchronised recipient mares. Genetic testing was performed to determine parentage of the two foals. Results: For both foals, DNA parentage testing excluded the second stallion as the genetic sire and confirmed that the first stallion, whose semen was inseminated on the previous oestrous cycle, was the actual genetic sire. Main limitations: Rare event in horses; two clinical cases are described. Conclusions: It is hypothesised that either marked delayed embryonic development or extended sperm survival occurred in the donor mares. Without genetic testing, parentage assignment based solely on breeding records would have been incorrect. [ABSTRACT FROM AUTHOR]

Background: Globoid cell leukodystrophy (GCL) is a fatal autosomal recessive disease caused by variants in the galactosylceramidase (GALC) gene. Two dog breed‐specific variants are reported. Objectives: Characterize the putatively causative GALC variant for GCL in a family of dogs and determine population allele frequency. Animals: Four related mixed‐breed puppies with signs of neurologic disease were evaluated. Subsequently, 33 related dogs were tested for genetic markers for parentage and the identified GALC variant. Additional GALC genotyping was performed on 278 banked samples from various breeds. Methods: The 4 affected puppies had neurological exams and necropsies. DNA was isolated from blood samples. Variants in GALC were identified via Sanger sequencing. Parentage testing was performed using short tandem repeat markers. Prevalence of the GALC variant of interest was investigated in other breeds. Results: GCL was confirmed histopathologically. A novel missense variant in GALC (NC_006590.4:g.58893972G>A) was homozygous in all affected animals (n = 4). A recessive mode of inheritance was confirmed by parentage testing as was variant linkage with the phenotype (LOD = 3.36). Among the related dogs (n = 33), 3 dogs were homozygous and 7 heterozygous. The variant allele was not detected in screening 278 dogs from 5 breeds. The novel variant is either unique to this family or has an extremely low allele frequency in the general population. Conclusions and Clinical Importance: A novel GALC variant was identified that likely explains GCL in this cohort. The identification of multiple causal variants for GCL in dogs is consistent with findings in humans. [ABSTRACT FROM AUTHOR]

Background: Equine recurrent uveitis (ERU) is the leading cause of blindness for horses; previous research implicated the leopard complex spotting allele (LP) as a genetic risk factor for insidious uveitis in the Appaloosa. There is limited information about risk in the Knabstrupper. Objective: To evaluate clinical manifestations, disease frequency and potential risk factors for ERU in Knabstrupper horses. Study design: Cross‐sectional study. Methods: Ocular examinations were performed on 116 horses, and based on identified anomalies, horses were classified as suspect, ERU‐affected or having no clinical signs. Microagglutination testing (MAT) of serum assessed exposure to Leptospira spp. Clinical signs, age, sex, base colour, coat pattern, LP and PATN1 genotypes, percent white at birth, progressive roaning and Leptospira were assessed as risk factors using multivariable exact logistic regression, accounting for clustering at the barn level. Additionally, a pedigree analysis was performed (n = 20 cases and 21 controls), and coefficients of coancestry (CC) and inbreeding were calculated. Results: Prevalence of insidious uveitis in this sample of Knabstruppers was 20.7%. Similar to findings for Appaloosas, LP homozygotes had higher odds of uveitis compared with true solid (N/N) horses (LP/LP OR = 7.64, 95% CI [0.8 to +INF], p = 0.04) and age was also identified as a risk factor. After accounting for LP, the 16–20 age group had higher odds compared with the youngest group (OR = 13.36, 95% CI [1.4–213.4], p = 0.009). The distributions of average CC were significantly different between cases and controls (p = 0.01). Main limitations: A relatively small sample size decreased the power for detecting additional associations. The progressive nature of insidious uveitis may have prevented identification of younger affected horses. Conclusions: Our data support genotyping for LP to assess risk of ERU in Knabstruppers. Additional studies are necessary to develop more robust risk models across LP breeds for earlier detection and improved clinical management. [ABSTRACT FROM AUTHOR]

Background: Equine familial isolated hypoparathyroidism (EFIH) and fragile foal syndrome (FFS) are both fatal recessive conditions reported in Thoroughbred foals. The causal variants for EFIH (RAPGEF5 c.2624C>A; EquCab3.0. chr4: g.54108297G>T) and FFS (PLOD1 c.2032G>A; EquCab3.0, chr2: g.39927817) were recently reported. Prevalence assessment for these variants in a large cohort of samples is needed to provide evidence‐based recommendations for genetic testing. Objectives: To estimate the frequency of the EFIH and FFS variant alleles in the United States Thoroughbred population between 1988 and 2019, and determine whether these are recent mutations or are increasing in frequency due to current breeding practices. Study design: Population allele frequency study. Methods: Genomic DNA from hair and serum samples were genotyped for the EFIH and FFS. Allele frequencies between cohorts, based on year of birth (1988–2000, n = 728) and (2001–2019, n = 1059), as well as across the seven geographical regions of the United States were compared by Fisher's Exact tests. Results: EFIH and FFS allele frequencies were not significantly different between the two time points studied (0.008 and 0.004, respectively, in the older cohorts and 0.008 and 0.009 in most recent years). No EFIH or FFS homozygotes were detected. A sample from 1992 was identified as a carrier for EFIH and one from 1993 a carrier for FFS. Non‐significant changes in geographical distribution of carriers for both traits were observed. Main limitations: The earliest samples available for study were from foals born in 1988. Conclusions: The EFIH and FFS variants are present at low frequency in the United States Thoroughbred population but are not recent mutations. There is no evidence to support changes in allele frequency over time. However, given the closed studbook and breeding practices, continued monitoring of breed allele frequencies and genetic testing is recommended to avoid the mating of carriers and production of affected foals. [ABSTRACT FROM AUTHOR]

Equine recurrent uveitis (ERU) is an ocular inflammatory disease that can be difficult to manage clinically. As such, it is the leading cause of bilateral blindness for horses. ERU is suspected to have a complex autoimmune etiology with both environmental and genetic risk factors contributing to onset and disease progression in some or all cases. Work in recent years has aimed at unraveling the primary triggers, such as infectious agents and inherited breed‐specific risk factors, for disease onset, persistence, and progression. This review has aimed at encompassing those factors that have been associated, implicated, or substantiated as contributors to ERU, as well as identifying areas for which additional knowledge is needed to better understand risk for disease onset and progression. A greater understanding of the risk factors for ERU will enable earlier detection and better prognosis through prevention and new therapeutics. [ABSTRACT FROM AUTHOR]

Summary: Individual variation in opioid sensitivity can have a profound impact on the safety and efficacy of equine veterinary treatments, with the ability to adequately manage equine pain in a clinical setting currently limited. This review aims to explore the overlap between biological mechanisms associated with opioid metabolism and those mechanisms associated with coat colour in horses as has been documented in humans, with particular focus on the melanocortin‐1 receptor (MC1R) gene. In the future, the use of the MC1R coat colour genotype could help to indicate variable opioid sensitivities thereby greatly improving the use of opioids in clinical settings. The MC1R gene has a well‐established role in melanogenesis and pigment switching, but involvement in the pain‐modulating periaqueductal grey (PAG) descending pathway and in immune responses, both of which contain opioid receptors, has also been suggested in humans. However, this relationship between opioid metabolism and the connection to the three known MC1R variants (EE, Ee and Eea) in horses is yet to be explored. [ABSTRACT FROM AUTHOR]

Equine recurrent uveitis (ERU) is a blinding ocular disorder among horses, and the Appaloosa horse breed is disproportionally affected by a chronic form of this intraocular inflammatory disease known as insidious uveitis. Strong breed predisposition and previous investigations suggest that there is a genetic component to the pathology of insidious uveitis among Appaloosa horses; however, no estimates of the heritability of the disease have previously been determined. This study aimed to characterize the genetic underpinning of the disease by estimating the heritability for insidious uveitis among Appaloosas. After combining two genotyping array datasets from the Illumina Equine SNP70 BeadChip and the Axiom Equine 670 K Genotyping Array, heritability was estimated for 59 affected and 83 unaffected horses using both restricted maximum likelihood (REML) and phenotype correlation – genotype correlation solvers from the linkage disequilibrium adjusted kinship software. Based on previous research, age and sex were used as covariates, and the locus responsible for the characteristic Appaloosa coat pattern (LP), previously associated with ERU risk, was included as a fixed effect ('top predictor'). Using prevalence values from 0.05 to 0.42, the heritability estimate for insidious uveitis ranged from 0.95 (SE = 0.14) to 1.74 (SE = 0.25) with LP contributing 0.16–0.33 to the estimate. This study suggests that insidious uveitis is highly heritable (REML 95% CI, h2 = 0.68–1.0) and additional loci outside of LP are contributing to the genetic risk for insidious uveitis for Appaloosas. Once identified, these other genetic factors may lead to new disease mitigation efforts in veterinary care and breeding practices. [ABSTRACT FROM AUTHOR]

Summary: Background: Warmblood Fragile Foal Syndrome Type 1 (WFFS) is an autosomal recessive disorder reported previously only in warmbloods and thought to be caused by a variant in the gene procollagen‐lysine,2‐oxoglutarate 5‐dioxygenase 1 (PLOD1, c.2032G>A, p.Gly678Arg). Given the presentation of this Thoroughbred case, we hypothesised that a similar genetic mechanism caused this phenotype. Objectives: To describe the pathological and genetic findings on a foal presenting to a veterinary practice in the UK with skin lesions similar to other Ehlers‐Danlos Syndromes, including those documented for warmbloods with WFFS. Study design: A single case report describing a genetic investigation. Methods: A Thoroughbred foal presenting as dystocia was euthanised for multiple skin lesions and developmental abnormalities. DNA extracted from the foal was tested for the PLOD1 variant (c.2032G>A, p.Gly678Arg) using the commercially available assay. To confirm causality and further interrogate potential novel causes of Ehlers‐Danlos Syndrome, 1799 functional candidate genes, including PLOD1, were analysed using whole genome sequencing data generated from DNA extracted from the foal's muscle. These data were compared to 34 control samples from at least 11 other breeds. Variants were prioritised for further evaluation based on predicted impact on protein function. Results: Post‐mortem evaluation concluded that this foal suffered from a condition of collagen dysplasia. The foal was homozygous for the c.2032G>A PLOD1 variant. Only two other missense variants identified from whole genome sequencing data were also computationally predicted to be deleterious to protein function, (NPHP3 c.1253T>C, p.Leu418Pro, EPDR1 c.154G>C, p.Glu52Gln). Neither of these genes have been linked to similar phenotypes, or Ehlers‐Danlos Syndrome in humans or other species and thus further investigation of these variants as the cause of EDS was not warranted. Main limitations: This study is a single case report in the Thoroughbred with no additional cases from this breed yet identified to replicate this finding. Conclusions: Given the clinical presentation similar to WFFS, homozygosity for the PLOD1 variant, and absence of another more plausible causal variant from the WGS experiment, we conclude that PLOD1 c.2032G>A is the likely cause of this foal's condition. This is the first documented evidence of fragile foal syndrome caused by the PLOD1 variant in a breed outside of warmbloods, the Thoroughbred. We therefore recommend a change in the name of this disorder to fragile foal syndrome type 1 (FFS) and utilisation of genetic testing in Thoroughbreds to avoid producing affected foals. [ABSTRACT FROM AUTHOR]

Summary: Equine recurrent uveitis (ERU) is an autoimmune disease defined by inflammation of the uveal tract of the eye. The cause of ERU is thought to be complex, involving both genetic and environmental factors. The purpose of this study was to investigate potential genetic risk factors for ERU in the Icelandic horse. Fifty‐six Icelandic horses (11 affected with ERU and 45 controls) living in Denmark and the USA, eight years or older, were included in the study. A case–control GWAS was performed using the GGP Equine 80K array on the Illumina Infinium HD Beadchip using 40 horses. A mixed linear model analysis identified a single SNP on ECA 11 (BIEC2_141650; NC_009154.3:g.3817009A>G) that reached genome‐wide significance (p = 1.79 × 10−7). This variant was within an intron of tissue inhibitor of metalloproteinase 2 (TIMP2), a gene previously implicated in ERU. Sanger sequencing identified a single coding variant in this gene; however it was a synonymous mutation (NC_009154.3:g.3858193C>T) and was not perfectly concordant with ERU phenotype (p = 0.68). Further investigation of TIMP2 is warranted. Additional horses and markers are needed to identify other potential loci worthy of further investigation as contributors to ERU risk in Icelandic horses. [ABSTRACT FROM AUTHOR]

Background: The prevalence of clinical signs and factors triggering muscle atrophy and rhabdomyolysis associated with an MYH1E321G mutation in Quarter Horses and related breeds (QH) remain poorly understood. Hypothesis/Objectives: Determine the prevalence and potential triggers of atrophy and stiffness in horses homozygous reference (N/N), heterozygous (My/N), and homozygous (My/My) for the MYH1E321G mutation. Animals: Two‐hundred seventy‐five N/N, 100 My/N, and 10 My/My QH. Methods: A retrospective case‐control study using a closed‐ended questionnaire completed by clients of the Veterinary Genetics Laboratory at the University of California, Davis. History of clinical signs, disease, vaccination and performance were analyzed by genotype using contingency testing. Results: Atrophy occurred in proportionately more horses with MYH1E321G (My) than N/N QH and more frequently in My/My than My/N QH (P <.001; My/My 8/10 [80%], My/N 17/100 [17%], N/N 29/275 [11%]). More My/My horses had rapid atrophy (P <.001), with recurrence in 50%. Fewer My/My horses recovered versus My/N QH (P <.001). Stiffness was common across genotypes (P =.100; My/My 4/10 [40%], My/N 18/100 [18%], N/N 48/275 [17%]). Three months before the observed atrophy and stiffness, 47% of MYH1E321G QH were vaccinated or had respiratory or gastrointestinal disease. Horses achieving 100% expected performance did not differ across genotypes (50% My/My, 71% My/N, 55% N/N), but, only 4/10 My/My QH were competing. My/N horses achieved national or world championships or both. Conclusion and Clinical Importance: Approximately 20% of My/N QH develop rapid atrophy. Atrophy is more common (80%) in homozygous My/My QH and less likely to resolve. Inciting causes such as vaccination and infection are inapparent in over half of cases. [ABSTRACT FROM AUTHOR]

Summary: Tabby patterns of fur coats are defining characteristics in wild and domestic felids. Historically, three autosomal alleles at one locus (Tabby): Abyssinian (Ta; a.k.a. ticked), mackerel (Tm; a.k.a. striped) and blotched (tb; a.k.a. classic, blotched) were thought to control these patterns in domestic cats and their breeds. Currently, at least three loci influence cat tabby markings, two of which are designated Tabby and Ticked. The Tabby locus is laeverin (LVRN) and affects the mackerel and blotched patterns. The unidentified gene for the Ticked locus on cat chromosome B1 was suggested to control the presence or absence of the ticked pattern (Tabby – Abyssinian (Ta; a.k.a. ticked). The cat reference genome (Cinnamon, the Abyssinian) has the ticked phenotype and the variant dataset and coat phenotypes from the 99 Lives Cat Genome Consortium (195 cats) were used to identify candidate genes and variants associated with the Ticked locus. Two strategies were used to find the Ticked allele(s), one considered Cinnamon with the reference allele or heterozygous (Strategy A) and the other considered Cinnamon as having the variant allele or heterozygous (Strategy B). For Strategy A, two variants in Dickkopf Wnt Signaling Pathway Inhibitor 4 (DKK4), a p.Cys63Tyr (B1:41621481, c.188G>A) and a less common p.Ala18Val (B1:42620835, c.53C>T) variant are suggested as two alleles influencing the Ticked phenotype. Bioinformatic and molecular modeling analysis suggests that these changes disrupt a key disulfide bond in the Dkk4 cysteine‐rich domain 1 or Dkk4 signal peptide cleavage respectively. All coding variants were excluded as Ticked alleles using Strategy B. [ABSTRACT FROM AUTHOR]

Background: The only known genetic cause of congenital stationary night blindness (CSNB) in horses is a 1378 bp insertion in TRPM1. However, an affected Tennessee Walking Horse was found to have no copies of this variant. Objectives: To identify the genetic cause for CSNB in an affected Tennessee Walking Horse. Study design: Case report detailing a whole‐genome sequencing (WGS) approach to identify a causal variant. Methods: A complete ophthalmic exam, including an electroretinogram (ERG), was performed on suspected CSNB‐affected horse. WGS data were generated from the case and compared with data from seven other breeds (n = 29). One hundred candidate genes were evaluated for coding variants homozygous in the case and absent in all other horses. Protein modelling was used to assess the functional effects of the identified variant. A random cohort of 90 unrelated Tennessee Walking Horses and 273 horses from additional breeds were screened to estimate allele frequency of the GRM6 variant. Results: ERG results were consistent with CSNB. WGS analysis identified a missense mutation in metabotropic glutamate receptor 6 (GRM6) (c.533C>T p.Thr178Met). This single nucleotide polymorphism (SNP) is predicted to be deleterious and protein modelling supports impaired binding of the neurotransmitter glutamate. This variant was not detected in 273 horses from three additional breeds. The estimated allele frequency in Tennessee Walking Horses is 10%. Main limitations: Limited phenotype information for controls and no additional cases with which to replicate this finding. Conclusions: We identified a likely causal recessive missense variant in GRM6. Based on protein modelling, this variant alters GRM6 binding, and thus signalling from the retinal rod cell to the ON‐bipolar cell, impairing vision in low light conditions. Given the 10% population allele frequency, it is likely that additional affected horses exist in this breed and further work is needed to identify and examine these animals. [ABSTRACT FROM AUTHOR]

Objective: To characterize clinical manifestations, measure frequency, and evaluate risk factors for equine recurrent uveitis (ERU) in Appaloosa horses in western Canada. Animals: 145 Appaloosa horses. Procedures: Ophthalmic examinations were completed and eyes were classified as having no or mild clinical signs, or moderate, or severe damage from ERU. Clinical signs, age, sex, base coat color, and pattern were recorded. Whole blood and/or mane hair follicles were collected for DNA extraction, and all horses were tested for the leopard complex (LP) spotting pattern allele. Pedigree analysis was completed on affected and unaffected horses, and coefficients of coancestry (CC) and inbreeding (COI) were determined. Results: Equine recurrent uveitis was confirmed in 20 (14%) horses. The mean age of affected horses was 12.3 years (±5.3; range 3-25). Age was a significant risk factor for ERU diagnosis (ORyear = 1.15) and classification (ORyear = 1.19). The fewspot coat pattern was significantly associated with increased risk for ERU compared to horses that were minimally patterned or true solids. The LP/LP genotype was at a significantly greater risk for ERU compared to lp/lp (OR = 19.4) and LP/lp (OR = 6.37). Classification of ERU was greater in the LP/LP genotype compared to LP/lp. Affected horses had an average CC of 0.066, and there was a significant difference in the distribution of CC for affected horses versus the control group (P = .021). One affected horse was the sire or grandsire of nine other affected. Conclusions: Age, coat pattern, and genetics are major risk factors for the diagnosis and classification of ERU in the Appaloosa. [ABSTRACT FROM AUTHOR]

Equine recurrent uveitis (ERU) is an immune‐mediated disease causing repeated or persistent inflammatory episodes which can lead to blindness. Currently, there is no cure for horses with this disease. Mesenchymal stem cells (MSCs) are effective at reducing immune cell activation in vitro in many species, making them a potential therapeutic option for ERU. The objectives of this study were to define the lymphocyte phenotype of horses with ERU and to determine how MSCs alter T‐cell phenotype in vitro. Whole blood was taken from 7 horses with ERU and 10 healthy horses and peripheral blood mononuclear cells were isolated. The markers CD21, CD3, CD4, and CD8 were used to identify lymphocyte subsets while CD25, CD62L, Foxp3, IFNγ, and IL10 were used to identify T‐cell phenotype. Adipose‐derived MSCs were expanded, irradiated (to control proliferation), and incubated with CD4+ T‐cells from healthy horses, after which lymphocytes were collected and analyzed via flow cytometry. The percentages of T‐cells and B‐cells in horses with ERU were similar to normal horses. However, CD4+ T‐cells from horses with ERU expressed higher amounts of IFNγ indicating a pro‐inflammatory Th1 phenotype. When co‐incubated with MSCs, activated CD4+ T‐cells reduced expression of CD25, CD62L, Foxp3, and IFNγ. MSCs had a lesser ability to decrease activation when cell‐cell contact or prostaglandin signaling was blocked. MSCs continue to show promise as a treatment for ERU as they decreased the CD4+ T‐cell activation phenotype through a combination of cell‐cell contact and prostaglandin signaling. [ABSTRACT FROM AUTHOR]

Objective: To document a case of limbal squamous cell carcinoma (SCC) in a Rocky Mountain Horse stallion determined to be homozygous for the genetic risk factor (DDB2 c.1013C>T) strongly associated with the disease in Haflinger and Belgian horses, and to determine the frequency of this allele in a larger population of Rocky Mountain Horses. Animals studied: One privately owned Rocky Mountain Horse and 84 Rocky Mountain Horses screened for allelic frequency. Procedures: A complete ophthalmic examination was performed on a Rocky Mountain Horse stallion for assessment of a mass affecting the right eye. A clinical diagnosis of suspected limbal SCC was made, and routine keratoconjunctivectomy and adjunctive strontium irradiation were performed. Genotyping for the DDB2 c.1013C > T (rs1139682898) risk variant was performed utilizing an allele‐specific PCR assay on DNA isolated from whole blood and hair follicles. Results: Histopathology confirmed the limbal mass to be consistent with SCC. The horse was genotyped as homozygous for the DDB2 c.1013C >T risk variant. The frequency of the variant allele among a population of 84 Rocky Mountain Horses was found to be 0.20. Conclusion: The Rocky Mountain Horse breed possesses the DDB2 variant allele determined to be a significant risk factor for ocular SCC in the Haflinger and Belgian breeds. Genotyping additional Rocky Mountain Horses diagnosed with ocular SCC as well as confirmed healthy controls for this variant should be undertaken to determine whether a significant association exists between ocular SCC and the variant in the Rocky Mountain Horse breed. [ABSTRACT FROM AUTHOR]

Squamous cell carcinoma (SCC) is the most common cancer of the equine eye, frequently originating at the limbus, with the potential to invade the cornea, cause visual impairment, and result in loss of the eye. Several breeds of horses have a high occurrence of limbal SCC implicating a genetic basis for limbal SCC predisposition. Pedigree analysis in the Haflinger breed supports a simple recessive mode of inheritance and a genome-wide association study ( N = 23) identified a 1.5 Mb locus on ECA12 significantly associated with limbal SCC ( Pcorrected= 0.04). Sequencing the most physiologically relevant gene from this locus, damage specific DNA binding protein 2 ( DDB2), identified a missense mutation (c.1013 C > T p.Thr338Met) that was strongly associated with limbal SCC ( P = 3.41 × 10−10). Genotyping 42 polymorphisms narrowed the ECA12 candidate interval to 483 kb but did not identify another variant that was more strongly associated. DDB2 binds to ultraviolet light damaged DNA and recruits other proteins to perform global genome nucleotide excision repair. Computational modeling predicts this mutation to be deleterious by altering conformation of the β loop involved in photolesion recognition. This DDB2 variant was also detected in two other closely related breeds with reported cases of ocular SCC, the Belgian and the Percheron, suggesting it may also be a SCC risk factor in these breeds. Furthermore, in humans xeroderma pigmentosum complementation group E, a disease characterized by sun sensitivity and increased risk of cutaneous SCC and melanomas, is explained by mutations in DDB2. Cross-species comparison remains to be further evaluated. [ABSTRACT FROM AUTHOR]

The Functional Annotation of Animal Genomes ( FAANG) Consortium recently held a Gathering On FAANG ( GO- FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at . In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO- FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established. [ABSTRACT FROM AUTHOR]

Objective To describe the prevalence of LSCC in Haflinger horses and to analyze affected horses' pedigrees investigating the genetic mode of inheritance. Animals Fifteen horses met inclusion criterion of (i) being of the Haflinger breed, as confirmed by North American Haflinger Registry pedigree and (ii) being diagnosed with LSCC, as confirmed by clinical examination by a veterinary ophthalmologist or by histopathology. Pedigrees could not be obtained for four additional horses diagnosed with LSCC that had been identified as Haflingers. Procedure Retrospective medical record review of all 19 horses was used to determine patient sex and age at diagnosis. The four-generation pedigrees available for 15 of the horses were used to perform pedigree analysis. Results Average age of 19 Haflingers at diagnosis with LSCC was 8.7 years. Eleven were males and eight were females. Thirteen of 15 affected horses for whom pedigrees were available shared a common ancestor within five generations, and all 15 shared a common ancestor from the A stallion line in the breed pedigree. Pedigree analysis identified a common sire of two of the affected male horses. Clinical examination of this sire that had no history of LSCC showed no current clinical signs of LSCC, suggesting an autosomal recessive mode of inheritance. Conclusions Haflingers may be over-represented amongst horses with LSCC and may be diagnosed at a younger age than other breeds. Affected Haflingers appear closely related, suggesting a possible heritable basis for LSCC. The genetic basis for LSCC will be investigated further by a GWAS approach. [ABSTRACT FROM AUTHOR]

Objective To determine if congenital stationary night blindness (CSNB) exists in the miniature horse in association with leopard complex spotting patterns ( LP), and to investigate if CSNB in the miniature horse is associated with three single nucleotide polymorphisms (SNPs) in the region of TRPM1 that are highly associated with CSNB and LP in Appaloosas. Animals studied Three groups of miniature horses were studied based on coat patterns suggestive of LP/LP ( n = 3), LP/lp ( n = 4), and lp/lp genotype ( n = 4). Procedures Horses were categorized based on phenotype as well as pedigree analysis as LP/LP, LP/lp, and lp/lp. Neurophthalmic examination, slit-lamp biomicroscopy, indirect ophthalmoscopy, and scotopic flash electroretinography were performed on all horses. Hair samples were processed for DNA analysis. Three SNPs identified and associated with LP and CSNB in the Appaloosa were investigated for association with LP and CSNB in these Miniature horses. Results All horses in the LP/LP group were affected by CSNB, while none in the LP/lp or lp/lp groups were affected. All three SNPs were completely associated with LP genotype (χ2 = 22, P << 0.0005) and CSNB status (χ2 = 11, P < 0.0005). Conclusions The Miniature Horse breed is affected by CSNB and it appears to be associated with LP as in the Appaloosa breed. The SNPs tested could be used as a DNA test for CSNB until the causative mutation is determined. [ABSTRACT FROM AUTHOR]

Variants in the EDNRB, KIT, MITF, PAX3 and TRPM1 genes are known to cause white spotting phenotypes in horses, which can range from the common white markings up to completely white horses. In this study, we investigated these candidate genes in 169 horses with white spotting phenotypes not explained by the previously described variants. We identified a novel missense variant, PAX3:p.Pro32Arg, in Appaloosa horses with a splashed white phenotype in addition to their leopard complex spotting patterns. We also found three novel variants in the KIT gene. The splice site variant c.1346+1G>A occurred in a Swiss Warmblood horse with a pronounced depigmentation phenotype. The missense variant p.Tyr441Cys was present in several part-bred Arabians with sabino-like depigmentation phenotypes. Finally, we provide evidence suggesting that the common and widely distributed KIT:p.Arg682His variant has a very subtle white-increasing effect, which is much less pronounced than the effect of the other described KIT variants. We termed the new KIT variants W18-W20 to provide a simple and unambiguous nomenclature for future genetic testing applications. [ABSTRACT FROM AUTHOR]

The article presents a study which analyzes whether gene encoding biglycan (BGN) variants are as simple X-linked causative mutations for bilateral corneal stromal loss (BCSL) in Friesian horses. It mentions that pedigree analysis and gene sequencing was employed in the study. The study ruled out BGN as a candidate gene for a simple X-linked inheritance for BCSL.