The Genetics of Deafness in Domestic Animals

Sensorineural deafness in purebred white Devon Rex cats

BACKGROUND

Data regarding congenital sensorineural deafness (CSD) in client-owned, white Devon Rex cats is limited because most of the information on this disease comes from experiments on mixed-breed cats.

OBJECTIVES

Provide data on the occurrence of CSD in a population of client-owned purebred white Devon Rex cats.

ANIMALS

Forty client-owned, purebred, white Devon Rex cats examined at 2 different facilities. Median age of the examined cats was 19 weeks.

METHODS

Hearing status was defined by use of brainstem auditory evoked responses.

RESULTS

The occurrence of sensorineural deafness in the studied population of Devon Rex cats was estimated at 10%. Unilateral and bilateral deafness occurred equally often, with 2 individuals having each (ie, 5.0%). No association between the occurrence of CSD and sex could be found, χ2 (1, n = 40) = 0.001 (P > .99). No association between blue irises and deafness was noted in the studied population, χ2 (1, n = 40) < 0.01 (P > .99).

CONCLUSIONS

The occurrence of CSD in a population of client-owned, white Devon Rex cats was found to be lower compared with data obtained in previously conducted studies of deafness in purebred cats. In the studied population of Devon Rex cats, no association between blue irises and CSD was found.

Genetic insights into fiber quality, coat color and adaptation in Changthangi and Muzzafarnagri sheep: A comparative skin transcriptome analysis

Changthangi sheep, which inhabit the high-altitude regions of Ladakh, are known for their fine fiber production and are characterized by grey skin and either black or white coats. In contrast, Muzzafarnagri sheep from the plains of Uttar Pradesh produce coarse wool and have white skin and coats. We conducted comparative global gene expression profiling on four biological replicates of skin from each breed. Notably, our analysis identified 149 up-regulated genes and 2,139 down-regulated genes in Changthangi sheep compared to Muzzafarnagri sheep, with a p-adjusted value (padj) of ≤0.05 and a Log2 fold change of ≥1.5. Gene Ontology analysis of the up-regulated genes revealed an enrichment of terms related to melanin biosynthesis and developmental pigmentation. Additionally, enriched KEGG pathways included tyrosine metabolism and metabolic pathways. Among the melanogenesis-related genes that exhibited higher expression in Changthangi sheep were TYR, TYRP1, DCT, SLC45A2, PMEL, MLANA, and OCA2. These findings confirm melanin's role in both the animals' black coat color and UV protection at high-altitude. Furthermore, we observed more pronounced expression of genes related to fiber quality, namely KRTAP6, KRTAP7, KRTAP13, and KRTAP2, in the fine wool-producing sheep from Ladakh. The results of the RNA sequencing were validated using real-time PCR on 10 genes governing fiber quality and coat color, with ACTB and PPIB serving as reference genes. In conclusion, our comparative skin transcriptome analysis of Changthangi and Muzzafarnagri sheep sheds light on the genetic differences associated with distinct phenotypic traits and environmental adaptability, offering valuable insights into the underlying mechanisms.

Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data

The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the first intron of KIT by its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.

A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison)

Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.

Evaluation of the prevalence of congenital sensorineural deafness in a population of 72 client-owned purebred white cats examined from 2007 to 2021

Background

Data on sensorineural deafness (CSD) in purebred white client-owned cats is limited as most of the information on this disease entity is assured from mixed-breed experimental colonies. It is known that cats with blue irises are more predisposed to CSD having been described as a condition in which many structures in the inner ear are damaged resulting in hearing loss. Cats with CSD are born deaf or lose their hearing irreversibly within the first 4-5 weeks of life. It is important to diagnose cats with this hereditary condition in order to eliminate affected individuals from breeding. The objectives of this study were to ensure data on prevalence of CSD in a population of 72 client-owned purebred white cats in Poland according to the color of the irises and to determine if there are any predispositions with regard to CSD among different breeds of cats in which the dominant W gene is present.

Results

Conducted study included 72 purebred white cats from six different breeds. The prevalence of CSD in the conducted study was 16.7%, CI₉₅ [8.9%; 23.3%]. Unilateral deafness (11.1%, CI₉₅ [4.9%; 20.7%]) was more common than bilateral CSD (5.6%, CI₉₅ [1.5%; 13.6%]). The studies did not show any association between sex and CSD, p = .46. No association between the blue color of irises and deafness in the studied population could be found, p = .91. When compared to the rest of the examined population, no association was found between CSD and a particular breed.

Conclusions

Overall prevalence of CSD regarding the examined population of purebred client-owned cats was reported as lower when compared to previous studies concerning purebred cats. Cats with blue irises are more likely to be deaf in accordance to the current state of knowledge, however in the conducted study, no significant association between the presence of blue irises and deafness in white purebred cats could be identified. In order to eliminate CSD from the population, it is necessary to conduct examinations and diagnose CSD in white cats with blue irises as well as with irises of color other than blue. Association between particular breed and CSD wasn’t identified.

De-novo and genome-wide meta-analyses identify a risk haplotype for congenital sensorineural deafness in Dalmatian dogs

Congenital sensorineural deafness (CSD) has been reported to affect up to 30% of Dalmatian dogs world-wide and while unilaterally deaf dogs can live a close to normal life, dogs suffering bilateral deafness are frequently euthanized. Extreme-white coat patterning as encoded by the gene Melanocyte Inducing Transcription Factor (MITF) has long been postulated as the major risk factor for CSD in the Dalmatian breed. While attempts to identify causative risk variants associated with CSD have been numerous, no genome-wide association study has positively identified MITF as a risk locus for either bilateral or unilateral deafness in the Dalmatian breed to date. In this study, we identified an association with CSD on CFA20 in the vicinity of MITF within Australian Dalmatian dogs. Although not genome-wide significant, the association signal was validated by reanalysing publicly available data and merging the wider data resource with the local data to improve statistical power. The merged data, representing three major global populations of Dalmatian dogs, enabled us to identify a single, well-defined genome-wide significant risk haplotype for CSD. The haplotype was formed by three genome-wide significant associated markers (BICF2G630233852T>C, BICF2G630233861T>C, BICF2G630233888G>A) on CFA20 with 62% of bilaterally deaf dogs homozygous for the risk haplotype (CCA), while 30% of bilaterally deaf and 45% of hearing dogs carried one copy of the risk haplotype. Animals homozygous or heterozygous for the low-risk haplotype were less likely to be unilaterally deaf. While the association between the risk haplotype and deafness is incomplete, animals homozygous for the risk haplotype were 10-times more likely to be bilaterally deaf. Although the underlying causative variants are yet to be discovered, results from this study can now assist with reducing deafness in Dalmatian dogs.

Early onset adult deafness in the Rhodesian Ridgeback dog is associated with an in-frame deletion in the EPS8L2 gene

Domestic dogs exhibit diverse types of both congenital and non-congenital hearing losses. Rhodesian Ridgebacks can suffer from a progressive hearing loss in the early stage of their life, a condition known as early onset adult deafness (EOAD), where they lose their hearing ability within 1–2 years after birth. In order to investigate the genetic basis of this hereditary hearing disorder, we performed a genome-wide association study (GWAS) by using a sample of 23 affected and 162 control Rhodesian Ridgebacks. We identified a genomic region on canine chromosome 18 (CFA18) that is strongly associated with EOAD, and our subsequent targeted Sanger sequencing analysis identified a 12-bp inframe deletion in EPS8L2 (CFA18:25,868,739–25,868,751 in the UMICH_Zoey_3.1/canFam5 reference genome build). Additional genotyping confirmed a strong association between the 12-bp deletion and EOAD, where all affected dogs were homozygous for the deletion, while none of the control dogs was a deletion homozygote. A segregation pattern of this deletion in a 2-generation nuclear family indicated an autosomal recessive mode of inheritance. Since EPS8L2 plays a critical role in the maintenance and integrity of the inner ear hair cells in humans and other mammals, the inframe deletion found in this study represents a strong candidate causal mutation for EOAD in Rhodesian Ridgebacks. Genetic and clinical similarities between childhood deafness in humans and EOAD in Rhodesian Ridgebacks emphasizes the potential value of this dog breed in translational research in hereditary hearing disorders.

Congenital malformations of the external and middle ear accompanied by temporal bone anomaly in a calf

A 7-month-old female Holstein calf presented with bilateral microtia and absent external acoustic meatus. The real-time polymerase chain reaction test was negative for bovine viral diarrhea virus and bovine leukemia virus. The calf’s dam had a normal reproductive history. Computed tomography confirmed bilateral atresia of external auditory canals, aplasia of tympanic cavities and the ossicular chain, and temporomandibular joint abnormality. Necropsy revealed a severe malformation of the temporal bone. In the tympanic region, the external acoustic pore, tympanic bulla, and muscular process were absent bilaterally. The bilateral inner ear structure was normal. Based on these findings, we diagnosed the present case as congenital malformations of the external and middle ear accompanied by temporal bone anomaly.

Gentamicin-induced sensorineural auditory loss in healthy adult horses

Background

Irreversible sensorineural auditory loss has been reported in humans treated with aminoglycosides but not in horses.

Objective

Investigate if auditory loss occurs in horses treated using the recommended IV daily dosage of gentamicin for 7 consecutive days.

Animals

Ten healthy adult horses (7‐15 years; females and males, 5 each).

Methods

Prospective study. Physical and neurological examinations and renal function tests were performed. Gentamicin sulfate was administered at a dosage of 6.6 mg/kg via the jugular vein on alternating sides for 7 days. Gentamicin peak and trough concentrations were measured. Horses were sedated using detomidine hydrochloride IV to perform brainstem auditory evoked responses (BAER) before the first dose, immediately after the last dose, and 30 days after the last dose. Peaks latencies, amplitudes, and amplitude ratios were recorded. Data from the second and last BAER were compared to results at baseline. Bone conduction was performed to rule out conduction disorders.

Results

Seven horses had auditory loss: complete bilateral (N = 1), complete unilateral (N = 2), and partial unilateral (N = 4). Based on physical examination and BAER results, sensorineural auditory loss was suspected. Absent bone conduction ruled out a conduction disorder and further supported sensorineural auditory loss in horses with completely absent BAER. Auditory dysfunction was reversible in 4 of 7 horses.

Conclusions and Clinical Importance

Gentamicin at recommended doses may cause sensorineural auditory loss in horses that might be irreversible. Follow‐up studies are needed to investigate if other dosing protocols present a similar risk.

Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in genome-wide association study analyses

Pigment-associated deafness is a common hereditary condition in a range of dog breeds. The aim of this study was to perform a genome-wide association analysis to investigate the genetic architecture of deafness in Australian Cattle Dogs. Genotypes for 104 757 polymorphisms in 216 dogs were available for analyses after quality control. A genomic relationship matrix was used in the mixed model analyses to account for polygenic effects, as we tested each polymorphism for its association with deafness, in a case/control experimental design. Three approaches were used to code the genotypes and test for additive, recessive and dominant SNP effects. The genome-wide association study analyses identified a clear association peak on CFA20, with the most significant SNPs on this chromosome (1.29 × 10^-4 ) in the vicinity of MITF. Variants in MITF have been associated with white pigmentation in dogs and with deafness in humans and other species, supporting the premise that canine deafness is associated with variants in or near this gene. A recessive inheritance for the peak in CFA20 is possible given the significant results in the recessive model; however, the estimated heritability was low (4.54 × 10^-5 ). Further validation, identification of variants and testing in other dog breeds are needed.

Missense variant in LOXHD1 is associated with canine nonsyndromic hearing loss

Hearing loss is a common sensory deficit in both humans and dogs. In canines, the genetic basis is largely unknown, as genetic variants have only been identified for a syndromic form of hearing impairment. We observed a congenital or early-onset sensorineural hearing loss in a Rottweiler litter. Assuming an autosomal recessive inheritance, we used a combined approach of homozygosity mapping and genome sequencing to dissect the genetic background of the disorder. We identified a fully segregating missense variant in LOXHD1, a gene that is known to be essential for cochlear hair cell function and associated with nonsyndromic hearing loss in humans and mice. The canine LOXHD1 variant was specific to the Rottweiler breed in our study cohorts of pure-bred dogs. However, it also was present in some mixed-breed dogs, of which the majority showed Rottweiler ancestry. Low allele frequencies in these populations, 2.6% and 0.04%, indicate a rare variant. To summarize, our study describes the first genetic variant for canine nonsyndromic hearing loss, which is clinically and genetically similar to human LOXHD1-related hearing disorder, and therefore, provides a new large animal model for hearing loss. Equally important, the affected breed will benefit from a genetic test to eradicate this LOXHD1-related hearing disorder from the population.

A natural knockout of the MYO7A gene leads to pre-weaning mortality in pigs

The pig breeding system provides a unique framework to study recessive defects and the consequence on the phenotype. We examined a commercial synthetic Duroc population for recessive defects and identified a haplotype on chromosome 9 significantly affecting pre‐weaning mortality. To identify the causal variant underlying the mortality, we examined sequence data of four carrier animals and 21 non‐carrier animals from the same population. The results yield a strong candidate causal stop‐gained variant (NM_001099928.1:c.541C>T) affecting the MYO7A gene in complete linkage disequilibrium with the lethal haplotype. The variant leads to an impaired (p.Gln181*) MYO7A protein that truncates 2032 amino acids from the protein. We examined a litter from a carrier sow inseminated by a carrier boar. From the resulting piglets, two confirmed homozygous piglets suffered from severe balance difficulties and the inability to walk properly. The variant segregates at a carrier frequency of 8.2% in the evaluated population and will be gradually purged from the population, improving animal welfare. Finally, this 'natural knockout' will increase our understanding of the functioning of the MYO7A gene and provides a potential model for Usher syndrome in humans.

Congenital sensorineural deafness in Dogo Argentino dogs: Prevalence and phenotype associations

BACKGROUND

The Dogo Argentino dog breed is affected by hereditary congenital sensorineural deafness (CSD) associated with white pigmentation, but prevalence data and associations with phenotypes have not been reported.

METHODS

In a retrospective study, animals were tested by the brainstem auditory evoked response, and phenotype data of sex, iris color, patch presence/absence and parent hearing status were collected. Chi-square analyses were performed to identify associations between deafness and phenotype traits.

RESULTS

BAER results and phenotype data were collected for 811 dogs. Hearing status was 74.23% bilaterally hearing, 20.35% unilaterally deaf and 5.43% bilaterally deaf or an overall prevalence of 25.77%. CSD was not associated with sex, but dogs without a patch had a significantly higher prevalence rate than patched dogs. Blue-eyed dogs had higher prevalence rates than brown-eyed dogs, but because of small sample size the χ² association was not considered valid. Insufficient numbers of dogs with a unilaterally deaf parent were present to assess the effects of parent hearing status.

CONCLUSION

Approximately one fourth of a US Dogo Argentino population was deaf in one or both ears, but dogs with a patch had a lower prevalence. Dogs with a blue eye were more likely to be deaf, but the association significance could not be reliably assessed.

A Missense Mutation in the KLF7 Gene Is a Potential Candidate Variant for Congenital Deafness in Australian Stumpy Tail Cattle Dogs

Congenital deafness is prevalent among modern dog breeds, including Australian Stumpy Tail Cattle Dogs (ASCD). However, in ASCD, no causative gene has been identified so far. Therefore, we performed a genome-wide association study (GWAS) and whole genome sequencing (WGS) of affected and normal individuals. For GWAS, 3 bilateral deaf ASCDs, 43 herding dogs, and one unaffected ASCD were used, resulting in 13 significantly associated loci on 6 chromosomes, i.e., CFA3, 8, 17, 23, 28, and 37. CFA37 harbored a region with the most significant association (−log₁₀(9.54 × 10⁻²¹) = 20.02) as well as 7 of the 13 associated loci. For whole genome sequencing, the same three affected ASCDs and one unaffected ASCD were used. The WGS data were compared with 722 canine controls and filtered for protein coding and non-synonymous variants, resulting in four missense variants present only in the affected dogs. Using effect prediction tools, two variants remained with predicted deleterious effects within the Heart development protein with EGF like domains 1 (HEG1) gene (NC_006615.3: g.28028412G>C; XP_022269716.1: p.His531Asp) and Kruppel-like factor 7 (KLF7) gene (NC_006619.3: g.15562684G>A; XP_022270984.1: p.Leu173Phe). Due to its function as a regulator in heart and vessel formation and cardiovascular development, HEG1 was excluded as a candidate gene. On the other hand, KLF7 plays a crucial role in the nervous system, is expressed in the otic placode, and is reported to be involved in inner ear development. 55 additional ASCD samples (28 deaf and 27 normal hearing dogs) were genotyped for the KLF7 variant, and the variant remained significantly associated with deafness in ASCD (p = 0.014). Furthermore, 24 dogs with heterozygous or homozygous mutations were detected, including 18 deaf dogs. The penetrance was calculated to be 0.75, which is in agreement with previous reports. In conclusion, KLF7 is a promising candidate gene causative for ASCD deafness.

Brainstem auditory evoked responses and bone conduction assessment in alpacas

Auditory loss has been reported in camelids using brainstem auditory evoked responses (BAER). Differentiation between conductive versus sensorineural dysfunction has not been investigated. Therefore, the objective of the study was to investigate auditory function using BAER and bone conduction (BC). Twenty-four alpacas: 15 females, 9 intact males (2-16 years of age) were included in a randomized clinical trial. BAER and BC were recorded using two derivations (vertex to mastoid and vertex to cranial aspect of second cervical vertebra). All alpacas underwent complete physical examinations and were sedated with xylazine hydrochloride at 0.6 mg/kg IM. Peaks, when present, were identified and latencies, amplitudes, and amplitude ratios were determined. Eleven alpacas had normal responses and 13 had auditory loss based on BAER. The latter consisted of complete absence of peaks bilaterally (n = 3), absence of peaks unilaterally (n = 1), delayed latencies bilaterally (n = 4), and delayed latencies unilaterally (n = 5). Distinct peaks on BC supported conductive auditory loss in 6 alpacas, difficult to interpret due to stimulus artifact and additional undefined peaks in 4, and absent peaks in 3 alpacas. The cause of auditory loss was presumed to be due to otitis in 6, aging in 4 (10-16 years old), and congenital sensorineural (absent peaks on BAER and BC) in 3 alpacas with unpigmented fiber and irises. BAER and BC are useful and non-invasive to perform techniques for the investigation of auditory loss in alpacas, and further characterization as conductive or sensorineural.

Genomic Regions Associated with Variation in Pigmentation Loss in Saddle Tan Beagles

Loss of pigmentation is a hallmark of domestication, and dogs offer a unique model for understanding the genetics of fur coloration. The aim of this study was to use dense genetic mapping to map loci underlying variations in color and whiteness in a population of laboratory beagles. A total of 190 beagles with well-defined pedigrees were phenotyped for the amount of white color in six different body parts, including the saddle. All individuals were genotyped on 85,172 informative and valid SNP-markers and the genome-wide associations for the amount of white in each body part were determined. There was a large variation in the amount of white on different parts of the body, and the whiteness was highly correlated within individuals, except for saddle color which was only moderately correlated with overall whiteness. The GWAS showed significant associations with two loci, one on chromosome 5, containing the MC1R gene, and one on chromosome 20, containing the MITF gene. Our results suggest that the variation in loss of pigmentation is largely a function of regulatory variation related to these genes.

Comparison of the efficacy of 2 sedative protocols in pediatric dogs undergoing brainstem auditory-evoked response testing

This study compared the quality of sedation with dexmedetomidine or alfaxalone during brainstem auditory-evoked response (BAER) tests in 6- to 17-week-old dogs. This was a prospective, randomized clinical study involving 19 client-owned pediatric dogs of breeds with reported congenital deafness. Group A (G_A) received alfaxalone, 2 mg/kg body weight (BW) (n = 9) and group D (G_D) dexmedetomidine, 0.005 mg/kg BW, and postprocedure antagonism with atipamezole (n = 10) intramuscularly. Time from injection to sedation, duration of sedation, sedation scores, need for re-dosing, rectal temperature, pulse and respiratory rate were recorded at baseline, before and after the BAER test, and once recovered from sedation. Pulse rate was significantly lower in G_D (P = 0.004) and the number of re-dosing was significantly higher in G_A (P = 0.011). Both sedation protocols allowed good quality BAER test recordings in pediatric dogs. Sedation with dexmedetomidine required less re-dosing, whereas alfaxalone maintained more physiological pulse rates.

Are dogs with congenital hearing and/or vision impairments so different from sensory normal dogs? A survey of demographics, morphology, health, behaviour, communication, and activities

The births of domestic dogs with pigment deletion and associated congenital hearing and/or vision impairments are increasing, as a result of mutations of certain genes expressing popular coat colour patterns (Merle, piebald, Irish spotting). The future of these dogs is often pessimistic (early euthanasia or placement in rescues/fosters, lack of interactions and activities for adults). These pessimistic scenarios result from popular assumptions predicting that dogs with congenital hearing/vision impairments exhibit severe Merle-related health troubles (cardiac, skeletal, neurological), impairment-related behavioural troubles (aggressiveness, anxiety), and poor capacities to communicate, to be trained, and to be engaged in leisure or work activities. However, there is no direct scientific testing, and hence no evidence or refutation, of these assumptions. We therefore addressed an online questionnaire to owners of 223 congenitally sensory impaired (23 vision impaired, 63 hearing impaired, 137 hearing and vision impaired) and 217 sensory normal dogs from various countries. The sensory normal cohort was matched in age, lifetime with owner, breed and sex with the sensory impaired cohort, and was used as a baseline. The questionnaire assessed demographics, morphology, sensory impairments, health and behavioural troubles, activities, and dog-owner communication. Most hearing and/or vision impaired dogs exhibited abnormal pigment deletion in their coat and irises. Vision impaired dogs additionally exhibited ophthalmic abnormalities typically related to Merle. The results are opposed to all above-listed assumptions, except for neurological troubles, which were more frequently reported in sensory impaired dogs. However, we suggest that this finding could be partially accounted for by a lack of diagnosis of breed-related drug sensitivity and impairment-related compulsive behaviours. Results about communication and activities are particularly optimistic. The need for future studies of numerous dogs from various breeds tested for Merle, piebald and medical-drug-resistance genes, and the beneficial effects that present and future research may have on the future of sensory impaired dogs, are discussed.

Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

BACKGROUND

Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca.

RESULTS

Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α.

CONCLUSIONS

The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.

Decline in prevalence of congenital sensorineural deafness in Dalmatian dogs in the United Kingdom

Background

Congenital sensorineural deafness (CSD) is the most common type of deafness in Dalmatian dogs.

Objectives

To use results of CSD screening in Dalmatian dogs in the United Kingdom in genetic analysis and to determine any changes in the prevalence of CSD in this breed over time.

Animals

A total of 8955 Dalmatian puppies undergoing hearing function screening using brainstem auditory evoked response (BAER) between July 1992 and February 2019.

Methods

Results of BAER testing and pigmentation phenotypic data were linked to the UK Kennel Club Dalmatian pedigree database. Mixed model analysis was used to estimate variance parameters.

Results

The overall prevalence of CSD was 17.8% (13.4%, unilateral; 4.4%, bilateral). Heritability of CSD was approximately 0.3 (across models) and significantly >0. Genetic correlations between CSD and blue irises (+0.6) and pigmented head patch (−0.86) were large in magnitude and significantly different form 0. Significant improving phenotypic and genetic trends were identified, likely as the result of selection against deafness, equivalent to avoiding breeding with the 4% to 5% of animals with the highest genetic risk of CSD.

Conclusions and Clinical Importance

A decrease in the prevalence and genetic risk of CSD implies breeders have been selecting for hearing dogs. Selective breeding based on estimated breeding values (EBVs) can help further decrease the prevalence of CSD in Dalmatians in the future.

A genome-wide association study of deafness in three canine breeds

Congenital deafness in the domestic dog is usually related to the presence of white pigmentation, which is controlled primarily by the piebald locus on chromosome 20 and also by merle on chromosome 10. Pigment-associated deafness is also seen in other species, including cats, mice, sheep, alpacas, horses, cows, pigs, and humans, but the genetic factors determining why some piebald or merle dogs develop deafness while others do not have yet to be determined. Here we perform a genome-wide association study (GWAS) to identify regions of the canine genome significantly associated with deafness in three dog breeds carrying piebald: Dalmatian, Australian cattle dog, and English setter. We include bilaterally deaf, unilaterally deaf, and matched control dogs from the same litter, phenotyped using the brainstem auditory evoked response (BAER) hearing test. Principal component analysis showed that we have different distributions of cases and controls in genetically distinct Dalmatian populations, therefore GWAS was performed separately for North American and UK samples. We identified one genome-wide significant association and 14 suggestive (chromosome-wide) associations using the GWAS design of bilaterally deaf vs. control Australian cattle dogs. However, these associations were not located on the same chromosome as the piebald locus, indicating the complexity of the genetics underlying this disease in the domestic dog. Because of this apparent complex genetic architecture, larger sample sizes may be needed to detect the genetic loci modulating risk in piebald dogs.

STRING data mining of GWAS data in canine hereditary pigment-associated deafness

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Genome-wide association studies may fail to identify significant associations between a disorder and causative genes in complex hereditary disorders.

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STRING software is a bioinformatics data mining tool that identifies known and predicted physical and functional relationship networks among the proteins of candidate genes.

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STRING analysis provides a mechanism to identify gene-gene interactions that might not otherwise have been recognized.

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Relationships identified from STRING analysis can uncover function-based gene-gene relationships that may not be easily extracted from literature, thereby providing genes for pursuit as a cause of a complex hereditary disorder.

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In this study STRING analysis was applied to identification of candidate genes to pursue as the cause of pigment-associated hereditary deafness in dogs.

Most canine deafness is linked to white pigmentation caused by the piebald locus, shown to be the gene MITF (melanocyte inducing transcription factor), but studies have failed to identify a deafness cause. The coding regions of MITF have not been shown to be mutated in deaf dogs, leading us to pursue genes acting on or controlled by MITF. We have genotyped DNA from 502 deaf and hearing Australian cattle dogs, Dalmatians, and English setters, breeds with a high deafness prevalence. Genome-wide significance was not attained in any of our analyses, but we did identify several suggestive associations. Genome-wide association studies (GWAS) in complex hereditary disorders frequently fail to identify causative gene variants, so advanced bioinformatics data mining techniques are needed to extract information to guide future studies.

STRING diagrams are graphical representations of known and predicted networks of protein-protein interactions, identifying documented relationships between gene proteins based on the scientific literature, to identify functional gene groupings to pursue for further scrutiny. The STRING program predicts associations at a preset confidence level and suggests biological functions based on the identified genes.

Starting with (1) genes within 500 kb of GWAS-suggested SNPs, (2) known pigmentation genes, (3) known human deafness genes, and (4) genes identified from proteomic analysis of the cochlea, we generated STRING diagrams that included these genes. We then reduced the number of genes by excluding genes with no relationship to auditory function, pigmentation, or relevant structures, and identified clusters of genes that warrant further investigation.

Eriodictyon angustifolium extract, but not Eriodictyon californicum extract, reduces human hair greying

OBJECTIVE

Yerba Santa (Eriodictyon angustifolium and Eriodictyon californicum) has been used for many years in traditional medicine. However, the effect of Yerba Santa on melanogenesis has not yet been investigated. We aimed to assess the biological effects of Yerba Santa on hair pigmentation.

METHODS

Yerba Santa extracts were assessed for their cytological effects following X-ray irradiation treatment and then tested directly for the prevention of human hair greying. Ultra-performance liquid chromatography (UPLC) was utilized to identify the individual extract components.

RESULTS

Eriodictyon angustifolium extract significantly increased melanin synthesis in the melanoma cell line through activation of the WNT/MITF/tyrosinase-signalling pathway. In contrast, E. californicum had no effect on melanin synthesis. E. angustifolium extract also demonstrated a protective effect against the damage induced by X-ray irradiation in human keratinocytes. Application of the extracts to subjects who had grey beards demonstrated a reduced number of grey beard hair per year specifically with the E. angustifolium extract. A significant decrease in grey head hair was also observed after application of E. angustifolium extract. Upregulation of gene expression related to melanin production and WNT signalling was observed after the application of E. angustifolium extract. Sterubin was the most abundant flavonoid detected by UPLC in E. angustifolium extract. In addition, sterubin showed the highest difference in terms of quantity, between E. angustifolium and E. californicum extract.

CONCLUSION

Eriodictyon angustifolium extract, which is abundant in sterubin, may be suitable as a potential cosmetic and medical agent for the prevention and improvement of hair greying.

Congenital sensorineural deafness in English setters in the United Kingdom: prevalence and association with phenotype and sex

BACKGROUND

The English setter (ES) is predisposed to congenital sensorineural deafness (CSD). CSD prevalence and association with phenotype in the UK ES population are previously unreported.

METHODS

The database of the authors' institution was searched for ES puppies undergoing brainstem auditory evoked response (BAER) testing for CSD screening (2000-2018). Inclusion criteria were BAER performed at 5-10 weeks of age, testing of complete litters and available phenotypic data. The age, sex, presence of patches at birth, coat colour, iris colour, hearing status and BAER-determined parental hearing status of each puppy were recorded. Multivariable binary logistic regression was performed to determine the significance of these variables as predictors for the likelihood of puppies being unilaterally or bilaterally deaf.

RESULTS

Inclusion criteria were met for 447 puppies. Hearing was bilaterally normal in 427 (95.5 per cent) puppies. The prevalence of unilateral and bilateral CSD was 3.6 per cent and 0.9 per cent, respectively. Females were 3.3 times more likely to be deaf than males, and puppies with both parents of unknown hearing status were 4.6 times more likely to be deaf than those with at least one normal parent.

CONCLUSION

The prevalence of CSD was 4.5 per cent, with female puppies and those with two parents of unknown hearing status at greatest risk.

Refined Auditory Brainstem Response Measurement Identified Potential Models of Congenital Deafness in Laboratory Mouse Strains

Introduction

To detect congenital hearing loss in mice, an objective measure is needed other than mouse behavioral observation. This study aimed to refine the methodology of auditory brainstem response measurement and identify potential congenital hearing loss models in laboratory mouse strains.

Methods

Mice were anesthetized and fitted with head electrodes. Each mouse underwent four ABR measurements according to four testing conditions: A - no chamber; conventional tone; B - chamber; conventional tone; C - no chamber; short tone; D - chamber; short tone. Potential congenital hearing loss models were identified using 10 mice from each strain (C57BL, BALB/c, CH3, ICR, and ddY) through sound-attenuated ABR measurements with short-tone bursts. Potential congenital hearing loss models exhibited hearing thresholds ≥30 dB in both ears. Data were analyzed for normal distribution and variance homogeneity using the D'Agostino-Pearson/Kolmogorov-Smirnov and F value tests, respectively. One-way analysis of variance (ANOVA), with the Tukey-Kramer test, was used to conduct parametric analysis, and the Kruskal-Wallis/Friedman test, with a Dunn's test for post hoc analysis, was used to perform non-parametric analysis.

Results

The simultaneous use of a sound-attenuating chamber and short-tone bursts provided clearly defined wave patterns, even at lower sound intensities. Inbred strains, especially C57BL/6 sub-strains, constitute suitable congenital hearing loss models.

Conclusions

Our study shows that environmental factors should be addressed in animal studies of hearing function. Potential congenital hearing loss models may be found amongst commercially available inbred strains.

OSBPL2-disrupted pigs recapitulate dual features of human hearing loss and hypercholesterolaemia

Oxysterol binding protein like 2 (OSBPL2), an important regulator in cellular lipid metabolism and transport, was identified as a novel deafness-causal gene in our previous work. To resemble the phenotypic features of OSBPL2 mutation in animal models and elucidate the potential genotype-phenotype associations, the OSBPL2-disrupted Bama miniature (BM) pig model was constructed using CRISPR/Cas9-mediated gene editing, somatic cell nuclear transfer (SCNT) and embryo transplantation approaches, and then subjected to phenotypic characterization of auditory function and serum lipid profiles. The OSBPL2-disrupted pigs displayed progressive hearing loss (HL) with degeneration/apoptosis of cochlea hair cells (HCs) and morphological abnormalities in HC stereocilia, as well as hypercholesterolaemia. High-fat diet (HFD) feeding aggravated the development of HL and led to more severe hypercholesterolaemia. The dual phenotypes of progressive HL and hypercholesterolaemia resembled in OSBPL2-disrupted pigs confirmed the implication of OSBPL2 mutation in nonsydromic hearing loss (NSHL) and contributed to the potential linkage between auditory dysfunction and dyslipidaemia/hypercholesterolaemia.

Prevalence of congenital sensorineural deafness in a population of client-owned purebred kittens in the United Kingdom

Background

Data about congenital sensorineural deafness (CSD) in white blue‐eyed cats derive mainly from research colonies, and information about client‐owned cats is limited.

Objectives

To describe the prevalence of CSD in a client‐owned population of white purebred kittens and colored littermates in the United Kingdom.

Animals

One hundred thirty‐two solid white client‐owned purebred kittens and 61 colored littermates, 6 to 21 weeks of age.

Methods

Retrospective (56 cases) and prospective (137 cases) study. Hearing was assessed by brainstem auditory evoked response testing, and the entire litter was tested.

Results

Congenital sensorineural deafness was diagnosed only in solid white kittens, with a prevalence of 30.3% (15.9% bilateral, 14.4% unilateral). The prevalence of CSD was significantly higher in white kittens with 1 (44.4%) or 2 (50%) blue irises than in those without blue irises (22.2%). Kittens with at least 1 blue iris were 3.2 times more likely to have CSD than kittens without blue irises. In solid white kittens, CSD was diagnosed in 7 of 15 (46.7%) Turkish Vankedisi, 8 of 18 (44.0%) Maine Coon, 18 of 41 (43.9%) Norwegian Forest, 3 of 11 (27.3%) British Shorthair, 2 of 12 (16.7%) Devon Rex, 2 of 12 (8.3%) Persian, 1 of 21 (4.8%) Russian, and 0 of 2 Sphinx. The prevalence of CSD was significantly different in Norwegian Forest, Maine Coon, and Turkish Vankedisi kittens compared with Persian or Russian kittens.

Conclusion and Clinical Importance

We identified a high prevalence of CSD in a population of client‐owned purebred white kittens in the United Kingdom and suggest differences in breed‐specific prevalence of CSD.

A missense mutation in MYO7A is associated with bilateral deafness and vestibular dysfunction in the Doberman pinscher breed

Bilateral deafness with concurrent vestibular dysfunction was first reported in the Doberman pinscher in 1980. Here, we identify a coding mutation in the MYO7A gene that is perfectly associated with the disorder. The lack of visual deficits in affected dogs suggests that, like rodents but unlike humans, MYO7A is not required for retinal function. DNA testing of the mutation will enable dog breeders to manage the incidence of this genetic defect.

Cochleosaccular (Scheibe) dysplasia in dogs: A temporal bone study

The objective of this study was to evaluate any otopathologic changes in temporal bone specimens from dogs with deafness related to cochleosaccular (Scheibe) dysplasia (CSD). We used the canine temporal bone collections of the Otopathology Laboratory at the University of Minnesota and of the Massachusetts Eye and Ear Infirmary at Harvard University in Boston. Our morphometric analysis included measuring the areas of the stria vascularis and the spiral ligament and counting the number of spiral ganglion cells. In addition, we noted the presence of the organ of Corti and cochlear hair cells, assessed the location of Reissner's membrane and the saccular membrane, and counted the number of both Type I and Type II vestibular hair cells in the macule of the saccule and vestibular ganglion cells. In the group of specimens from dogs with cochleosaccular dysplasia, we observed generalized degeneration in the cochlea and a significantly decreased number of Type I and Type II vestibular hair cells and vestibular ganglion cells. As hereditary deafness is presently untreatable with known therapeutic methods, dogs with cochleosaccular dysplasia should not be considered for breeding. Future therapeutic approaches, such as stem cell therapies, should be designed to target all the elements of the cochlea in addition to the saccule as it was found that both are affected in dogs with CSD.

Hearing disorders in cats

Practical relevance: Auditory function is a sense that is central to life for cats - being important in situational awareness of potential predators, pursuit of prey, and for communication with conspecifics, humans and other species. Deafness in cats is most frequently the result of a genetic disorder, strongly associated with white fur and blue eyes, but may also result from acquired causes such as advancing age, ototoxic drugs, infection, environmental noise and physical trauma. Deafness can be sensorineural, where there is loss of cochlear hair cells, or conductive, where sound is muffled on its way to the inner ear. Clinical challenges: Establishing whether a cat is deaf can be difficult as behavioral testing of hearing is subjective and does not reliably detect unilateral deafness. Brainstem auditory evoked response testing is an objective measure but is limited in its availability. Currently, sensorineural deafness is irreversible because no treatments are available to restore lost hair cells. Conductive hearing loss can usually be treated, although full hearing recovery following otitis media may take weeks as the body clears the middle ear of debris. Evidence base: The author draws on the published literature and his extensive research on clinical aspects and molecular genetics of deafness, principally in companion animals, to review types and forms of deafness in cats. He also discusses current diagnostic approaches and provides brief advice for managing cats with hearing loss.

A comparison of the brainstem auditory evoked response in healthy ears of unilaterally deaf dogs and bilaterally hearing dogs

AIMS

Auditory plasticity in response to unilateral deafness has been reported in various animal species. Subcortical changes occurring in unilaterally deaf young dogs using the brainstem auditory evoked response have not been evaluated yet. The aim of this study was to assess the brainstem auditory evoked response findings in dogs with unilateral hearing loss, and compare them with recordings obtained from healthy dogs.

METHODS

Brainstem auditory evoked responses (amplitudes and latencies of waves I, II, III, V, the V/I wave amplitude ratio, wave I-V, I-III and III-V interpeak intervals) were studied retrospectively in forty-six privately owned dogs, which were either unilaterally deaf or had bilateral hearing. The data obtained from the hearing ears in unilaterally deaf dogs were compared to values obtained from their healthy littermates.

RESULTS

Statistically significant differences in the amplitude of wave III and the V/I wave amplitude ratio at 75 dB nHL were found between the group of unilaterally deaf puppies and the control group. The recordings of dogs with single-sided deafness were compared, and the results showed no statistically significant differences in the latencies and amplitudes of the waves between left- (AL) and right-sided (AR) deafness.

CONCLUSIONS

The recordings of the brainstem auditory evoked response in canines with unilateral inborn deafness in this study varied compared to recordings from healthy dogs. Future studies looking into electrophysiological assessment of hearing in conjunction with imaging modalities to determine subcortical auditory plasticity and auditory lateralization in unilaterally deaf dogs are warranted.

Prevalence, heritability and genetic correlations of congenital sensorineural deafness and coat pigmentation phenotype in the English bull terrier

Background

Congenital sensorineural deafness (CSD) is the most common type of deafness in dogs and it occurs in numerous canine breeds including the English bull terrier. This study estimates prevalence, heritability and genetic correlations of CSD and coat pigmentation phenotypes in the English bull terrier in England.

Results

Hearing status was assessed by brainstem auditory evoked response in 1060 English bull terrier puppies tested at 30–78 (mean 43.60) days of age as complete litters. Gender, coat and iris colour and parental hearing status were recorded.

The prevalence of CSD in all 1060 puppies was 10.19 % with 8.21 % unilaterally deaf and 1.98 % bilaterally deaf. The coat was predominately coloured in 49.15 % puppies and white with or without a patch in 50.85 % puppies. The majority (96.29 %) of deaf puppies had a white coat (with or without a patch); 19.29 % of the puppies with a white coat (with or without a patch) were deaf.

Heritability and genetic correlations were estimated using residual maximum likelihood. Heritability of hearing status as a trichotomous trait (bilaterally normal/unilaterally deaf/bilaterally deaf) was estimated at 0.15 to 0.16 and was significantly different to zero (P < 0.01). Heritability of coat pigmentation phenotype (all white/white with patches/coloured) was 0.49 (standard error 0.077). Genetic correlation of CSD with coat pigmentation phenotype was estimated at −0.36 to −0.37 (CSD associated with all white coat), but was not significantly larger than zero (P > 0.05). Analysis of CSD in all white and white patched puppies only estimated the heritability of CSD as 0.25 and was significantly greater than zero (P < 0.01), and the heritability of coat colour (all white/white with patches) as 0.20 (standard error 0.096). The genetic correlation was estimated at −0.53 to −0.54 (CSD associated with all white coat) but was just above the statistical threshold determining significant difference to zero (P = 0.06).

Conclusions

These results indicate that CSD occurs predominantly in white English bull terriers and there is genetic variation in CSD beyond that associated with coat colour.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0777-6) contains supplementary material, which is available to authorized users.

Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation

The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.