Mucopolysaccharidosis VI in cats - clarification regarding genetic testing

Debate. Published online: 02 July 2016.The release of new DNA-based diagnostic tools has increased tremendously in companion animals. Over 70 different DNA variants are now known for the cat, including DNA variants in disease-associated genes and genes causing aesthetically interesting traits. The impact genetic tests have on animal breeding and health management is significant because of the ability to control the breeding of domestic cats, especially breed cats. If used properly, genetic testing can prevent the production of diseased animals, causing the reduction of the frequency of the causal variant in the population, and, potentially, the eventual eradication of the disease. However, testing of some identified DNA variants may be unwarranted and cause undo strife within the cat breeding community and unnecessary reduction of gene pools and availability of breeding animals. Testing for mucopolysaccharidosis Type VI (MPS VI) in cats, specifically the genetic testing of the L476P (c.1427T>C) and the D520N (c.1558G>A) variants in arylsulfatase B (ARSB), has come under scrutiny. No health problems are associated with the D520N (c.1558G>A) variant, however, breeders that obtain positive results for this variant are speculating as to possible correlation with health concerns. Birman cats already have a markedly reduced gene pool and have a high frequency of the MPS VI D520N variant. Further reduction of the gene pool by eliminating cats that are heterozygous or homozygous for only the MPS VI D520N variant could lead to more inbreeding depression effects on the breed population. Herein is debated the genetic testing of the MPS VI D520N variant in cats. Surveys from different laboratories suggest the L476P (c.1427T>C) disease-associated variant should be monitored in the cat breed populations, particularly breeds with Siamese derivations and outcrosses. However, the D520N has no evidence of association with disease in cats and testing is not recommended in the absence of L476P genotyping. Selection against the D520N is not warranted in cat populations. More rigorous guidelines may be required to support the genetic testing of DNA variants in all animal species.Leslie A. Lyons, Robert A. Grahn, Francesca Genova, Michela Beccaglia, John J. Hopwood and Maria Longer

LTA4H and FXR1 Gene and Protein Expression in Canine Oral Melanoma

Introduction: Canine oral melanoma is a common neoplasm that is usually considered malignant, although the correlation between histology and prognosis is still controversial. Therefore, research of new biological markers is ongoing. In this study, LTA4H (an enzyme of the arachidonic acid cascade) and FXR1 (a RNA binding protein) are investigated. Both have been investigated previously for their possible role in metastasis of ocular melanoma, and are studied here in canine oral melanoma. Materials and Methods: Twenty-nine samples of formalin-fixed and paraffin wax-embedded canine oral melanomas were analyzed. Routine HE sections were evaluated on light microscopy and received a histological description, including mitotic activity index (MI). Immunohistochemistry (IHC) for LTA4H, FXR1 and Ki67 was performed. LTA4H and FXR1 were scored semiquantitatively and Ki67 was scored quantitatively. The expression of LTA4H and FXR1 genes was also quantified by RT-PCR. Results: Most of the cases were epithelioid, poorly pigmented melanomas. MI ranged from 0.1 to 9.2 (median 1.1). Ki67 index ranged from 7.9 to 44.4% (median 19%). IHC was positive in 29/29 LTA4H and 28/29 FXR1, with variable intensity and percentage of positivity. RT-PCR relative expression values ranged from 0.49 to 9.11 for LTA4H and 0.15 to 10.33 for FXR1 (in four cases was under the detection limit). Conclusions: LTA4H and FXR1 were detected in all tested melanomas. Marked differences between cases were noted with RT-PCR, although target gene expression levels were not consistent with histological parameters or Ki67 index. Conversely, immunohistochemical positivity was elevated in most cases with negligible expression differences. Further work is ongoing to clarify the prognostic significance of different levels of expression

Genetic screening of the inherited Ichtyosis causative mutation in Chianina cattle

Inherited Ichthyosis is a genetic disorder reported in both humans and animals, including bovines. Two inherited forms were reported in cattle and both are transmitted in an autosomal recessive manner: Ichthyosis Fetalis (IF) and Ichthyosis Congenita (IC). A causative mutation of IF in Chianina cattle was recently indentified in the ABC12 gene. This work reports the first genetic screening using this recently available genetic test on Chianina cattle. Tests were performed on both the population of farm breeding selected young bulls (131 samples randomly chosen) and high breeding value sires (16 samples). Results confirm a low total prevalence of carriers in the selected sire population (2/131; 1.5%) and the presence of the disease allele among the high value selected sires (1/16; 6.3%). This result strengthens the importance to continue the genetic screening program, particularly in performance tested bulls approved for use in AI or natural servic

A genome-wide perspective on the population structure of Italian cattle breeds

Despite the growing diffusion of cosmopolite specialized breeds, several autochthonous populations are still farmed in Italy. The aim of this study was to provide a high-resolution picture of the genome-wide diversity and population structure of Italian local cattle breeds using medium-density genome-wide SNP markers. After data editing, the dataset included 800 samples from 32 breeds that were genotyped for 31,013 SNPs. For several breeds we observed a low level of polymorphism and genetic diversity that confirmed threat of extinction. Shared ancestry, admixture events, and reticulations observed on the phylogenetic tree between some breeds, all suggest high levels of gene flow. Clear clusters and relationships between breeds that originated from the same geographical area were detected. However, in spite of the complex admixture history, many of the local Italian cattle breeds have retained unique identities and are clearly differentiated breeds. Differences in their origin, in climate characteristics of farming areas, the genetic isolation, and the inbreeding can be the main reasons for such differentiation. This study represents the first exhaustive genome-wide analysis of Italian cattle diversity. The results largely agreed with the breeding history of the Italian cattle breeds. The population structure and the low genetic diversity presented here for several breeds should be evaluated in adopting conservation strategies. Thus, efforts should be made to improve genetic diversity in these breeds. Control of inbreeding, breeding stations development and improvement of recording system are strategies to conserve these breeds under in situ conservation situation, and in this context, genomic information may play a crucial role for the preservation and management of these populations

BOVITA: a first overview on genome-wide genetic diversity of Italian autochthonous cattle breeds

Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local cattle breeds. Despite the growing diffusion of some cosmopolite specialized breeds, several autochthonous breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local cattle breeds, to provide information on their genetic status that will be useful for the management of the genetic variability, as a contribution to biodiversity conservation and prioritization actions. A total of about 800 animals (20-32 per breed) belonging to thirty Italian cattle breeds (Agerolese, Bar\ue0-Pustertaler, Burlina, Cabannina, Calvana, Chianina, Cinisara, Garfagnina, Italian Brown, Italian Holstein, Italian Simmental, Marchigiana, Maremmana, Modenese, Modicana, Mucca Pisana, Pezzata Rossa d\u2019Oropa, Piedmontese, Pinzgau, Podolica, Pontremolese, Pustertaler, Reggiana, Rendena, Romagnola, Rossa Siciliana, Sarda, Sardo-Bruna, Sardo-Modicana and Ottonese-Varzese) and two cosmopolitan breeds (Charolaise and Limousine) genotyped with the Illumina BovineSNP50 v2 BeadChip array were collected for the analysis. The genotypes of several breeds were detected in the frame of the project, whereas for some breeds these data are derived by previous studies. The dataset will be analyzed to: study several aspects of population genetic diversity, multi-dimensional scaling plot, population structure, linkage disequilibrium, and runs of homozygosity. In addition, comparative analysis of conserved haplotypes will be conducted to identify genomic segments under selection pressure. Such information also provides important insights into the mechanisms of evolution and is useful for the annotation of significant functional genomics regions. Data analysis will also be useful to select SNPs suitable for parentage test and breed genetic traceability. The analysis of the data will pinpoint the genetic distinctiveness of Italian breeds. Moreover, the obtained results contribute to a better characterization of history and genetic structure of Italian cattle breeds

The ascent of cat breeds : genetic evaluations of breeds and worldwide random-bred populations

The diaspora of the modern cat was traced with microsatellite markers from the presumed site of domestication to distant regions of the world. Genetic data were derived from over 1100 individuals, representing 17 random-bred populations from five continents and 22 breeds. The Mediterranean was reconfirmed to be the probable site of domestication. Genetic diversity has remained broad throughout the world, with distinct genetic clustering in the Mediterranean basin, Europe/America, Asia and Africa. However, Asian cats appeared to have separated early and expanded in relative isolation. Most breeds were derived from indigenous cats of their purported regions of origin. However, the Persian and Japanese bobtail were more aligned with European/American than with Mediterranean basin or Asian clusters. Three recently derived breeds were not distinct from their parental breeds of origin. Pure breeding was associated with a loss of genetic diversity; however, this loss did not correlate with breed popularity or age

An international parentage and identification panel for the domestic cat (Felis catus)

Seventeen commercial and research laboratories participated in two comparison tests under the auspices of the International Society for Animal Genetics to develop an internationally tested, microsatellite-based parentage and identification panel for the domestic cat (Felis catus). Genetic marker selection was based on the polymorphism information content and allele ranges from seven random-bred populations (n = 261) from the USA, Europe and Brazil and eight breeds (n = 200) from the USA. Nineteen microsatellite markers were included in the comparison test and genotyped across the samples. Based on robustness and efficiency, nine autosomal microsatellite markers were ultimately selected as a single multiplex ‘core’ panel for cat identification and parentage testing. Most markers contained dinucleotide repeats. In addition to the autosomal markers, the panel included two gender-specific markers, amelogenin and zinc-finger XY, which produced genotypes for both the X and Y chromosomes. This international cat parentage and identification panel has a power of exclusion comparable to panels used in other species, ranging from 90.08% to 99.79% across breeds and 99.47% to 99.87% in random-bred cat populations

Precision medicine in cats:novel niemann-pick type C1 diagnosed by whole-genome sequencing

State-of-the-art health care includes genome sequencing of the patient to identify genetic variants that contribute to either the cause of their malady or variants that can be targeted to improve treatment. The goal was to introduce state-of-the-art health care to cats using genomics and a precision medicine approach. To test the feasibility of a precision medicine approach in domestic cats, a single cat that presented to the University of Missouri, Veterinary Health Center with an undiagnosed neurologic disease was whole-genome sequenced. The DNA variants from the cat were compared to the DNA variant database produced by the 99 Lives Cat Genome Sequencing Consortium. Approximately 25× genomic coverage was produced for the cat. A predicted p.H441P missense mutation was identified in NPC1, the gene causing Niemann-Pick type C1 on cat chromosome D3.47456793 caused by an adenine-to-cytosine transversion, c.1322A>C. The cat was homozygous for the variant. The variant was not identified in any other 73 domestic and 9 wild felids in the sequence database or 190 additionally genotyped cats of various breeds. The successful effort suggested precision medicine is feasible for cats and other undiagnosed cats may benefit from a genomic analysis approach. The 99 Lives DNA variant database was sufficient but would benefit from additional cat sequences. Other cats with the mutation may be identified and could be introduced as a new biomedical model for NPC1. A genetic test could eliminate the disease variant from the population

High Diversity at PRDM9 in Chimpanzees and Bonobos

BACKGROUND: The PRDM9 locus in mammals has increasingly attracted research attention due to its role in mediating chromosomal recombination and possible involvement in hybrid sterility and hence speciation processes. The aim of this study was to characterize sequence variation at the PRDM9 locus in a sample of our closest living relatives, the chimpanzees and bonobos. METHODOLOGY/PRINCIPAL FINDINGS: PRDM9 contains a highly variable and repetitive zinc finger array. We amplified this domain using long-range PCR and determined the DNA sequences using conventional Sanger sequencing. From 17 chimpanzees representing three subspecies and five bonobos we obtained a total of 12 alleles differing at the nucleotide level. Based on a data set consisting of our data and recently published Pan PRDM9 sequences, we found that at the subspecies level, diversity levels did not differ among chimpanzee subspecies or between chimpanzee subspecies and bonobos. In contrast, the sample of chimpanzees harbors significantly more diversity at PRDM9 than samples of humans. Pan PRDM9 shows signs of rapid evolution including no alleles or ZnFs in common with humans as well as signals of positive selection in the residues responsible for DNA binding. CONCLUSIONS AND SIGNIFICANCE: The high number of alleles specific to the genus Pan, signs of positive selection in the DNA binding residues, and reported lack of conservation of recombination hotspots between chimpanzees and humans suggest that PRDM9 could be active in hotspot recruitment in the genus Pan. Chimpanzees and bonobos are considered separate species and do not have overlapping ranges in the wild, making the presence of shared alleles at the amino acid level between the chimpanzee and bonobo species interesting in view of the hypothesis that PRDM9 plays a universal role in interspecific hybrid sterility