State of cat genomics

Feline Cognition and the Role of Nutrition: An Evolutionary Perspective and Historical Review

Research into cognition in cats and the impact of nutrition on cat cognitive health lags behind that in dogs but is receiving increased attention. In this review, we discuss the evolutionary history of the domesticated cat, describe possible drivers of domestication, and explore the interrelationships between nutrition and cat cognition. While most cat species are solitary, domesticated cats can live in social groups, engage in complex social encounters, and form strong attachments to humans. Researchers have recently started to study cat cognition using similar methods as those developed for dogs, with an initial primary focus on perception and social cognition. Similar to dogs, cats also show cognitive and behavioral changes associated with stress and aging, but these signs are often gradual and often considered a consequence of natural aging. Despite the fundamental role of nutrition in cognitive development, function, and maintenance, research into the association between nutrition and cognition in cats is only preliminary. Ultimately, additional research is needed to gain a full understanding of cat cognition and to explore the role of nutrition in the cognitive health of cats to help improve their welfare.

Cryo-EM structure of ex vivo fibrils associated with extreme AA amyloidosis prevalence in a cat shelter

AA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at high SAA serum levels during chronic inflammation. Prion-like transmission was reported as possible cause of extreme AA amyloidosis prevalence in captive animals, e.g. 70% in cheetah and 57-73% in domestic short hair (DSH) cats kept in zoos and shelters, respectively. Herein, we present the 3.3 Å cryo-EM structure of AA amyloid extracted post-mortem from the kidney of a DSH cat with renal failure, deceased in a shelter with extreme disease prevalence. The structure reveals a cross-β architecture assembled from two 76-residue long proto-filaments. Despite >70% sequence homology to mouse and human SAA, the cat SAA variant adopts a distinct amyloid fold. Inclusion of an eight-residue insert unique to feline SAA contributes to increased amyloid stability. The presented feline AA amyloid structure is fully compatible with the 99% identical amino acid sequence of amyloid fragments of captive cheetah.

Evolutionary Biology and Gene Editing of Cat Allergen, Fel d 1

Allergy to domestic cat affects up to 15% of the population, and sensitization to cat allergen is associated with asthma. Despite the pervasiveness of cat allergic disease, current treatments have limited impact. Here, we present a bioinformatics analysis of the major cat allergen, Fel d 1, and demonstrate proof of principle for CRISPR gene editing of the allergen. Sequence and structural analyses of Fel d 1 from 50 domestic cats identified conserved coding regions in genes CH1 and CH2 suitable for CRISPR editing. Comparative analyses of Fel d 1 and orthologous sequences from eight exotic felid species determined relatively low-sequence identities for CH1 and CH2, and implied that the allergen may be nonessential for cats, given the apparent lack of evolutionary conservation. In vitro knockouts of domestic cat Fel d 1 using CRISPR-Cas9 yielded editing efficiencies of up to 55% and found no evidence of editing at predicted potential off-target sites. Taken together, our data indicate that Fel d 1 is both a rational and viable candidate for gene deletion, which may profoundly benefit cat allergy sufferers by removing the major allergen at the source.

Genetic diversity and population structure for ocelots (Leopardus pardalis) in Costa Rica

Ocelots (Leopardus pardalis) are a wide-ranging felid species, occurring from southern United States to northern Argentina. They occupy various habitats and are usually considered the most abundant wild cat species in the Neotropics. However, genetic studies that include free-ranging Mesoamerican ocelots are rare and generally based on small sample sizes. This is the first conservation genetics study on ocelots in Costa Rica and the second one in Mesoamerica that has conducted a genetic assessment of the species at a countrywide scale. We evaluated genetic diversity and population structure of ocelots using 15 microsatellite loci in 28 successfully genotyped individuals from throughout the country. We also compared genetic diversity of Costa Rican ocelots with that of jaguars (Panthera onca) and pumas (Puma concolor) in the country, and with ocelots in Belize. Genetic diversity of ocelots in Costa Rica was relatively high as measured by rarified allelic richness (AR = 5.50 ± 1.36) and expected heterozygosities (HE = 0.79 ± 0.08). We did not detect patterns of genetic substructure, suggesting high levels of gene flow throughout the country and no strong barriers to movement. As expected, genetic diversity of Costa Rican ocelots was higher than co-occurring jaguars and pumas. Additionally, levels of genetic diversity were slightly higher in Costa Rican ocelots when compared with their counterparts in Belize, confirming the south to north decrease in genetic diversity reported in other studies. Our study provides critical baseline information to understand the status of wild ocelot populations in Costa Rica. Future studies on ocelots and other threatened or keystone species should also integrate genetic monitoring and conservation genetics analysis to properly inform management decisions, guarantee their long-term survival, and improve the resilience of ecosystems.

Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi

The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.

Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats

The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.

How to Build a Super Predator: From Genotype to Phenotype

We present a drawing discovery lab that crosscuts multiple disciplines in biology and links concepts in genetics and evolutionary thinking to enhance understanding of the genotype-to-phenotype transformation. These combined concepts are also linked to ecological frameworks in nature through the model of biological plasticity. Students and teachers explore drawing skills to flesh out the future of a predator while engaging with the computational software MEGA, which introduces students and teachers to nucleotide changes, mutations, variation, phylogenetics, and molecular evolution.

Genetic relationships and inbreeding levels among geographically distant populations of Felis catus from Japan and the United States

Pedigreed cats have traditionally been mated with close relatives, which increases the risks for inbreeding depression and genetic disorders. We evaluated the genome-wide population structure and the degree of inbreeding of 1022 cats, including 13 pedigreed and two random bred populations from Japan and the USA, using single nucleotide polymorphism array-based data. Ancestry structure analysis revealed Japan's American Curl, Norwegian Forest, and Siamese cat populations were genetically distinct from their American counterparts. Furthermore, we found an ancestral genetic component shared between five pedigreed and random bred Japanese cats, suggesting the breeds were admixed with Japanese cats or cats of east Asian origin. Between-country differences in inbreeding estimates based on runs of homozygosity were found for Maine Coon, Siamese, and random bred cats. To reduce the risks of inbreeding depression and genetic disorders, particularly for highly inbred breeds, such as Abyssinian cats, as well as Russian Blue and Siamese cats in the USA, appropriate breeding practices must be observed, including mating practices that increase the genetic diversity.

Knowledge and perception on ticks and tick-borne diseases among veterinary medicine students from the North African countries of Algeria, Egypt, and Tunisia

Ticks are important vectors of both animal and human pathogens. The epidemiology of tick-borne diseases (TBDs) has dramatically changed in several regions in the world. As parasitology is a continuously growing field, assessing the knowledge of veterinary medicine students provides useful indicators and information on the level of intervention required to adapt parasitological courses to meet the demands in a changing world.

This study aimed to assess, in three North African veterinary education establishments, the basic parasitology knowledge of veterinary medicine students. Such a study is essential to build up core competencies regarding ticks and TBDs, and to suggest suitable adjustment measures to parasitology courses.

The present study was based on a self-administered and anonymous questionnaire on ticks and TBDs basic knowledge and perception. The survey was completed by 558 veterinary medicine students in Algeria, Egypt, and Tunisia in 2018. The students were divided into two groups: the “before” group – students who had not yet completed the parasitology course, and the “after” group – students who had already completed it.

In all studied countries, the “after” students' group gave significantly more correct answers (83.16%) than the “before” students' group (16.84%) (p < 0.001). Similarly, the percentage of “no answer” was higher in the “before” students' group (51.02%) compared to the “after” students' group (48.98%) (p < 0.001). The most frequent false answers provided by the “after” students' group regarded the number of tick species present in their own countries (5.14% of correct answers), and the most common tick species in their countries (18.11% of correct answers).

Almost 58.38% (216/370) of the “after” students' group knew that ticks transmit zoonotic pathogens to humans; among them, only 63 (29.17%) gave the correct names of the zoonotic diseases in their country.

Among the three countries, more than 80% of the “after” students' group thought that climate has an influences on ticks. According to this group, the most frequent factor that has influences on ticks' abundance is heat (53.02%).

As North African countries share several similitudes, we suggest creating a network of parasitological teachers where common teaching sources and resources could be developed for both teachers and students in the region. This network would allow the exchange of teaching approaches and materials to introduce harmonization into veterinary parasitological courses across North African countries. This is particularly important when considering the increasing incidence of ticks and TBDs in the region.

Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France

European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the subspecies and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization remain largely unknown. In France, wildcats are mainly present in the northeast and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the northeastern wildcat population. The two wildcat populations were significantly differentiated (F ST = 0.072) to an extent close to what has been reported (F ST = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.

Breed differences of heritable behaviour traits in cats

Cat domestication and selective breeding have resulted in tens of breeds with major morphological differences. These breeds may also show distinctive behaviour differences; which, however, have been poorly studied. To improve the understanding of feline behaviour, we examined whether behavioural differences exist among cat breeds and whether behaviour is heritable. For these aims, we utilized our extensive health and behaviour questionnaire directed to cat owners and collected a survey data of 5726 cats. Firstly, for studying breed differences, we utilized logistic regression models with multiple environmental factors and discovered behaviour differences in 19 breeds and breed groups in ten different behaviour traits. Secondly, the studied cat breeds grouped into four clusters, with the Turkish Van and Angora cats alone forming one of them. These findings indicate that cat breeds have diverged not only morphologically but also behaviourally. Thirdly, we estimated heritability in three breeds and obtained moderate heritability estimates in seven studied traits, varying from 0.4 to 0.53, as well as phenotypic and genetic correlations for several trait pairs. Our results show that it is possible to partition the observed variation in behaviour traits into genetic and environmental components, and that substantial genetic variation exists within breed populations.

Cats use hollow papillae to wick saliva into fur

The cat tongue is covered in sharp, rear-facing spines called papillae, the precise function of which is a mystery. In this combined experimental and theoretical study, we use high-speed film, grooming force measurements, and computed tomography (CT) scanning to elucidate the mechanism by which papillae are used to groom fur. We examine the tongues of six species of cats from domestic cat to lion, spanning 30-fold in body weight. The papillae of these cats each feature a hollow cavity at the tip that spontaneously wicks saliva from the mouth and then releases it onto hairs. The unique shape of the cat's papillae may inspire ways to clean complex hairy surfaces. We demonstrate one such application with the tongue-inspired grooming (TIGR) brush, which incorporates 3D-printed cat papillae into a silicone substrate. The TIGR brush experiences lower grooming forces than a normal hairbrush and is easier to clean.

Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence

Since the discovery of the human pathogen Helicobacter pylori, various other Helicobacter species have been identified in the stomach of domesticated and wild mammals. To better understand the evolutionary history of these ecologically similar but genetically distinct species, we analyzed 108 gastric Helicobacter genomes and included 54 enterohepatic Helicobacter genomes for comparison purposes. An admixture analysis supported the presence of an ecological barrier, preventing the genetic exchange between the gastric and enterohepatic Helicobacter species, and unraveled many gene flow events within and across species residing in the stomach. As pets can be colonized by multiple gastric Helicobacter species, the genetic exchange between the canine and feline strains was evident, with H. heilmannii and H. bizzozeronii showing the highest interspecies recombination. An admixture between H. pylori (in particular, the ancestral African strains), H. acinonychis from wild felines and H. cetorum from marine mammals was also identified. Because these latter species do not share the same host, this phenomenon is most likely a remaining signal of shared ancestry. A reconstruction of the time of divergence of the gastric Helicobacter spp. revealed that the domestic animal-related Helicobacter species evolved in parallel with H. pylori and its two closest relatives (H. acinonychis and H. cetorum), rather than together.

Hindering the illegal trade in dog and cat furs through a DNA-based protocol for species identification

In Western countries dogs and cats are the most popular pets, and people are increasingly opposed to their rearing for the fur industry. In 2007, a Regulation of the European Union (EU) banned the use and trade of dog and cat furs, but an official analytical protocol to identify them as source species was not provided, and violations of law are still frequent in all Member States. In this paper we report on the development and validation of a simple and affordable DNA method for species detection in furs to use as an effective tool to combat illegal trade in fur products. A set of mitochondrial primers was designed for amplification of partial cytochrome b, control region and ND1 gene in highly degraded samples, like furs and pelts. Our amplification workflow involved the use of a non-specific primer pair to perform a first test to identify the species through sequencing, then the application of species-specific primer pairs to use in singleplex end-point PCRs as confirmation tests. The advantage of this two-step procedure is twofold: on the one hand it minimises the possibility of negative test results from degraded samples, since failure of amplification with a first set of primers can be offset by successful amplification of the second, and on the other it adds confidence and reliability to final authentication of species. All designed primers were validated on a reference collection of tissue samples, obtaining solid results in terms of specificity, sensitivity, repeatability and reproducibility. Application of the protocol on real caseworks from seized furs yielded successful results also from old and dyed furs, suggesting that age and chemical staining do not necessarily affect positive amplifications. Major pros of this approach are: (1) sensitive and informative primer sets for detection of species; (2) short PCR amplicons for the analysis of poor quality DNA; (3) binding primers that avoid contamination from human DNA; (4) user-friendly protocol for any laboratory equipped for analysis of low-copy-number DNA. Our molecular procedure proved to be a good starting point for enforcing the EU Regulation against dog and cat fur trade in forensic contexts where source attribution is essential to the assignment of responsibilities.

Translational pain assessment: could natural animal models be the missing link?

Failure of analgesic drugs in clinical development is common. Along with the current "reproducibility crisis" in pain research, this has led some to question the use of animal models. Experimental models tend to comprise genetically homogeneous groups of young, male rodents in restricted and unvarying environments, and pain-producing assays that may not closely mimic the natural condition of interest. In addition, typical experimental outcome measures using thresholds or latencies for withdrawal may not adequately reflect clinical pain phenomena pertinent to human patients. It has been suggested that naturally occurring disease in veterinary patients may provide more valid models for the study of painful disease. Many painful conditions in animals resemble those in people. Like humans, veterinary patients are genetically diverse, often live to old age, and enjoy a complex environment, often the same as their owners. There is increasing interest in the development and validation of outcome measures for detecting pain in veterinary patients; these include objective (eg, locomotor activity monitoring, kinetic evaluation, quantitative sensory testing, and bioimaging) and subjective (eg, pain scales and quality of life scales) measures. Veterinary subject diversity, pathophysiological similarities to humans, and diverse outcome measures could yield better generalizability of findings and improved translation potential, potentially benefiting both humans and animals. The Comparative Oncology Trial Consortium in dogs has pawed the way for translational research, surmounting the challenges inherent in veterinary clinical trials. This review describes numerous conditions similarly applicable to pain research, with potential mutual benefits for human and veterinary clinicians, and their respective patients.

Early weaning increases aggression and stereotypic behaviour in cats

Behaviour problems are common in companion felines, and problematic behaviour may be a sign of chronic stress. In laboratory animals, early weaning increases the risk for aggression, anxiety, and stereotypic behaviour. However, very few studies have focused on early weaning in one of the world’s most popular pets, the domestic cat, although weaning soon after the critical period of socialisation is common practice. To study the effects of early weaning (<12 weeks) on behaviour, a large data set (N = 5726, 40 breeds) was collected from home-living domestic cats through a questionnaire survey. The results show that weaning before 8 weeks of age increases the risk for aggression, but not fearful behaviour. Moreover, cats weaned after 14 weeks of age have a lower probability for aggression towards strangers than early weaned cats and a lower probability for stereotypic behaviour (excessive grooming) than cats weaned at 12 weeks. The effect of weaning age on stereotypic behaviour is partially explained by the effects on aggression. These findings indicate that early weaning has a detrimental effect on behaviour, and suggest delayed weaning as a simple and inexpensive approach to significantly improve the welfare of millions of domestic cats.

Phylogeography of Toxoplasma gondii points to a South American origin

Toxoplasma gondii, a protozoan found ubiquitously in mammals and birds, is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide, including about 200,000 new cases of congenital toxoplasmosis each year. Clinical severity has been shown to vary across geographical regions, with South America exhibiting the highest burden. Unfortunately, the drivers of these heterogeneities are still poorly understood, and the geographical origin and historical spread of the pathogen worldwide are currently uncertain. A worldwide sample of 168 T. gondii isolates gathered in 13 populations was sequenced for five fragments of genes (140 single nucleotide polymorphisms from 3153bp per isolate). Phylogeny based on Maximum likelihood methods with estimation of the time to the most recent common ancestor (TMRCA) and geostatistical analyses were performed for inferring the putative origin of T. gondii. We show that extant strains of the pathogen likely evolved from a South American ancestor, around 1.5 million years ago, and reconstruct the subsequent spread of the pathogen worldwide. This emergence is much more recent than the appearance of ancestral T. gondii, believed to have taken place about 11 My ago, and follows the arrival of felids in this part of the world. We posit that an ancestral lineage of T. gondii likely arrived in South America with felids and that the evolution of oral infectivity through carnivorism and the radiation of felids in this region enabled a new strain to outcompete the ancestral lineage and undergo a pandemic radiation.

Comparison of the activation peptide regions of protease-activated receptors (PAR) in members of the Family Felidae

BACKGROUND

There is limited information regarding the nucleotides encoding or the predicted amino acid composition of protease-activated receptors (PAR) in cats.

OBJECTIVES

The purpose of the study was to determine the nucleotide sequence and predicted amino acid composition of the activation peptide regions of protease-activated receptors PAR1, PAR3, and PAR4 in Felidae family members.

METHODS

Genomic DNA isolated from whole blood samples collected from 10 domestic cats and 45 big cats representing 11 species was subjected to PCR using primers flanking the coding regions for the activation peptides of PAR1, PAR3, and PAR4. PCR products were isolated from agarose gels and submitted for sequencing. Nucleotide sequence data was used to predict the amino acid composition of the activation peptide and flanking regions of the 3 receptors. Predicted amino acid sequences were compared between Felidae members and to human beings.

RESULTS

Variations in the predicted amino acid composition of the activation peptides and flanking regions of the various PAR were observed when comparing Felidae family members to each other and to human beings.

CONCLUSIONS

While the activation peptide regions of the various PAR tend to be conserved, there are differences that may impact the ability of some agonists to mediate biased signaling events documented to occur in human platelets.

Cytogenomics of Feline Cancers: Advances and Opportunities

Relative to the dog, integration of the cat into the “One Health” concept has been more restricted, particularly in the field of molecular oncology. Beyond the continual need to enhance the sophistication of feline healthcare per se, the unique spectrum of naturally-occurring cancers in the cat offers tremendous opportunities for comparative and translational advances that may have mutual benefit for human and veterinary medicine. The study of feline cancers additionally may generate new insight into underexplored aspects of tumor biology that are less accessible in other species, such as the relationship between chronic inflammation and neoplasia, and the role of viruses in malignant transformation. Several factors that have hindered molecular studies of feline cancers have now been surmounted, with the most fundamental step forward coming from the development of a high-quality reference genome sequence assembly for the cat. This article reviews landmark studies that have led to our current appreciation of feline genome architecture, and outlines techniques used in cancer cytogenomics, from conventional karyotyping analysis through to the development of genomic microarrays and beyond. A summary of progress in the identification and characterization of chromosomal aberrations in feline cancers is provided using examples from studies of injection-site sarcomas, lymphomas and mammary tumors.

Changes in serum and urine SAA concentrations and qualitative and quantitative proteinuria in Abyssinian cats with familial amyloidosis: a five-year longitudinal study (2009-2014)

BACKGROUND

Diagnosis of familial amyloidosis (FA) in Abyssinian cats usually is made on postmortem examination.

HYPOTHESIS/OBJECTIVES

Sequential analysis of serum SAA (sSAA), urinary SAA (uSAA), urinary protein:creatinine (UPC) ratio, or sodium-dodecylsulfate agarose gel electrophoresis (SDS-AGE) may facilitate early identification of cats with FA.

ANIMALS

Twenty-three Abyssinian cats belonging to cattery A or B (low and high prevalence of FA, respectively).

METHODS

Prospective longitudinal study using 109 blood and 100 urine samples collected over 4-year period every 4 months, if possible, or more frequently in case of illness. Cats that died during study were necropsied. Health status of live cats was checked 5 years after enrollment. Serum amyloid A (sSAA) and urinary SAA (uSAA) were measured using ELISA kit. The UPC ratio and SDS-AGE also was performed.

RESULTS

Familial amyloidosis was not identified in cattery A, whereas 7/14 cats from cattery B had FA. Serum amyloid A concentrations were not significantly different between cats in catteries A and B or between cats with or without FA, despite frequent peaks in cats from cattery B. Conversely, uSAA was significantly higher in cattery B, especially in the terminal phases of FA. Proteinuria occasionally was found in cats from both catteries, especially in those with FA. Urine protein electrophoresis identified mixed proteinuria only in cats with FA.

CONCLUSIONS AND CLINICAL IMPORTANCE

Serum amyloid A and UPC ratio are not helpful for early identification of Abyssinian cats with FA. Conversely, increases in uSAA with or without mixed proteinuria may be found before onset of clinical signs in cats with FA.

Molecular cloning, sequencing, and distribution of feline GnRH receptor (GnRHR) and resequencing of canine GnRHR

GnRH receptors play vital roles in mammalian reproduction via regulation of gonadotropin secretion, which is essential for gametogenesis and production of gonadal steroids. GnRH receptors for more than 20 mammalian species have been sequenced, including human, mouse, and dog. This study reports the molecular cloning and sequencing of GnRH receptor (GnRHR) cDNA from the pituitary gland of the domestic cat, an important species in biomedical research. Feline GnRHR cDNA is composed of 981 nucleotides and encodes a 327 amino acid protein. Unlike the majority of mammalian species sequenced so far, but similar to canine GnRHR, feline GnRHR protein lacks asparagine in position three of the extracellular domain of the protein. At the amino acid level, feline GnRHR exhibits 95.1% identity with canine, 93.8% with human, and 88.9% with mouse GnRHR. Comparative sequence analysis of GnRHRs for multiple mammalian species led to resequencing of canine GnRHR, which differed from that previously published by a single base change that translates to a different amino acid in position 193. This single base change was confirmed in dogs of multiple breeds. Reverse transcriptase PCR analysis of GnRHR messenger RNA in different tissues from four normal cats indicated the presence of amplicons of varying lengths, including full-length as well as shortened GnRHR amplicons, pointing to the existence of truncated GnRHR transcripts in the domestic cat. This study is the first insight into molecular composition and expression of feline GnRHR and promotes better understanding of receptor organization, and distribution in various tissues of this species.

Pathogenesis and molecular biology of a transmissible tumor in the Tasmanian devil

The emergence of a fatal transmissible cancer known as devil facial tumor disease (DFTD) is threatening the iconic Tasmanian devil with extinction in the wild within the next few decades. Since the first report of the disease in 1996, DFTD has spread to over 85% of the devils' distribution and dramatically reduced devil numbers. Research into DFTD has focused on gaining a deeper understanding of the disease on multiple levels, including an accurate assessment of the tissue origin of the tumor, elucidation of how the tumor evades immune detection, and determination of how the tumor is transmitted between individuals and how it is evolving as it spreads through the population. Knowledge gained from these studies has important implications for DFTD management and devil conservation.

Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K

Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.

Haematological and biochemical reference intervals of four feline breeds

Many feline breeds have been generated from a small number of ancestors. Thus, breed-specific peculiarities can be expected, which could include haematological and biochemical measurements. Despite this, there are only a few reports on breed-specific reference intervals (RI). This information is essential in routine practice where results from individual patients are usually compared with an RI. The aim was to compare haematological and biochemical data from clinically healthy Abyssinian, Holy Birman, Norwegian Forest and Siberian cats with published RIs to assess whether the published RIs are acceptable in these breeds. Comparison with established RIs using guidelines from the National Committee for Clinical Laboratory Standards and the American Society of Veterinary Clinical Pathology, revealed a number of breed-related clinicopathological differences. New RIs were established, but in most cases the new RIs overlapped with published RIs, and the use of the breed-specific data would minimally affect the clinical interpretation of laboratory results. Important differences that could result in misinterpretation of laboratory results were as follows: microcytosis and high α2-globulin concentrations in Abyssinian cats; high serum creatinine, α2-globulin and glucose concentrations in Holy Birman cats; high serum alkaline phosphatase activity and calcium and phosphate concentration in Norwegian Forest cats; low β2-globulin and γ-globulin concentrations in Norwegian Forest and Siberian cats. Breed-specific RIs should be used for these analytes. In addition, care should be taken in interpreting clinicopathological data in purebred cats for which specific RIs have not been established.

Felinine excretion in domestic cat breeds: a preliminary investigation

The aim of this study was to determine possible differences in felinine excretion between domesticated cat breeds. For this purpose, urine was collected from a total of 83 privately owned entire male cats from eight different breeds in the Netherlands during the period of November 2010 till November 2011. In the collected samples, free felinine and creatinine concentrations were measured. Free felinine concentrations were expressed relative to the urinary creatinine concentration to compensate for possible variations in renal output. The mean (±SD) felinine:creatinine (Fel:Cr) ratio as measured over all cats was 0.702 (±0.265). Both the Abyssinian and Sphynx breeds showed the highest Fel:Cr ratio (0.878 ± 0.162 and 0.878 ± 0.341 respectively) which significantly differed from the ratios of the British Shorthairs (0.584 ± 0.220), Birmans (0.614 ± 0.266), Norwegian Forest cats (0.566 ± 0.296) and Siberian cats (0.627 ± 0.124). The Fel:Cr ratios of the Persians (0.792 ± 0.284) and Ragdolls (0.673 ± 0.256) showed no statistical difference with either of the other breeds. A significant proportion of the observed variation between the different feline breeds could be explained by hair growth, as both hair growth and felinine production compete for available cysteine. Shorthaired and hairless cat breeds generally showed a higher Fel:Cr ratio compared to longhaired cat breeds, with the exception of Persian cats. Further research is warranted to more closely study the effect of hair growth on felinine production.

Identification and classification of feline endogenous retroviruses in the cat genome using degenerate PCR and in silico data analysis

The purpose of this study was to identify and classify endogenous retroviruses (ERVs) in the cat genome. Pooled DNA from five domestic cats was subjected to degenerate PCR with primers specific to the conserved retroviral pro/pol region. The 59 amplified retroviral sequences were used for in silico analysis of the cat genome (Felis_catus-6.2). We identified 219 ERV γ and β elements from cat genome contigs, which were classified into 42 ERV γ and 4 β families and further analysed. Among them, 99 γ and 5 β ERV elements contained the complete retroviral structure. Furthermore, we identified 757 spuma-like ERV elements based on the sequence homology to murine (Mu)ERV-L and human (H)ERV-L. To the best of our knowledge, this is the first detailed genome-scale analysis examining Felis catus endogenous retroviruses (FcERV) and providing advanced insights into their structural characteristics, localization in the genome, and diversity.

Genetic tracking of mice and other bioproxies to infer human history

The long-distance movements made by humans through history are quickly erased by time but can be reconstructed by studying the genetic make-up of organisms that travelled with them. The phylogeography of the western house mouse (Mus musculus domesticus), whose current widespread distribution around the world has been caused directly by the movements of (primarily) European people, has proved particularly informative in a series of recent studies. The geographic distributions of genetic lineages in this commensal have been linked to the Iron Age movements within the Mediterranean region and Western Europe, the extensive maritime activities of the Vikings in the 9th to 11th centuries, and the colonisation of distant landmasses and islands by the Western European nations starting in the 15th century. We review here recent insights into human history based on phylogeographic studies of mice and other species that have travelled with humans, and discuss how emerging genomic methodologies will increase the precision of these inferences.

Mutation analysis of GM1 gangliosidosis in a Siamese cat from Japan in the 1960s

GM1 gangliosidosis is a fatal, progressive neurodegenerative lysosomal storage disease caused by mutations of the β-galactosidase (GLB1) gene. In feline GM1 gangliosidosis, a pathogenic mutation (c.1448G>C) of the feline GLB1 gene was identified in Siamese and Korat cats previously diagnosed with the disease in the USA and Italy, respectively. The present study demonstrated the same mutation in a Siamese cat that had been diagnosed with GM1 gangliosidosis in Japan in the 1960s. The mutation was confirmed using DNA extracted from stored paraffin-embedded brain tissue by a direct sequencing method and a polymerase chain reaction-restriction fragment length polymorphism assay. This pathogenic mutation seems to have been distributed around the world.

Identification of Bangladeshi domestic cats with GM1 gangliosidosis caused by the c.1448G>C mutation of the feline GLB1 gene: case study

GM1 gangliosidosis is a fatal, progressive neurodegenerative lysosomal storage disease caused by mutations in the β-galactosidase (GLB1) gene. In feline GM1 gangliosidosis, a pathogenic mutation (c.1448G>C) in the feline GLB1 gene was identified in Siamese cats in the United States and Japan and in Korat cats in Western countries. The present study found the homozygous c.1448G>C mutation in 2 apparent littermate native kittens in Bangladesh that were exhibiting neurological signs. This is the first identification of GM1 gangliosidosis in native domestic cats in Southeast Asia. This pathogenic mutation seems to have been present in the domestic cat population in the Siamese region and may have been transferred to pure breeds such as Siamese and Korat cats originating in this region.

Antiviral restriction factor transgenesis in the domestic cat

This paper reports transgenesis by genetic modification of gametes in the domestic cat. The approach is used to generate transgenic cats expressing a virus restriction factor from rhesus macaque.

Studies of the domestic cat have contributed to many scientific advances, including the present understanding of the mammalian cerebral cortex. A practical capability for cat transgenesis is needed to realize the distinctive potential of research on this neurobehaviorally complex, accessible species for advancing human and feline health. For example, humans and cats are afflicted with pandemic AIDS lentiviruses that are susceptible to species-specific restriction factors. Here we introduced genes encoding such a factor, rhesus macaque TRIMCyp, and eGFP, into the cat germline. The method establishes gamete-targeted transgenesis for the first time in a carnivore. We observed uniformly transgenic outcomes, widespread expression, no mosaicism and no F1 silencing. TRIMCyp transgenic cat lymphocytes resisted feline immunodeficiency virus replication. This capability to experimentally manipulate the genome of an AIDS-susceptible species can be used to test the potential of restriction factors for HIV gene therapy and to build models of other infectious and noninfectious diseases.

Human impact on genetic diversity of Toxoplasma gondii: example of the anthropized environment from French Guiana

In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.

The replication rate of human hematopoietic stem cells in vivo

Hematopoietic stem cells (HSCs) replicate (self-renew) to create 2 daughter cells with capabilities equivalent to their parent, as well as differentiate, and thus can both maintain and restore blood cell production. Cell labeling with division-sensitive markers and competitive transplantation studies have been used to estimate the replication rate of murine HSCs in vivo. However, these methods are not feasible in humans and surrogate assays are required. In this report, we analyze the changing ratio with age of maternal/paternal X-chromosome phenotypes in blood cells from females and infer that human HSCs replicate on average once every 40 weeks (range, 25-50 weeks). We then confirm this estimate with 2 independent approaches, use the estimate to simulate human hematopoiesis, and show that the simulations accurately reproduce marrow transplantation data. Our simulations also provide evidence that the number of human HSCs increases from birth until adolescence and then plateaus, and that the ratio of contributing to quiescent HSCs in humans significantly differs from mouse. In addition, they suggest that human marrow failure, such as the marrow failure that occurs after umbilical cord blood transplantation and with aplastic anemia, results from insufficient numbers of early progenitor cells, and not the absence of HSCs.

Ursodeoxycholic acid promotes intestinal adaptation in a cat model of short bowel syndrome

The aim of this study was to assess the effect of ursodeoxycholic acid (UDCA) on the morphological and functional adaptive response of the jejunal remnant after massive intestinal resection in a cat model of short bowel syndrome (SBS). UDCA was administered to animals at a daily oral dose of 15 mg/kg for 6 weeks following a 85% jejunoileal resection. Resection alone caused extensive hyperplasia of jejunal mucosa, as evidenced by a significant increase in the weight of jejunal mucosa per unit length as well as by significant increases in DNA and protein concentration but no change in the protein/DNA ratio. Morphometric analysis using microscopy revealed no changes in jejunal mucosa thickness, jejunal crypt depth, villus height and villus surface area, although villus thickness was increased. The specific activities of jejunal sucrase and alkaline phosphatase were unaffected. UDCA treatment of resected animals, using doses that caused no toxicity, as evidenced by the absence of serum biochemistry abnormalities and histopathology, did not induce, compared to resection alone, any changes in mucosal cellularity and did not affect villus morphometry. On the other hand, UDCA administration increased crypt depth and, also, induced a profound increase in the specific activity of sucrase. UDCA improved diarrhoea, a core SBS symptom, reflected in a considerably reduced frequency of defaecation and improved form and texture of faeces. It is concluded that UDCA administration may enhance the natural adaptive response of the intestinal remnant following massive jejunoileal resection and may, thus, be beneficial in SBS treatment.

Evidence for compromised metabolic function and limited glucose uptake in spermatozoa from the teratospermic domestic cat (Felis catus) and cheetah (Acinonyx jubatus)

Cheetahs and certain other felids consistently ejaculate high proportions (≥ 60%) of malformed spermatozoa, a condition known as teratospermia, which is prevalent in humans. Even seemingly normal spermatozoa from domestic cat teratospermic ejaculates have reduced fertilizing capacity. To understand the role of sperm metabolism in this phenomenon, we conducted a comparative study in the normospermic domestic cat versus the teratospermic cat and cheetah with the general hypothesis that sperm metabolic function is impaired in males producing predominantly pleiomorphic spermatozoa. Washed ejaculates were incubated in chemically defined medium containing glucose and pyruvate. Uptake of glucose and pyruvate and production of lactate were assessed using enzyme-linked fluorescence assays. Spermatozoa from domestic cats and cheetahs exhibited similar metabolic profiles, with minimal glucose metabolism and approximately equimolar rates of pyruvate uptake and lactate production. Compared to normospermic counterparts, pyruvate and lactate metabolism were reduced in teratospermic cat and cheetah ejaculates, even when controlling for sperm motility. Rates of pyruvate and lactate (but not glucose) metabolism were correlated positively with sperm motility, acrosomal integrity, and normal morphology. Collectively, our findings reveal that pyruvate uptake and lactate production are reliable, quantitative indicators of sperm quality in these two felid species and that metabolic function is impaired in teratospermic ejaculates. Furthermore, patterns of substrate utilization are conserved between these species, including the unexpected lack of exogenous glucose metabolism. Because glycolysis is required to support sperm motility and capacitation in certain other mammals (including dogs), the activity of this pathway in felid spermatozoa is a target for future investigation.

Extremophiles and their application to veterinary medicine

Extremophiles can be defined as organisms that can survive in extreme environments that cannot support mammalian life. They include microorganisms that can tolerate temperature extremes, extremes of pH, salinity, hydrostatic pressure and ionizing radiation, as well as low oxygen tension, desiccation and the presence of heavy metals. Psychrophilic organisms also include fish in polar waters and animals that withstand freezing. Rare examples of thermophilic pathogens exist, and the main category of extremophilic animal pathogens comprises psychrophilic and psychrotrophic microorganisms that cause fish diseases, e.g. Flavobacterium psychrophilum, Moritella viscosa, Aliivibrio wodanis and Aliivibrio salmonicida. The most widely known application of an extremophile product in veterinary medicine is DNA polymerase from thermophiles, which is a mainstay of PCR-based diagnostics for an extensive range of animal pathogens. DNA polymerases and other extremophile enzymes are also used in many molecular biology applications and animal genomics. Other extremophile products may find application in veterinary medicine in the future. These include enzymes in biosensors, compatible solutes in skin care products, drug excipients, treatments for respiratory disease, radioprotectants, peptide antibiotics, archaeal lipids for drug delivery and anti-cancer therapeutics.

Light whole genome sequence for SNP discovery across domestic cat breeds

BACKGROUND

The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus--FeLV, feline coronavirus--FECV, feline immunodeficiency virus--FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery.

DESCRIPTION

To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a SNP validation rate of 99%.

CONCLUSIONS

These data provide a large collection of mapped feline SNPs across the cat genome that will allow for the development of SNP genotyping platforms for mapping feline diseases.

Future Veterinary Diagnostics

The development of rapid, accurate, and sensitive diagnostic methods for detecting pathogens is the basis for treating, controlling, and eradicating infectious diseases of veterinary importance. Scientific and technological advancements have revolutionized the field of veterinary diagnostics. Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. The integration of advances in biochemistry, proteomics, engineering, and medicine offers enormous potential for the rapid and accurate diagnosis of viral, microbial, genetic, and metabolic disease. In the future, polymerase chain reaction assays, microarray testing, genomic analysis, and metabolic profiling will be accomplished in a rapid, portable, sensitive, and cost-efficient manner.

Behavioral profiles of feline breeds in Japan

To clarify the behavioral profiles of 9 feline purebreds, 2 Persian subbreeds and the Japanese domestic cat, a questionnaire survey was distributed to 67 small-animal veterinarians. We found significant differences among breeds in all behavioral traits examined except for "inappropriate elimination". In addition, sexual differences were observed in certain behaviors, including "aggression toward cats", "general activity", "novelty-seeking", and "excitability". These behaviors were more common in males than females, whereas "nervousness" and "inappropriate elimination" were rated higher in females. When all breeds were categorized into four groups on the basis of a cluster analysis using the scores of two behavioral trait factors called "aggressiveness/sensitivity" and "vivaciousness", the group including Abyssinian, Russian Blue, Somali, Siamese, and Chinchilla breeds showed high aggressiveness/sensitivity and low vivaciousness. In contrast, the group including the American Shorthair and Japanese domestic cat displayed low aggressiveness/sensitivity and high vivaciousness, and the Himalayan and Persian group showed mild aggressiveness/sensitivity and very low vivaciousness. Finally, the group containing Maine Coon, Ragdoll, and Scottish Fold breeds displayed very low aggressiveness/sensitivity and low vivaciousness. The present results demonstrate that some feline behavioral traits vary by breed and/or sex.

Devil Facial Tumour Disease (DFTD): Using Genetics and Genomics to Investigate Infectious Disease in an Endangered Marsupial

The Tasmanian devil (Sarcophilus harrisii), so named for its blood-curdling, nocturnal shrieks and snarls, is the largest of the carnivorous marsupials. Although once widely persecuted, concerted efforts are now being made to save the devil from extinction following the emergence of a fatal transmissible malignancy known as devil facial tumour disease (DFTD). DFTD is unusual in that the infectious agent is the cancer cell itself. This chapter discusses the aetiology and pathogenesis of DFTD as well as the profound impact the spread of DFTD has had on the devil’s conservation status. Strategies for managing DFTD and conserving the devil will be explored and the contribution of new sequencing technology to the field of conservation genetics and genomics will be examined with regard to the Tasmanian devil and DFTD.

Restriction of feline retroviruses: lessons from cat APOBEC3 cytidine deaminases and TRIM5alpha proteins

The interplay between viral and cellular factors determines the outcome of an initial contact between a given virus and its natural host or upon encounter of a novel host. Thus, the potential of inducing disease as well as crossing host species barriers are the consequences of the molecular interactions between the parasite and its susceptible, tolerant or resistant host. Cellular restriction factors, for instance APOBEC3 and TRIM5 proteins, targeting defined pathogens or groups of pathogens as well as viral genes counter-acting these cellular defense systems are of prime importance in this respect and may even represent novel targets for prevention and therapy of virus infections. Due to the importance of host-encoded antiviral restriction and viral counter-defense for pathogenicity and host tropism, the responsible molecular factors and mechanisms are currently under intense investigation. In this review we will introduce host restriction and retroviral counter-defense systems with a special emphasis on the cat and its naturally occurring exogenous retroviruses which is a valid model for human disease, a model that will contribute to increase our basic understanding and potential applications of these important aspects of host-virus interaction.

Update on genomics in veterinary oncology

The release of an annotated human genome sequence assembly and the emergence of genomics technologies have led to significant advances in our understanding of many human diseases including cancers. As DNA sequencing technology has become less costly, the field of comparative genomics has progressed rapidly and attention has turned now to generating whole genome assemblies and dedicated genomics resources for veterinary species. Such progress brings a whole new series of opportunities to advance veterinary medicine. Many human and animal diseases share a pathogenetic basis, and although veterinary species need advances in biomedical research in their own right, the consideration of companion animals also as good comparative models for human disease saw the emergence of the "one medicine" concept. The future of many areas of human and veterinary biomedical research is very much interdependent, with one of the closest associations being in oncology. It is inevitable that veterinary oncology will benefit enormously from data derived from genomics and that this era will see a huge shift in the ways in which companion animal cancer patients are evaluated and subsequently treated. Here, we will review some of the advancements of genomics as they relate to veterinary oncology.

An autosomal genetic linkage map of the domestic cat, Felis silvestris catus

We report on the completion of an autosomal genetic linkage (GL) map of the domestic cat (Felis silvestris catus). Unlike two previous linkage maps of the cat constructed with a hybrid pedigree between the domestic cat and the Asian leopard cat, this map was generated entirely with domestic cats, using a large multi-generational pedigree (n=256) maintained by the Nestlé Purina PetCare Company. Four hundred eighty-three simple tandem repeat (STR) loci have been assigned to linkage groups on the cat's 18 autosomes. A single linkage group spans each autosome. The length of the cat map, estimated at 4370 cM, is long relative to most reported mammalian maps. A high degree of concordance in marker order was observed between the third-generation map and the 1.5 Mb-resolution radiation hybrid (RH) map of the cat. Using the cat 1.9x whole-genome sequence, we identified map coordinates for 85% of the loci in the cat assembly, with high concordance observed in marker order between the linkage map and the cat sequence assembly. The present version represents a marked improvement over previous cat linkage maps as it (i) nearly doubles the number of markers that were present in the second-generation linkage map in the cat, (ii) provides a linkage map generated in a domestic cat pedigree which will more accurately reflect recombination distances than previous maps generated in a hybrid pedigree, and (iii) provides single linkage groups spanning each autosome. Marker order was largely consistent between this and the previous maps, though the use of a hybrid pedigree in the earlier versions appears to have contributed to some suppression of recombination. The improved linkage map will provide an added resource for the mapping of phenotypic variation in the domestic cat and the use of this species as a model system for biological research.

Canine RD3 mutation establishes rod-cone dysplasia type 2 (rcd2) as ortholog of human and murine rd3

Rod-cone dysplasia type 2 (rcd2) is an autosomal recessive disorder that segregates in collie dogs. Linkage disequilibrium and meiotic linkage mapping were combined to take advantage of population structure within this breed and to fine map rcd2 to a 230-kb candidate region that included the gene C1orf36 responsible for human and murine rd3, and within which all affected dogs were homozygous for one haplotype. In one of three identified canine retinal RD3 splice variants, an insertion was found that cosegregates with rcd2 and is predicted to alter the last 61 codons of the normal open reading frame and further extend the open reading frame. Thus, combined meiotic linkage and LD mapping within a single canine breed can yield critical reduction of the disease interval when appropriate advantage is taken of within-breed population structure. This should permit a similar approach to tackle other hereditary traits that segregate in single closed populations.