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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 34689

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Prof. Dr. Tosso Leeb

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Institute of Genetics, University of Bern, Bern, Switzerland
Interests: veterinary genetics; domestic animals; mammals; skin (dermatology); coat colour; mendelian traits
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genes has devoted several Special Issues to cats, dogs and other companion animal species in the past. Companion animals are the beloved friends of humans and share the environment with their owners. Due to their close phylogenetic relationship with humans and their specific physiological characteristics, they often represent excellent models for human traits and diseases. The importance of genetic research on companion animals is recognized with this Special Issue.

This Special Issue will cover all aspects of companion animal genetics and genomics, including studies on domestication and breed development, genetic diversity, determinants of morphology and coat color, behavioral genetics and genetics of athletic performance, genetics of inherited diseases and cancer genetics. The ever advancing technological developments in sequencing and data analysis, together with large publicly available resource datasets, facilitate new approaches to tackle open questions. We are looking forward to receiving your exciting research manuscripts that will inform biology and (veterinary) medicine.

Prof. Dr. Tosso Leeb
Guest Editor

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Keywords

cat
dog
horse
breed
domestication
diversity
morphology
behavior
disease
cancer
precision medicine

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Published Papers (10 papers)

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Research

14 pages, 10671 KiB

Open AccessEditor’s ChoiceArticle

Selection Signatures Reveal Candidate Genes for the Cornish Rex Breed-Specific Phenotype

by Minja Zorc, Tajda Horvat, Anja Tanšek, Tamara Ferme and Peter Dovč

Genes 2024, 15(3), 368; https://doi.org/10.3390/genes15030368 - 16 Mar 2024

Cited by 1 | Viewed by 2551

Abstract

Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp deletion in the LPAR6 gene has been found to cause a frame shift and a premature stop codon. In addition to the rexoid coat, Cornish Rex cats also have a characteristic head, ear shape and body type. Analysis of the selection signatures in the Cornish Rex genome revealed several regions that are under selective pressure. One of these is located in CFA B4, in the region where the ALX1 gene is located. The ALX1 gene in Burmese cats disrupts the cranial morphogenesis and causes brachycephaly in the heterozygous state. In our study, we confirmed the presence of a deletion in LPAR6 in 20 Cornish Rex and in four F1 hybrids between Cornish Rex and domestic cat. However, we did not confirm the presence of the deletion in ALX1 in Cornish Rex cats. Genome-wide selection signature analysis was performed using ROH islands and integrated haplotype score (iHS) statistics based on publicly available SNP array data of 11 Cornish Rex cats. The selection signatures were detected on chromosomes A1, A3, C2, B1, B4 and D1. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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17 pages, 2114 KiB

Open AccessEditor’s ChoiceArticle

Cross-Species Comparison of the Pan-RAF Inhibitor LY3009120’s Anti-Tumor Effects in Equine, Canine, and Human Malignant Melanoma Cell Lines

by Yu Gao, Eva-Maria Packeiser, Sophia Wendt, Anett Sekora, Jessika-Maximiliane V. Cavalleri, Barbara Pratscher, Moosheer Alammar, Maja Hühns, Bertram Brenig, Christian Junghanss, Ingo Nolte and Hugo Murua Escobar

Genes 2024, 15(2), 202; https://doi.org/10.3390/genes15020202 - 3 Feb 2024

Cited by 1 | Viewed by 2471

Abstract

Malignant melanomas (MMs) are the abnormal proliferation of melanocytes and are one of the lethal skin cancers in humans, equines, and canines. Accordingly, MMs in companion animals can serve as naturally occurring animal models, completing conventional cancer models. The common constitutive activation of the MAPK and PI3K pathways in MMs has been described in all three species. Targeting the related pathways is considered a potential option in comparative oncologic approaches. Herein, we present a cross-species comparative analysis exposing a set of ten melanoma cell lines (one human, three equine, and six canine) derived from primary tumors or metastasis to a pan-RAF and RAF dimer inhibitor (LY3009120). Cellular response (proliferation, biomass, metabolism, early and late apoptosis/necrosis, and morphology) and the presence of pathogenic single-nucleotide variants (SNVs) within the mutational hotspot genes BRAF exon 11 and 15, NRAS exon 2 and 3, KRAS exon 2, and KIT exon 11 were analyzed. This study showed that equine malignant melanoma (EMM) cells (MelDuWi) harbor the KRAS p.Q61H mutation, while canine malignant melanoma (CMM) cells (cRGO1 and cRGO1.2) carry NRAS p.G13R. Except for EMM metastasis cells eRGO6 (wild type of the above-mentioned hotspot genes), all melanoma cell lines exhibited a decrease in dose dependence after 48 and 72 h of exposure to LY3009120, independent of the mutation hotspot landscape. Furthermore, LY3009120 caused significant early apoptosis and late apoptosis/necrosis in all melanoma cell lines except for eRGO6. The anti-tumor effects of LY3009120 were observed in nine melanoma cell lines, indicating the potential feasibility of experimental trials with LY3009120. The present study reveals that the irradiation-resistant canine metastasis cells (cRGO1.2) harboring the NRAS p.G13R mutation are significantly LY3009120-sensitive, while the equine metastases-derived eRGO6 cells show significant resistance to LY3009120, which make them both valuable tools for studying resistance mechanisms in comparative oncology. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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14 pages, 3333 KiB

Open AccessEditor’s ChoiceArticle

Association of FGF4L1 Retrogene Insertion with Prolapsed Gland of the Nictitans (Cherry Eye) in Dogs

by Jamie Freyer, Julia D. Labadie, Jason T. Huff, Michael Denyer, Oliver P. Forman, Rebecca Chodroff Foran and Jonas Donner

Genes 2024, 15(2), 198; https://doi.org/10.3390/genes15020198 - 1 Feb 2024

Cited by 2 | Viewed by 3664

Abstract

Cherry eye is the common name for prolapse of the nictitans gland, a tear-producing gland situated under the third eyelid of dogs. Cherry eye is characterized by a red fleshy protuberance in the corner of the eye, resembling a cherry. This protrusion is a displacement of the normal gland of the third eyelid, thought to be caused by a defect in the connective tissue that secures the gland in place. Options for treatment may include anti-inflammatory medications in mild cases, but surgical replacement of the gland is usually indicated. Cherry eye is most often seen in dogs under the age of two years, with certain breeds having a higher incidence, suggesting a potential genetic association. Integration of panel genetic testing into routine clinical practice allows for the generation of large numbers of genotyped individuals paired with clinical records and enables the investigation of common disorders using a genome-wide association study (GWAS) approach at scale. In this investigation, several thousand cases and controls for cherry eye in both purebred dogs and mixed breeds are used for a large-scale GWAS, revealing a single peak of genome-wide significance on canine chromosome 18, directly at the location of the previously identified FGF4 insertion known to cause chondrodysplasia in several breeds. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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11 pages, 635 KiB

Open AccessEditor’s ChoiceArticle

Sequence Analysis of Six Candidate Genes in Miniature Schnauzers with Primary Hypertriglyceridemia

by Nicole M. Tate, Michaela Underwood, Alison Thomas-Hollands, Katie M. Minor, Jonah N. Cullen, Steven G. Friedenberg, James R. Mickelson, Panagiotis G. Xenoulis, Joerg M. Steiner and Eva Furrow

Genes 2024, 15(2), 193; https://doi.org/10.3390/genes15020193 - 31 Jan 2024

Cited by 1 | Viewed by 2056

Abstract

Miniature Schnauzers are predisposed to primary hypertriglyceridemia (HTG). In this study, we performed whole genome sequencing (WGS) of eight Miniature Schnauzers with primary HTG and screened for risk variants in six HTG candidate genes: LPL, APOC2, APOA5, GPIHBP1, LMF1, and APOE. Variants were filtered to identify those present in ≥2 Miniature Schnauzers with primary HTG and uncommon (<10% allele frequency) in a WGS variant database including 613 dogs from 61 other breeds. Three variants passed filtering: an APOE TATA box deletion, an LMF1 intronic SNP, and a GPIHBP1 missense variant. The APOE and GPIHBP1 variants were genotyped in a cohort of 108 Miniature Schnauzers, including 68 with primary HTG and 40 controls. A multivariable regression model, including age and sex, did not identify an effect of APOE (estimate = 0.18, std. error = 0.14; p = 0.20) or GPIHBP1 genotypes (estimate = −0.26, std. error = 0.42; p = 0.54) on triglyceride concentration. In conclusion, we did not identify a monogenic cause for primary HTG in Miniature Schnauzers in the six genes evaluated. However, if HTG in Miniature Schnauzers is a complex disease resulting from the cumulative effects of multiple variants and environment, the identified variants cannot be ruled out as contributing factors. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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7 pages, 1024 KiB

Open AccessEditor’s ChoiceCommunication

Idiopathic Epilepsy Risk Allele Trends in Belgian Tervuren: A Longitudinal Genetic Analysis

by Nathan Kinsey, Janelle M. Belanger, Paul J. J. Mandigers, Peter A. Leegwater, Tiina Heinonen, Marjo K. Hytönen, Hannes Lohi, Elaine A. Ostrander and Anita M. Oberbauer

Genes 2024, 15(1), 114; https://doi.org/10.3390/genes15010114 - 18 Jan 2024

Viewed by 2610

Abstract

Idiopathic epilepsy (IE) has been known to be inherited in the Belgian Tervuren for many decades. Risk genotypes for IE in this breed have recently been identified on Canis familiaris chromosomes (CFA) 14 and 37. In the current study, the allele frequencies of these loci were analyzed to determine whether dog breeders had employed a purposeful selection against IE, leading to a reduction in risk-associated allele frequency within the breed over time. The allele frequencies of two generational groupings of Belgian Tervuren with and without IE were compared. Allele frequencies for risk-associated alleles on CFA14 were unchanged between 1985 and 2015, whereas those on CFA37 increased during that time in the control population (p < 0.05). In contrast, dogs with IE showed a decrease (p < 0.05) in the IE risk-associated allele frequency at the CFA37 locus. Seizure prevalence in the Belgian Tervuren appears to be increasing. These results suggest that, despite awareness that IE is inherited, selection against IE has not been successful. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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23 pages, 4803 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Global Frequency Analyses of Canine Progressive Rod-Cone Degeneration–Progressive Retinal Atrophy and Collie Eye Anomaly Using Commercial Genetic Testing Data

by Jessica A. Clark, Heidi Anderson, Jonas Donner, Susan Pearce-Kelling and Kari J. Ekenstedt

Genes 2023, 14(11), 2093; https://doi.org/10.3390/genes14112093 - 17 Nov 2023

Viewed by 3220

Abstract

Hundreds of genetic variants associated with canine traits and disorders have been identified, with commercial tests offered. However, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for the progressive rod-cone degeneration–progressive retinal atrophy (prcd-PRA) G>A missense PRCD variant (n = 86,667) and the collie eye anomaly (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science & Diagnostics). These data were analyzed using the chi-square goodness-of-fit test, time-trend graphical analysis, and regression modeling in order to evaluate how test results changed over time. The results span fifteen years, representing 82 countries and 67 breeds/breed mixes. Both diseases exhibited significant differences in genotype frequencies (p = 2.7 × 10⁻¹⁵² for prcd-PRA and 0.023 for CEA) with opposing graphical trends. Regression modeling showed time progression to significantly affect the odds of a dog being homozygous or heterozygous for either disease, as do variables including breed and breed popularity. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. However, the presence of dogs homozygous for the disease variant, especially for prcd-PRA, was still observed fourteen years after test availability, potentially due to crosses of unknown carriers. This suggests that genetic testing of dog populations should continue. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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13 pages, 4201 KiB

Open AccessArticle

Current Classification of Canine Muscular Dystrophies and Identification of New Variants

by G. Diane Shelton, Katie M. Minor, Steven G. Friedenberg, Jonah N. Cullen, Ling T. Guo and James R. Mickelson

Genes 2023, 14(8), 1557; https://doi.org/10.3390/genes14081557 - 29 Jul 2023

Cited by 6 | Viewed by 2984

Abstract

The spectrum of canine muscular dystrophies has rapidly grown with the recent identification of several more affected breeds and associated mutations. Defects include those in genes and protein products associated with the sarcolemma (dystrophin deficient X-linked muscular dystrophy and sarcoglycan-deficient limb–girdle muscular dystrophy) and with the extracellular matrix (collagen 6, laminin α2, and α-dystroglycan-deficient congenital muscular dystrophies). With the increasing application of whole genome sequencing and whole exome sequencing, the clinical and pathological spectra associated with specific neuromuscular genetic defects are constantly evolving. In this report, we provide a brief overview of the current status of gene defects reported in canine muscular dystrophies. We also report the causative mutations for novel forms of X-linked muscular dystrophy in Brittany spaniels and in a French bulldog. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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10 pages, 2078 KiB

Open AccessArticle

RALGAPA1 Deletion in Belgian Shepherd Dogs with Cerebellar Ataxia

by Matthias Christen, Isabel Zdora, Michael Leschnik, Vidhya Jagannathan, Christina Puff, Enrice Hünerfauth, Holger A. Volk, Wolfgang Baumgärtner, Tessa C. Koch, Wencke Schäfer, Miriam Kleiter and Tosso Leeb

Genes 2023, 14(8), 1520; https://doi.org/10.3390/genes14081520 - 25 Jul 2023

Cited by 1 | Viewed by 7343

Abstract

Several genetically distinct forms of cerebellar ataxia exist in Belgian shepherd dogs. We investigated a litter in which two puppies developed cerebellar ataxia. The clinical signs stabilized at around six weeks of age, but remained visible into adulthood. Combined linkage and homozygosity mapping delineated a 5.5 Mb critical interval. The comparison of whole-genome sequence data of one affected dog to 929 control genomes revealed a private homozygous ~4.8 kb deletion in the critical interval, Chr8:14,468,376_14,473,136del4761. The deletion comprises exon 35 of the RALGAPA1 gene, XM_038544497.1:c.6080-2893_6944+1003del. It is predicted to introduce a premature stop codon into the transcript, truncating ~23% of the wild-type open reading frame of the encoded Ral GTPase-activating protein catalytic subunit α 1, XP_038400425.1:(p.Val2027Glnfs*7). Genotypes at the deletion showed the expected co-segregation with the phenotype in the family. Genotyping additional ataxic Belgian shepherd dogs revealed three additional homozygous mutant dogs from a single litter, which had been euthanized at five weeks of age due to their severe clinical phenotype. Histopathology revealed cytoplasmic accumulation of granular material within cerebellar Purkinje cells. Genotyping a cohort of almost 900 Belgian shepherd dogs showed the expected genotype–phenotype association and a carrier frequency of 5% in the population. Human patients with loss-of-function variants in RALGAPA1 develop psychomotor disability and early-onset epilepsy. The available clinical and histopathological data, together with current knowledge about RALGAPA1 variants and their functional impact in other species, suggest the RALGAPA1 deletion is the likely causative defect for the observed phenotype in the affected dogs. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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8 pages, 952 KiB

Open AccessArticle

PKD1 Nonsense Variant in a Lagotto Romagnolo Family with Polycystic Kidney Disease

by Michaela Drögemüller, Nadine Klein, Rikke Lill Steffensen, Miriam Keiner, Vidhya Jagannathan and Tosso Leeb

Genes 2023, 14(6), 1210; https://doi.org/10.3390/genes14061210 - 1 Jun 2023

Cited by 2 | Viewed by 2284

Abstract

A female Lagotto Romagnolo dog with polycystic kidney disease (PKD) and her progeny, including PKD-affected offspring, were studied. All affected dogs appeared clinically inconspicuous, while sonography revealed the presence of renal cysts. The PKD-affected index female was used for breeding and produced two litters with six affected offspring of both sexes and seven unaffected offspring. The pedigrees suggested an autosomal dominant mode of inheritance of the trait. A trio whole genome sequencing analysis of the index female and her unaffected parents identified a de novo heterozygous nonsense variant in the coding region of the PKD1 gene. This variant, NM_001006650.1:c.7195G>T, is predicted to truncate 44% of the open reading frame of the wild-type PKD1 protein, NP_001006651.1:p.(Glu2399*). The finding of a de novo variant in an excellent functional candidate gene strongly suggests that the PKD1 nonsense variant caused the observed phenotype in the affected dogs. Perfect co-segregation of the mutant allele with the PKD phenotype in two litters supports the hypothesized causality. To the best of our knowledge, this is the second description of a PKD1-related canine form of autosomal dominant PKD that may serve as an animal model for similar hepatorenal fibrocystic disorders in humans. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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12 pages, 8695 KiB

Open AccessEditor’s ChoiceArticle

An ABCC9 Missense Variant Is Associated with Sudden Cardiac Death and Dilated Cardiomyopathy in Juvenile Dogs

by Eva Furrow, Nicole Tate, Katie Minor, Shannon Martinson, Shannon Larrabee, Marjukka Anttila, Meg Sleeper and Paula Henthorn

Genes 2023, 14(5), 988; https://doi.org/10.3390/genes14050988 - 27 Apr 2023

Viewed by 3726

Abstract

Sudden cardiac death in the young (SCDY) is a devastating event that often has an underlying genetic basis. Manchester Terrier dogs offer a naturally occurring model of SCDY, with sudden death of puppies as the manifestation of an inherited dilated cardiomyopathy (DCM). We performed a genome-wide association study for SCDY/DCM in Manchester Terrier dogs and identified a susceptibility locus harboring the cardiac ATP-sensitive potassium channel gene ABCC9. Sanger sequencing revealed an ABCC9 p.R1186Q variant present in a homozygous state in all SCDY/DCM-affected dogs (n = 26). None of the controls genotyped (n = 398) were homozygous for the variant, but 69 were heterozygous carriers, consistent with autosomal recessive inheritance with complete penetrance (p = 4 × 10⁻⁴² for the association of homozygosity for ABCC9 p.R1186Q with SCDY/DCM). This variant exists at low frequency in human populations (rs776973456) with clinical significance previously deemed uncertain. The results of this study further the evidence that ABCC9 is a susceptibility gene for SCDY/DCM and highlight the potential application of dog models to predict the clinical significance of human variants. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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