Hereditary sensory and autonomic neuropathy in a family of mixed breed dogs associated with a novel RETREG1 variant

An Overview of Canine Inherited Neurological Disorders with Known Causal Variants

Hereditary neurological conditions documented in dogs encompass congenital, neonatal, and late-onset disorders, along with both progressive and non-progressive forms. In order to identify the causal variant of a disease, the main two approaches are genome-wide investigations and candidate gene investigation. Online Mendelian Inheritance in Animals currently lists 418 Mendelian disorders specific to dogs, of which 355 have their likely causal genetic variant identified. This review aims to summarize the current knowledge on the canine nervous system phenes and their genetic causal variant. It has been noted that the majority of these diseases have an autosomal recessive pattern of inheritance. Additionally, the dog breeds that are more prone to develop such diseases are the Golden Retriever, in which six inherited neurological disorders with a known causal variant have been documented, and the Belgian Shepherd, in which five such disorders have been documented. DNA tests can play a vital role in effectively managing and ultimately eradicating inherited diseases.

Single-step genome-wide association studies and post-GWAS analyses for the number of oocytes and embryos in Gir cattle

Genome-Wide Association Studies (GWAS) are used for identification of quantitate trait loci (QTL) and genes associated with several traits. We aimed to identify genomic regions, genes, and biological processes associated with number of total and viable oocytes, and number of embryos in Gir dairy cattle. A dataset with 17,526 follicular aspirations, including the following traits: number of viable oocytes (VO), number of total oocytes (TO), and number of embryos (EMBR) from 1641 Gir donors was provided by five different stock farms. A genotype file with 2093 animals and 395,524 SNP markers was used to perform a single-step GWAS analysis for each trait. The top 10 windows with the highest percentage of additive genetic variance explained by 100 adjacent SNPs were selected. The genomic regions identified in our work were overlapped with QTLs from QTL database on chromosomes 1, 2, 5, 6, 7, 8, 9, 13, 17, 18, 20, 21, 22, 24, and 29. These QTLs were classified as External, Health, Meat and carcass, Production or Reproduction traits, and about 38% were related to Reproduction. In total, 117 genes were identified, of which 111 were protein-coding genes. Exclusively associations were observed for 42 genes with EMBR, and 1 with TO. Also, 42 genes were in common between VO and TO, 28 between VO and EMBR, and four genes were in common among all traits. In conclusion, great part of the identified genes plays a functional role in initial embryo development or general cell functions. The protein-coding genes ARNT, EGR1, HIF1A, AHR, and PAX2 are good markers for the production of oocytes and embryos in Gir cattle.

Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle

Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (F_ROH) and pedigree-based inbreeding (F_ped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH_1-2Mb: 58.17%), representing ancient inbreeding, ROH_2-4Mb (22.74%), ROH_4-8Mb (11.34%), ROH_8-16Mb (5.51%), and ROH_>16Mb (2.24%). Combining our results, we conclude that the increase in general F_ROH and F_ped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with F_ROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

SCN9A variant in a family of mixed breed dogs with congenital insensitivity to pain

BACKGROUND

Congenital insensitivity to pain (CIP) and hereditary sensory and autonomic neuropathies (HSANs) are a rare group of genetic disorders causing inability to feel pain. Three different associated variants have been identified in dogs: 1 in Border Collies, 1 in mixed breed dogs, and 1 in Spaniels and Pointers.

OBJECTIVES

To clinically and genetically characterize CIP in a family of mixed breed dogs.

ANIMALS

Two mixed breed dogs from the same litter were independently presented: 1 for evaluation of painless fractures, and the other for chronic thermal skin injuries.

METHODS

Physical, neurological, and histopathological evaluations were performed. Whole genome sequencing of 1 affected dog was used to identify homozygous protein-changing variants that were not present in 926 control genomes from diverse dog breeds.

RESULTS

Physical and neurological examinations showed the absence of superficial and deep pain perception in the entire body. Histopathological evaluations of the brain, spinal cord and sensory ganglia were normal. Whole genome sequencing identified a homozygous missense variant in SCN9A, XM_038584713.1:c.2761C>T or XP_038440641.1:(p.Arg921Cys). Both affected dogs were homozygous for the mutant allele, which was not detected in 926 dogs of different breeds.

CONCLUSIONS AND CLINICAL IMPORTANCE

We confirmed the diagnosis of CIP in a family of mixed breed dogs and identified a likely pathogenic variant in the SCN9A gene. The clinical signs observed in these dogs mimic those reported in humans with pathogenic SCN9A variants causing CIP. This report is the first of a spontaneous pathogenic SCN9A variant in domestic animals.

The number of mitochondrial DNA mutations as a genetic feature for hair cycle arrest (alopecia X) in Pomeranian dogs

BACKGROUND

Hair cycle arrest (HCA) is a noninflammatory alopecic disease affecting various dog breeds, particularly Pomeranian dogs. This disease is probably a hereditary disorder considering the strong breed predisposition. Despite efforts to identify the pathogenesis of this disease, an underlying specific cause is unknown.

OBJECTIVE

To identify candidate gene mutations for HCA in Pomeranian dogs.

ANIMALS

Four Pomeranian dogs diagnosed with HCA and four unaffected Pomeranian dogs.

MATERIALS AND METHODS

Whole blood was used for DNA extraction. Whole-genome sequencing (WGS) was performed, and variants were analysed using a Genome Analysis Toolkit (GATK) and SnpEff. All reads were aligned to the reference genome, Dog10K_Boxer_Tasha. Sanger sequencing was performed to define the complex mutations.

RESULTS

A total of 113 variants of mitochondrial DNA were found to be effective gene mutations in the eight dogs. The affected dogs showed significantly increased effective mutations (average 57 variants) compared with unaffected dogs (average eight variants; p < 0.05). There was no significant difference in the number of chromosomal DNA mutations between the two groups.

CONCLUSION AND CLINICAL IMPORTANCE

We suggest that an increased number of mitochondrial gene mutations are features for HCA in Pomeranian dogs.

Inheritance of Monogenic Hereditary Skin Disease and Related Canine Breeds

The plasticity of the genome is an evolutionary factor in all animal species, including canines, but it can also be the origin of diseases caused by hereditary genetic mutation. Genetic changes, or mutations, that give rise to a pathology in most cases result from recessive alleles that are normally found with minority allelic frequency. The use of genetic improvement increases the consanguinity within canine breeds and, on many occasions, also increases the frequency of these recessive alleles, increasing the prevalence of these pathologies. This prevalence has been known for a long time, but mutations differ according to the canine breed. These genetic diseases, including skin diseases, or genodermatosis, which is narrowly defined as monogenic hereditary dermatosis. In this review, we focus on genodermatosis sensu estricto, i.e., monogenic, and hereditary dermatosis, in addition to the clinical features, diagnosis, pathogeny, and treatment. Specifically, this review analyzes epidermolytic and non-epidermolytic ichthyosis, junctional epidermolysis bullosa, nasal parakeratosis, mucinosis, dermoid sinus, among others, in canine breeds, such as Golden Retriever, German Pointer, Australian Shepherd, American Bulldog, Great Dane, Jack Russell Terrier, Labrador Retriever, Shar-Pei, and Rhodesian Ridgeback.