Heritability and segregation analysis of deafness in U.S. Dalmatians

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.

Canine coat pigmentation genetics: a review

Our understanding of canine coat colour genetics and the associated health implications is developing rapidly. To date, there are 15 genes with known roles in canine coat colour phenotypes. Many coat phenotypes result from complex and/or epistatic genetic interactions among variants within and between loci, some of which remain unidentified. Some genes involved in canine pigmentation have been linked to aural, visual and neurological impairments. Consequently, coat pigmentation in the domestic dog retains considerable ethical and economic interest. In this paper we discuss coat colour phenotypes in the domestic dog, the genes and variants responsible for these phenotypes and any proven coat colour-associated health effects.

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.

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.

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.

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.

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.

The Genetics of Deafness in Domestic Animals

Although deafness can be acquired throughout an animal's life from a variety of causes, hereditary deafness, especially congenital hereditary deafness, is a significant problem in several species. Extensive reviews exist of the genetics of deafness in humans and mice, but not for deafness in domestic animals. Hereditary deafness in many species and breeds is associated with loci for white pigmentation, where the cochlear pathology is cochleo-saccular. In other cases, there is no pigmentation association and the cochlear pathology is neuroepithelial. Late onset hereditary deafness has recently been identified in dogs and may be present but not yet recognized in other species. Few genes responsible for deafness have been identified in animals, but progress has been made for identifying genes responsible for the associated pigmentation phenotypes. Across species, the genes identified with deafness or white pigmentation patterns include MITF, PMEL, KIT, EDNRB, CDH23, TYR, and TRPM1 in dog, cat, horse, cow, pig, sheep, ferret, mink, camelid, and rabbit. Multiple causative genes are present in some species. Significant work remains in many cases to identify specific chromosomal deafness genes so that DNA testing can be used to identify carriers of the mutated genes and thereby reduce deafness prevalence.

Congenital sensorineural deafness in dalmatian dogs associated with quantitative trait loci

A genome-wide association study (GWAS) was performed for 235 Dalmatian dogs using the canine Illumina high density bead chip to identify quantitative trait loci (QTL) associated with canine congenital sensorineural deafness (CCSD). Data analysis was performed for all Dalmatian dogs and in addition, separately for brown-eyed and blue-eyed dogs because of the significant influence of eye colour on CCSD in Dalmatian dogs. Mixed linear model analysis (MLM) revealed seven QTL with experiment-wide significant associations (-log10P>5.0) for CCSD in all Dalmatian dogs. Six QTL with experiment-wide significant associations for CCSD were found in brown-eyed Dalmatian dogs and in blue-eyed Dalmatian dogs, four experiment-wide significant QTL were detected. The experiment-wide CCSD-associated SNPs explained 82% of the phenotypic variance of CCSD. Five CCSD-loci on dog chromosomes (CFA) 6, 14, 27, 29 and 31 were in close vicinity of genes shown as causative for hearing loss in human and/or mouse.

Familial aggregation of chronic diarrhea disease (CDD) in rhesus macaques (Macaca mulatta)

Chronic diarrheal disease (CDD) is a critical problem for breeders of captive rhesus macaque (Macaca mulatta), as it results in significant levels of morbidity and death annually. As with other inflammatory disorders, CDD is thought to be caused by environmental and/or genetic factors. Although correspondence between the characters defined as Mendelian by pedigree or segregation analysis and functional genes is difficult to establish, such analyses provide essential entry points into understanding CDD in captive bred rhesus macaques. To investigate the familial aggregation of CDD in captive rhesus macaque, we performed pedigree, segregation and heritability analyses on genealogical data from 55 severely affected individuals (probands) through whom relatives with a history of CDD were ascertained from routine computerized colony records comprising vital and demographic statistics of 10,814 rhesus macaques. We identified 175 rhesus macaques with CDD and estimated its incidence as approximately 2% in the colony. The disease strongly clustered in eight multi-generation pedigrees. Inspection of the pedigrees, segregation analysis and heritability estimate of CDD suggest that susceptibility to the disease is under strong genetic control. Identification of the locations of susceptibility genes in the rhesus macaque genome could facilitate the reduction of their frequency in captive breeding facilities.

Prevalence of congenital hereditary sensorineural deafness in Australian Cattle Dogs and associations with coat characteristics and sex

Background

Congenital hereditary sensorineural deafness (CHSD) occurs in many dog breeds, including Australian Cattle Dogs. In some breeds, CHSD is associated with a lack of cochlear melanocytes in the stria vascularis, certain coat characteristics, and potentially, abnormalities in neuroepithelial pigment production. This study investigates phenotypic markers for CHSD in 899 Australian Cattle Dogs.

Results

Auditory function was tested in 899 Australian Cattle Dogs in family groups using brainstem auditory evoked response testing. Coat colour and patterns, facial and body markings, gender and parental hearing status were recorded.

Deafness prevalence among all 899 dogs was 10.8% with 7.5% unilaterally deaf, and 3.3% bilaterally deaf, and amongst pups from completely tested litters (n = 696) was 11.1%, with 7.5% unilaterally deaf, and 3.6% bilaterally deaf.

Univariable and multivariable analyses revealed a negative association between deafness and bilateral facial masks (odds ratio 0.2; P ≤ 0.001). Using multivariable logistic animal modelling, the risk of deafness was lower in dogs with pigmented body spots (odds ratio 0.4; P = 0.050).

No significant associations were found between deafness and coat colour.

Within unilaterally deaf dogs with unilateral facial masks, no association was observed between the side of deafness and side of mask. The side of unilateral deafness was not significantly clustered amongst unilaterally deaf dogs from the same litter. Females were at increased risk of deafness (odds ratio from a logistic animal model 1.9; P = 0.034) after adjusting for any confounding by mask type and pigmented body spots.

Conclusions

Australian Cattle Dogs suffer from CHSD, and this disease is more common in dogs with mask-free faces, and in those without pigmented body patches. In unilaterally deaf dogs with unilateral masks, the lack of observed association between side of deafness and side of mask suggests that if CHSD is due to defects in molecular pigment pathways, the molecular control of embryonic melanoblast migration from ectoderm to skin differs from control of migration from ectoderm to cochlea. In Australian Cattle Dogs, CHSD may be more common in females.

Canine deafness

Conductive deafness, caused by outer or middle ear obstruction, may be corrected, whereas sensorineural deafness cannot. Most deafness in dogs is congenital sensorineural hereditary deafness, associated with the genes for white pigment: piebald or merle. The genetic cause has not yet been identified. Dogs with blue eyes have a greater likelihood of hereditary deafness than brown-eyed dogs. Other common forms of sensorineural deafness include presbycusis, ototoxicity, noise-induced hearing loss, otitis interna, and anesthesia. Definitive diagnosis of deafness requires brainstem auditory evoked response testing.

Congenital sensorineural deafness in Australian stumpy-tail cattle dogs is an autosomal recessive trait that maps to CFA10

Background

Congenital sensorineural deafness is an inherited condition found in many dog breeds, including Australian Stumpy-tail Cattle Dogs (ASCD). This deafness is evident in young pups and may affect one ear (unilateral) or both ears (bilateral). The genetic locus/loci involved is unknown for all dog breeds. The aims of this study were to determine incidence, inheritance mechanism, and possible association of congenital sensorineural deafness with coat colour in ASCD and to identify the genetic locus underpinning this disease.

Methodology/Principal Findings

A total of 315 ASCD were tested for sensorineural deafness using the brain stem auditory evoked response (BAER) test. Disease penetrance was estimated directly, using the ratio of unilaterally to bilaterally deaf dogs, and segregation analysis was performed using Mendel. A complete genome screen was undertaken using 325 microsatellites spread throughout the genome, on a pedigree of 50 BAER tested ASCD in which deafness was segregating. Fifty-six dogs (17.8%) were deaf, with 17 bilaterally and 39 unilaterally deaf. Unilaterally deaf dogs showed no significant left/right bias (p = 0.19) and no significant difference was observed in frequencies between the sexes (p = 0.18). Penetrance of deafness was estimated as 0.72. Testing the association of red/blue coat colour and deafness without accounting for pedigree structure showed that red dogs were 1.8 times more likely to be deaf (p = 0.045). The within family association between red/blue coat colour and deafness was strongly significant (p = 0.00036), with red coat colour segregating more frequently with deafness (COR = 0.48). The relationship between deafness and coat speckling approached significance (p = 0.07), with the lack of statistical significance possibly due to only four families co-segregating for both deafness and speckling. The deafness phenotype was mapped to CFA10 (maximum linkage peak on CFA10 −log10 p-value = 3.64), as was both coat colour and speckling. Fine mapping was then performed on 45 of these 50 dogs and a further 48 dogs (n = 93). Sequencing candidate gene Sox10 in 6 hearing ASCD, 2 unilaterally deaf ASCD and 2 bilaterally deaf ASCD did not reveal any disease-associated mutations.

Conclusions

Deafness in ASCD is an incompletely penetrant autosomal recessive inherited disease that maps to CFA10.

Evaluation of deafness in American Paint Horses by phenotype, brainstem auditory-evoked responses, and endothelin receptor B genotype

OBJECTIVE

To evaluate deafness in American Paint Horses by phenotype, clinical findings, brainstem auditory-evoked responses (BAERs), and endothelin B receptor (EDNBR) genotype.

DESIGN

Case series and case-control studies.

ANIMALS

14 deaf American Paint Horses, 20 suspected-deaf American Paint Horses, and 13 nondeaf American Paint Horses and Pintos.

PROCEDURES

Horses were categorized on the basis of coat color pattern and eye color. Testing for the EDNBR gene mutation (associated with overo lethal white foal syndrome) and BAERs was performed. Additional clinical findings were obtained from medical records.

RESULTS

All 14 deaf horses had loss of all BAER waveforms consistent with complete deafness. Most horses had the splashed white or splashed white-frame blend coat pattern. Other patterns included frame overo and tovero. All of the deaf horses had extensive head and limb white markings, although the amount of white on the neck and trunk varied widely. All horses had at least 1 partially heterochromic iris, and most had 2 blue eyes. Ninety-one percent (31/34) of deaf and suspected-deaf horses had the EDNBR gene mutation. Deaf and suspected-deaf horses were used successfully for various performance events. All nondeaf horses had unremarkable BAER results.

CONCLUSIONS AND CLINICAL RELEVANCE

Veterinarians should be aware of deafness among American Paint Horses, particularly those with a splashed white or frame overo coat color pattern, blend of these patterns, or tovero pattern. Horses with extensive head and limb markings and those with blue eyes appeared to be at particular risk.

Amyloidosis in Black-footed Cats (Felis nigripes)

A high prevalence of systemic amyloidosis was documented in the black-footed cat ( Felis nigripes) based on a retrospective review of necropsy tissues ( n = 38) submitted as part of ongoing disease surveillance. Some degree of amyloid deposition was present in 33 of 38 (87%) of the examined cats, and amyloidosis was the most common cause of death (26/38, 68%). Amyloid deposition was most severe in the renal medullary interstitium (30/33, 91%) and glomeruli (21/33, 63%). Other common sites included the splenic follicular germinal centers (26/31, 84%), gastric lamina propria (9/23, 39%), and intestinal lamina propria (3/23, 13%). Amyloid in all sites stained with Congo red, and in 13 of 15 (87%) cats, deposits had strong immunoreactivity for canine AA protein by immunohistochemistry. There was no association with concurrent chronic inflammatory conditions ( P = .51), suggesting that amyloidosis was not secondary to inflammation. Adrenal cortical hyperplasia, a morphologic indicator of stress that can predispose to amyloid deposition, was similarly not associated ( P = .09) with amyloidosis. However, adrenals were not available from the majority of cats without amyloidosis; therefore, further analysis of this risk factor is warranted. Heritability estimation suggested that amyloidosis might be familial in this species. Additionally, tissues from a single free-ranging black-footed cat had small amounts of amyloid deposition, suggesting that there could be a predilection for amyloidosis in this species. Research to identify the protein sequence of serum amyloid A (SAA) in the black-footed cat is needed to further investigate the possibility of an amyloidogenic SAA in this species.

Genes affecting coat colour and pattern in domestic dogs: a review

Tremendous progress has been made in identifying genes involved in pigmentation in dogs in the past few years. Comparative genomics has both aided and benefited from these findings. Seven genes that cause specific coat colours and/or patterns in dogs have been identified: melanocortin 1 receptor, tyrosinase related protein 1, agouti signal peptide, melanophilin, SILV (formerly PMEL17), microphthalmia-associated transcription factor and beta-defensin 103. Although not all alleles have been yet identified at each locus, DNA tests are available for many. The identification of these alleles has provided information on interactions in this complex set of genes involved in both pigmentation and neurological development. The review also discusses pleiotropic effects of some coat colour genes as they relate to disease. The alleles found in various breeds have shed light on some potential breed development histories and phylogenetic relationships. The information is of value to dog breeders who have selected for and against specific colours since breed standards and dog showing began in the late 1800s. Because coat colour is such a visible trait, this information will also be a valuable teaching resource.

Heritability and complex segregation analysis of deafness in Jack Russell Terriers

BACKGROUND

The association between patterns of pigmentation and deafness in the dog has a long-documented history, with reports dating back over one hundred years. Long suspected of having a genetic basis, the search for loci with a pronounced influence in the expression of hearing loss in the dog has yet to be successful. No studies in the dog to date have found a possible influence of a specific colour locus associated with deafness. The present study is intended to evaluate the heritability of deafness in the Jack Russell Terrier (JRT), characterize the mode of inheritance, and evaluate the existence of a sex, coat colour, or coat texture influence on the expression of sensorineural deafness.

RESULTS

The estimation of heritability of deafness in the JRT was 0.22 when deafness was considered a binary (normal/deaf) trait and 0.31 when deafness was considered a three-category (normal/unilateral/bilateral deafness). The influence of coat colour in the incidence of JRT deafness was statistically significant, indicating that dogs with more white are more likely to be deaf. The influence of sex or coat texture was not statistically significant in the incidence of JRT deafness. Complex segregation analysis revealed a model of a single locus with a large effect on the binary measure of hearing loss is not supported.

CONCLUSION

This is the first attempt, to our knowledge, to characterize a genetic component responsible for deafness in the JRT. The heritability of deafness in the JRT was found to be 0.22 and 0.31 considering deafness to be a two-category or three-category trait, respectively. There appears to be an influence of coat colour on the expression of deafness. In an attempt to characterize the mode of inheritance of deafness in the JRT, a model of a single locus with a large effect on hearing loss is not supported with this data. Further study is needed to determine if a single locus may be influencing deafness in the JRT. While the absence of a clear mode of inheritance complicates genetic dissection of deafness in the JRT, the assembling of this pedigree provides a tool for eventually defining the genetic bases of this disorder.

Investigation of major gene for milk yield, milking speed, dry matter intake, and body weight in dairy cattle

The main aim of this study was to determine if there exist any major gene for milk yield (MY), milking speed (MS), dry matter intake (DMI), and body weight (BW) recorded at various stages of lactation in first-lactation dairy cows (2543 observations from 320 cows) kept at the research farm of the Swiss Federal Institute of Technology between April 1994 and April 2004. Data were modelled based a simple repeatability covariance structure and analysed by using Bayesian segregation analyses. Gibbs sampling was used to make statistical inferences on posterior distributions; inferences were based on a single run of the Markov chain for each trait with 500,000 samples, with each 10th sample collected because of the high correlation among the samples. The posterior mean (+/-SD) of major gene variance was 2.61 (+/-2.46) for MY, 0.83 (+/-1.26) for MS, 4.37 (+/-2.34) for DMI, and 2056.43 (+/-665.67) for BW. Highest posterior density regions for 3 of the 4 traits did not include 0 (except MS), which supported the evidence for major gene. With additional tests for agreement with Mendelian transmission probabilities, we could only confirm the existence of a major gene for MY, but not for MS, DMI, and BW. Expected Mendelian transmission probabilities and their model fits were also compared.

Genetic counseling in the era of molecular diagnostics

Veterinarians with an interest in theriogenology will often be asked by small animal clients for advice concerning hereditary diseases in their breeds. Many new DNA-based tests for analysis of genetic diseases and traits (e.g. coat color) are now available for use by both breeders and veterinarians. With appropriate interpretation, these tests can be invaluable tools in a breeding program. For example, they can be used to produce animals free of specific diseases, to quickly eliminate a disease from an entire breed, or to select for specific traits in breeding stock. Selection strategies that do not take into account maintaining genetic diversity of the breed may be detrimental and reduce the potential for future improvement.

The color of a Dalmatian's spots: linkage evidence to support the TYRP1 gene

Background

The distinctive coat pattern of a Dalmatian is the result of the interaction of several loci. While the encoded function of these genes is not fully understood, it is known the Piebald, Ticking, and Flecking loci interact to produce the Dalmatian's classic pigmented spots on a white background. The color of the pigmented spots in purebred Dalmatians can either be black or liver, but the locus responsible for color determination is unknown. Studies have been conducted to determine the underlying genes involved in coat color determination in the dog, e.g., in the Labrador Retriever, but none to date have addressed black versus liver in the Dalmatian.

Results

A genome scan was conducted in a multi-generational kindred of Dalmatians segregating black and liver spot color. Linkage analysis was performed using a total of 113 polymorphic microsatellite markers from the kindred. Linkage was found between spot color and a single microsatellite marker, FH2319 (LOD = 12.5) on chromosome 11.

Conclusion

The TYRP1 (Brown) locus is located at position 50.1 Mb on chromosome 11, which is approximately 0.4 Mb from marker FH2319. Given the recent characterization of TYRP1 genetic variations in the dog and the linkage evidence reported here, TYRP1 is likely responsible for the spot color variation of black versus liver seen in the Dalmatian.

Evidence of a major gene from Bayesian segregation analyses of liability to osteochondral diseases in pigs

Bayesian segregation analyses were used to investigate the mode of inheritance of osteochondral lesions (osteochondrosis, OC) in pigs. Data consisted of 1163 animals with OC and their pedigrees included 2891 animals. Mixed-inheritance threshold models (MITM) and several variants of MITM, in conjunction with Markov chain Monte Carlo methods, were developed for the analysis of these (categorical) data. Results showed major genes with significant and substantially higher variances (range 1.384-37.81), compared to the polygenic variance (sigmau2). Consequently, heritabilities for a mixed inheritance (range 0.65-0.90) were much higher than the heritabilities from the polygenes. Disease allele frequencies range was 0.38-0.88. Additional analyses estimating the transmission probabilities of the major gene showed clear evidence for Mendelian segregation of a major gene affecting osteochondrosis. The variants, MITM with informative prior on sigmau2, showed significant improvement in marginal distributions and accuracy of parameters. MITM with a "reduced polygenic model" for parameterization of polygenic effects avoided convergence problems and poor mixing encountered in an "individual polygenic model." In all cases, "shrinkage estimators" for fixed effects avoided unidentifiability for these parameters. The mixed-inheritance linear model (MILM) was also applied to all OC lesions and compared with the MITM. This is the first study to report evidence of major genes for osteochondral lesions in pigs; these results may also form a basis for underpinning the genetic inheritance of this disease in other animals as well as in humans.

Assignment of canine MSS1 microsatellite markers to chromosomes by linkage data

Recent advances in mapping the canine genome have led to an increase in the number of linkage studies aimed at dissecting the genetic causes of many hereditary diseases that affect the domestic dog. The first step in developing molecular tools for a whole genome scan was the characterization of a set of microsatellite markers, termed minimal screening set 1 (MSS1), that provided an estimated coverage of 10 cM. A limiting factor in use of the MSS1 is not all of the 172 MSS1 markers have been localized to specific chromosomes. Seventy-five of the markers were positioned on a total of 15 chromosomes with the original publication of the MSS1. The localization based on linkage data of 14 additional MSS1 markers to chromosomes using CRIMAP v. 2.4 to build a linkage map of 113 MSS1 markers that were polymorphic in a kindred of Dalmatians is reported here.

Le chien, un modèle pour la génétique des mammifères

Up to recently, studies on dog genetics were rather scare notwithstanding the enormous potential that the canine model can offer in the study of the genotype/phenotype relationship and the analysis of the causes of many genetic diseases, with simple or complex inheritance, that affect dogs but also the human population. This potentiality is essentially due to the natural history of dogs whose domestication from wolves dated back 15,000 years, at least. All modern dogs originated from a limited number of female wolves from Eastern Asia. By applying a combination of selections and strong inbreeding practices, humans have created over 350 breeds, each of them corresponding to a genetic isolate and altogether offering a unique panel of polymorphism never encountered in any other mammals. In this review we summarized what makes dogs an unavoidable model. Contrary to the classical models like the two yeasts, nematode, fish, fly, mouse, or rat mainly used to understand the function of genes, dog with the creation across the centuries of numerous breeds offers a unique opportunity to study the role of their alleles. We report recent data on the construction of genomic maps and on the sequencing program of the dog genome launched by the National Institute of Health (NIH). To take fully advantage of the canine model, we advocate for the systematic construction of a rich canine single nucleotide polymorphisms (SNP) ressource to perform linkage desiquilibrium studies of normal or pathological traits as well as to get insight into the genetic diversity of the canine species.