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Summary The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university‐based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping‐by‐sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo‐autosomal sexing marker (zinc‐finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.

Hypertrophic cardiomyopathy (HCM) is a common and potentially fatal heart disease in many cat breeds. An intronic variant in TNNT2, c.95-108G>A, was recently reported as the cause of HCM in the Maine Coon. The aim of this study was to determine this variant's allele frequency in different populations and its possible association with HCM. Based on 160 Maine Coon samples collected in Belgium, Italy, Sweden and the USA, the variant's allele frequency was estimated to be 0.32. Analysis of the 99 Lives feline whole genome sequencing database showed that the TNNT2 variant also occurs in other breeds, as well as mixed-breed cats. Comparison of 31 affected and 58 healthy cats did not reveal significantly increased odds for HCM in homozygotes. Based on the combined evidence and in agreement with the standards and guidelines for the interpretation of sequence variants, this variant is currently classified as a variant of unknown significance and should not be used for breeding decisions regarding HCM.

Kinesin-2 enables ciliary assembly and maintenance as an anterograde intraflagellar transport (IFT) motor. Molecular motor activity is driven by a heterotrimeric complex comprised of KIF3A and KIF3B or KIF3C plus one non-motor subunit, KIFAP3. Using exome sequencing, we identified heterozygous KIF3B variants in two unrelated families with hallmark ciliopathy phenotypes. In the first family, the proband presents with hepatic fibrosis, retinitis pigmentosa, and postaxial polydactyly; he harbors a de novo c.748G>C (p.Glu250Gln) variant affecting the kinesin motor domain encoded by KIF3B. The second family is a six-generation pedigree affected predominantly by retinitis pigmentosa. Affected individuals carry a heterozygous c.1568T>C (p.Leu523Pro) KIF3B variant segregating in an autosomal-dominant pattern. We observed a significant increase in primary cilia length in vitro in the context of either of the two mutations while variant KIF3B proteins retained stability indistinguishable from wild type. Furthermore, we tested the effects of KIF3B mutant mRNA expression in the developing zebrafish retina. In the presence of either missense variant, rhodopsin was sequestered to the photoreceptor rod inner segment layer with a concomitant increase in photoreceptor cilia length. Notably, impaired rhodopsin trafficking is also characteristic of recessive KIF3B models as exemplified by an early-onset, autosomal-recessive, progressive retinal degeneration in Bengal cats; we identified a c.1000G>A (p.Ala334Thr) KIF3B variant by genome-wide association study and whole-genome sequencing. Together, our genetic, cell-based, and in vivo modeling data delineate an autosomal-dominant syndromic retinal ciliopathy in humans and suggest that multiple KIF3B pathomechanisms can impair kinesin-driven ciliary transport in the photoreceptor.

The development of the large-scale intensive poultry production system caused, in recent past, an almost complete disappearance of native breeds. The Mericanel della Brianza (MB) is an Italian bantam chicken breed characterized by optimal rusticity and a very good attitude to broodiness. The aim of this study was to assess peculiar phenotypic characteristics, breeding performance and genetic makeup of a small MB chicken nucleus under an in situ conservation program at the Poultry Conservation Centre of Local Genetic Resources of the University of Milan since 2010. The number of selected breeders in the nucleus progressively increased over the 5 years time from 22 (8M+14F) in 2010 to 58 (10M+48F) in 2014. FAO guidelines for phenotypic characterization of animal genetic resources were used to describe the productive, the reproductive traits and the performance of the MB chickens. The mean number of eggs per hen per week increased progressively from 1.86 in 2010 to 2.33 in 2014. Overall mean egg weight was 33.8 g (SD 3.71 g and CV 11%) and proportion of fertile eggs was 84%. Genetic screening of breeders was performed in 2010, 2012 and 2014 using the panel of 30 microsatellite loci recommended by ISAG and FAO for biodiversity studies. A total of 120 blood samples from twenty-four families (eight in 2010, six in 2012 and ten in 2014) were included in the study. The Mean Number of Alleles (MNA), the allelic frequencies, the observed (H O ) and expected (H E ) heterozygosity, the Polymorphism Information Content (PIC) and the inbreeding coefficient (F IS ) value were estimated. All markers were polymorphic with the exception of the MCW0034 and MCW0248 loci. These two markers and other 4, not properly amplifying, were excluded from analyses. A total number of 77 alleles (MNA = 3.08) in 25 microsatellites have been detected in the overall population. The genetic diversity within and among families was determined with the Wright's F-statistics fixation index (F ST ). F ST showed similarities among breeders within the nucleus in 2012 and 2014, but disclosed a variation respect to the nucleus of individuals of 2010. The genetic distance observed across years was confirmed by the PCA analysis. Despite the selection applied to decrease the presence of undesired traits (i.e. both morphological and reproductive traits), the genetic variability was conserved in the nucleus population across years.

Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.

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Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.

BackgroundThe Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences.MethodsSeventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences.ResultsNucleic markers showed a high degree of polymorphism (Ho= 0.642; He= 0.649) and a low inbreeding level (FIS= 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.

Inherited forms of ichthyosis, or generalized scaling of the skin, have been reported in many animal species, including cattle, and are characterized by an autosomal recessive mode of inheritance. We investigated 2 calves affected with ichthyosis fetalis, a Polled Hereford and a Shorthorn. Both cases had hard white plaques on the skin consistent with excessive keratinization. This was confirmed by histopathology, which showed severe diffuse epidermal and follicular orthokeratotic hyperkeratosis. The known mutation (H1935R) in gene ABCA12, responsible for ichthyosis fetalis in Chianina cattle, was shown to be absent in both affected calves and their obligate heterozygous parents. These molecular findings indicate that allelic heterogeneity exists for this condition in cattle.

African black-footed cats (Felis nigripes) are endangered wild felids. One male and full-sibling female African black-footed cat developed vision deficits and mydriasis as early as 3 months of age. The diagnosis of early-onset progressive retinal atrophy (PRA) was supported by reduced direct and consensual pupillary light reflexes, phenotypic presence of retinal degeneration, and a non-recordable electroretinogram with negligible amplitudes in both eyes. Whole genome sequencing, conducted on two unaffected parents and one affected offspring was compared to a variant database from 51 domestic cats and a Pallas cat, revealed 50 candidate variants that segregated concordantly with the PRA phenotype. Testing in additional affected cats confirmed that cats homozygous for a 2 base pair (bp) deletion within IQ calmodulin-binding motif-containing protein-1 (IQCB1), the gene that encodes for nephrocystin-5 (NPHP5), had vision loss. The variant segregated concordantly in other related individuals within the pedigree supporting the identification of a recessively inherited early-onset feline PRA. Analysis of the black-footed cat studbook suggests additional captive cats are at risk. Genetic testing for IQCB1 and avoidance of matings between carriers should be added to the species survival plan for captive management.

British shorthair (BSH) kittens in multiple litters died as a result of a severe non-neoplastic lymphoproliferative disease that showed many similarities with human autoimmune lymphoproliferative syndrome (ALPS). Human ALPS is caused by inherited defects in FAS-mediated lymphocyte apoptosis and the possibility of similar defects was investigated in BSH cats. The whole genomes of two affected kittens were sequenced and compared to 82 existing cat genomes. Both BSH kittens had homozygous insertions of an adenine within exon 3 of the FAS-ligand gene. The resultant frameshift and premature stop codon were predicted to result in a severely truncated protein that is unlikely to be able to activate FAS. Three additional affected BSH kittens were homozygous for the variant, while 11 of 16 unaffected, but closely related, BSH cats were heterozygous for the variant. All BSH cats in the study were from a population with significant inbreeding. The variant was not identified in a further survey of 510 non-BSH cats. Identification of a genetic defect in the FAS-mediated apoptosis pathway confirms that the lymphoproliferative disease in BSH cats fulfills the diagnostic criteria for ALPS in humans. These results will enable the development of a genetic test to detect BSH carrier animals.

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 arylsulfataseB (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.

Three fowl breeds, Valdarnese Bianca, a traditional white feathered breed from Tuscany, Golden Comet® a commercial hybrid and Livornese Bianca, a white leghorn type, were genotyped at eight microsatellite loci. A total of 74 alleles were detected with locus ADL181 recorded the lowest (six alleles) and locus ADL136 the highest (15 alleles) allele frequencies respectively. Heterozygosity values ranged from 0.210 (locus ADL210) to 0.742 (locus ADL176). The Wright's fixation index values were 0.089 (FST), 0.300 (FIs) and 0.363 (FIT). Factorial correspondence analysis and a dendrogram individual tree constructed using individual genetic distances showed genetic differentiation of the three breeds.

The widespread use of elite sires by means of artificial insemination in livestock breeding leads to the frequent emergence of recessive genetic defects, which cause significant economic and animal welfare concerns. Here we show that the availability of genome-wide, high-density SNP panels, combined with the typical structure of livestock populations, markedly accelerates the positional identification of genes and mutations that cause inherited defects. We report the fine-scale mapping of five recessive disorders in cattle and the molecular basis for three of these: congenital muscular dystony (CMD) types 1 and 2 in Belgian Blue cattle and ichthyosis fetalis in Italian Chianina cattle. Identification of these causative mutations has an immediate translation into breeding practice, allowing marker assisted selection against the defects through avoidance of at-risk matings.

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 seventeen random bred populations from five continents and twenty-two 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 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.

Summary Some Devon Rex and Sphynx cats have a variably progressive myopathy characterized by appendicular and axial muscle weakness, megaesophagus, pharyngeal weakness and fatigability with exercise. Muscle biopsies from affected cats demonstrated variable pathological changes ranging from dystrophic features to minimal abnormalities. Affected cats have exacerbation of weakness following anticholinesterase dosing, a clue that there is an underlying congenital myasthenic syndrome (CMS). A genome‐wide association study and whole‐genome sequencing suggested a causal variant for this entity was a c.1190G>A variant causing a cysteine to tyrosine substitution (p.Cys397Tyr) within the C‐terminal domain of collagen‐like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase (COLQ). Alpha‐dystroglycan expression, which is associated with COLQ anchorage at the motor end‐plate, has been shown to be deficient in affected cats. Eighteen affected cats were identified by genotyping, including cats from the original clinical descriptions in 1993 and subsequent publications. Eight Devon Rex and one Sphynx not associated with the study were identified as carriers, suggesting an allele frequency of ~2.0% in Devon Rex. Over 350 tested cats from other breeds did not have the variant. Characteristic clinical features and variant presence in all affected cats suggest a model for COLQ CMS. The association between the COLQ variant and this CMS affords clinicians the opportunity to confirm diagnosis via genetic testing and permits owners and breeders to identify carriers in the population. Moreover, accurate diagnosis increases available therapeutic options for affected cats based on an understanding of the pathophysiology and experience from human CMS associated with COLQ variants.

Summary Recombinant chimeric sequences originating from a mixture of the sequences of two different alleles are frequently found after amplification and cloning in Escherichia coli of exon 2 of the major histocompatibility complex (MHC) DRB genes. Several authors have suggested that the recombinant molecules result from in vitro recombination during PCR; nevertheless, a clear experimental demonstration of this hypothesis is lacking. In order to understand the mechanism producing the chimeric sequences, we set up a simple experiment based on the different restriction patterns of parental and recombinant sequences. Our data demonstrate that in the analysed case most of the recombinant variants were not produced by in vitro recombination during PCR, but were the result of the mismatch repair of heteroduplex molecules during cloning in E. coli. The high mutation rate in the α-helix region of DRB expressed genes, both after cloning in E. coli and after the germ-line differentiation process in vertebrates, suggests that the observed mutations are the result of similar gene conversion processes, probably favoured by chi-dependent microrecombination events.

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.

Seven autochthonous Italian cattle breeds bred in the alpine area (Aosta Black Pied, Aosta Red Pied, Aosta Chestnut, Oropa Red Pied, Grey Alpine, Rendena and Burlina) were investigated in order to characterise their genetic structure and to study their phylogenetic origin. Two cattle breeds from Germany (Original German Brown and Holstein) and four from Switzerland (Simmental, Herens, Evolene and Brown Swiss) were included in the study in order to determine the genetic diversity existing among Italian local breeds, similar breeds bred on the other side of the Alps and in the well known Holstein. Seventeen microsatellites, of the internationally accepted panel for the study of cattle biodiversity, were used for the analysis. Microsatellites were highly polymorphic with a mean number of 5,5 alleles (ranging from 2 to 12 per locus). For each locus, allelic frequencies, heterozygosity (H) and the Polymorphism Information Content (PIC) were computed. The genetic equilibrium according to Hardy–Weinberg was calculated for each population and for each locus. Allele frequencies were used to estimate genetic distances and to draw a phylogenetic tree. The two closest breeds were Aosta Red Pied and Aosta Black Pied, while the two genetically most different were Holstein and Aosta Chestnut. Aosta valley breeds, Evolene and Herens constituted a tight cluster in the phylogenetic consensus tree. Principal component analysis showed a similar pattern for all the alpine breeds, while Holstein and Original German Brown were far away. The genetic differences among breeds were in accordance with their geographical and historical origins. Die genetische Diversitat von Rinderrassen der Alpenregion Sieben autotochthone italienische Rinderrassen der Alpenregion (Aosta Black Pied, Aosta Red Pied, Aosta Chestnut, Oropa Red Pied, Grey Alpine, Rendena und Burlina) wurden untersucht, um ihre genetische Struktur und ihren phylogenetischen Ursprung zu beschreiben. In die Studie wurden zwei deutsche Rinderrassen (Original Deutsches Braunvieh und Deutsche Holsteins) und vier Rassen der Schweiz (Simmentaler, Herens, Evolene und Brown Swiss) einbezogen, um deren genetische Diversitat mit den ahnlichen italienischen Rassen auf der anderen Seite der Alpen zu vergleichen. Siebzehn Mikrosatelliten eines international anerkannten Panels fur die Untersuchung genetischer Distanzen zwischen Rinderrassen wurden in dieser Studie genutzt. Die Mikrosatelliten waren hochpolymorph mit einer durchschnittlichen Anzahl von 5,5 Allelen und einem Spektrum von 2 bis 12 Allelen pro Locus. Fur die einzelnen Loci wurden Allelfrequenzen, der Heterozygotiegrad (H) und der Polymorphism Information Content (PIC) berechnet. Die Berechnung des genetischen Gleichgewichts nach Hardy–Weinberg erfolgte fur die Populationen und die Loci. Die Allelfrequenzen wurden zur Schatzung der genetischen Distanzen und zur Zeichnung eines phylogenetischen Baums genutzt. Die Rassen Aosta Red Pied and Aosta Black Pied waren am engsten verwandt, wahrend die Rassen Deutsche Holsteins und Aosta Chestnut am unterschiedlichsten waren. Die Rassen Evolene und Herens des Aosta-Tals bildeten ein enges Cluster im phylogenetischen Konsensus-Baum. Die Hauptkomponenten-Analyse zeigte ein ahnliches Bild fur alle Rassen der Alpenregion, wahrend Deutschen Holsteins und das Original Deutsche Braunvieh einen grosen Abstand zu den anderen Rassen aufwiesen. Die genetischen Differenzen zwischen den Rassen waren in Ubereinstimmung mit ihrem geographischen und historischen Ursprung.

Ichthyosis is a heterogeneous group of keratinization disorders reported both in human and animals. Two rare, inherited forms have been reported in cattle, both characterized by autosomal recessive transmission. Because mutations of transglutaminase 1 (TGM1) gene are associated with autosomal recessive ichthyosis in people, this gene was investigated as a candidate for the diseases in cattle. Three different polymorphisms were identified in 5' end region of cattle TGM1. Marker homozygosity was not found among affected calves. Linkage analysis excluded (logarithmic odds [LOD] score -2.0) TGM1 as the cause for ichthyosis phenotype in the analyzed Chianina cases.

This work aimed to confirm previously reported quantitative trait loci (QTL) affecting the somatic cell score (SCS) in dairy cattle on Bos taurus autosomes (BTA) 4 and 26. A granddaughter design with selective genotyping was implemented that included half-sib families from 12 male lines of Italian Holstein cattle. The animals were genotyped for 5 microsatellite markers each on regions of BTA 4 (average marker spacing 9.42 cM) and BTA 26 (average marker spacing 5.26 cM), previously reported by other authors as carrying QTL for somatic cell count. Quantitative trait loci analyses were performed using interval mapping by regressing sire breeding values for SCS onto genotype probabilities at 1-cM intervals along the 2 chromosome regions. Breeding values for SCS were estimated for the whole population using a test-day repeatability animal model. Results were not significant on a chromosome basis, but a possible QTL was found at BM4505 on BTA 26, confirming this region for further studies of QTL affecting SCS in the Italian Holstein population.

BACKGROUND: Two mutations in the MYBPC3 gene have been identified in Maine Coon (MCO) and Ragdoll (RD) cats with hypertrophic cardiomyopathy (HCM). OBJECTIVE: This study examined the frequency of these mutations and of the A74T polymorphism to describe their worldwide distribution and correlation with echocardiography. ANIMALS: 1855 cats representing 28 breeds and random-bred cats worldwide, of which 446 underwent echocardiographic examination. METHODS: This is a prospective cross-sectional study. Polymorphisms were genotyped by Illumina VeraCode GoldenGate or by direct sequencing. The disease status was defined by echocardiography according to established guidelines. Odds ratios for the joint probability of having HCM and the alleles were calculated by meta-analysis. Functional analysis was simulated. RESULTS: The MYBPC3 A31P and R820W were restricted to MCO and RD, respectively. Both purebred and random-bred cats had HCM and the incidence increased with age. The A74T polymorphism was not associated with any phenotype. HCM was most prevalent in MCO homozygote for the A31P mutation and the penetrance increased with age. The penetrance of the heterozygote genotype was lower (0.08) compared with the P/P genotype (0.58) in MCO. CONCLUSIONS AND CLINICAL IMPORTANCE: A31P mutation occurs frequently in MCO cats. The high incidence of HCM in homozygotes for the mutation supports the causal nature of the A31P mutation. Penetrance is incomplete for heterozygotes at A31P locus, at least at a young age. The A74T variant does not appear to be correlated with HCM.

ummary From a sample of 119 Friesian calves, serologically typed for BoLA class I, 47 subjects were chosen expressing 9 different MHC types (A6, A6.9, A10, A11, A14, A15, A30, W16, M103) with the same age and reared in the same farm conditions. The animals were s.c. injected with a water in oil suspension of killed M. bovis and the treatment was repeated two days later. Before the treatment and 21 days later, calves were bled and on PBM (peripheral blood mononuclear leucocytes) were performed the following tests: 1. Lymphocyte Stimulation with bovine and avian PPDs (Purified protein derivative of Mycobacterium bovis and Mycobacterium avium, respectively). 2. Phagocytic activity towards M. bovis. 3. Class II molecules expression on cell surface. 4. Percentage of leucocyte populations and subpopulations. In the in vitro Lymphocyte Stimulation test, all the animals and classes were responders. Animals bearing A10 BoLA class I presented c.p.m. (counts per minute) and index values higher than the other cattle; these values were significantly positively related both to bovine and avian PPDs (P < .01). By variance analysis A14 BoLA type showed a slight positive significant correlation with more efficient phagocytic activity. BoLA class I type did not seem to significantly affect percentage of class II positive cells and leucocyte percentages on PBM. Zusammenfassung Der BoLA Klasse I Polymorphismus und in vitro immunologische Antwort gegen die Antigene von M. bovis Aus einer Stichprobe von 119 fur BoLA Klasse I serologisch typisierten Friesian Kalber, wurden 47 Subjekte ausgewahlt, die 9 verschiedene MHC Typen ausdruckten (A6, A6.9, A10, A11, A14, A15, A30, W16, M103). Alle waren gleich alt und in gleichen Haltungsbedingungen. Die Tiere wurden mit einer Wasser-in-Ol Suspension abgetoteter M. bovis subkutan injiziert und die Behandlung nach zwei Tagen wiederholt. Vor und 21 Tage nach Behandlung wurden die folgenden Tests ausgefuhrt: 1. Lymphozyten-Stimulationstest mit bovinen und Geflugel PPDs. 2. Phagozyten Aktivitat gegen M. bovis. 3. Zeil-Oberflachen, Expression der Klasse II Molekule. 4. Anteile der Lymphozyten Populationen und Subpopulationen. Im in vitro Lymphozyten-Stimulationstest waren alle Tiere und Klassen responder. Tiere mit A10 BoLA I zeigten hohere c.p.m. und Indexwerte als die anderen; diese Werte waren in signifikant positiver Beziehung mit der PPD von M. bovis und auch mit M. avium (P < .01). BoLA Typ A14 zeigte leicht signifikant positive Korrelation mit wirksamerer Phagozyten Aktivitat. BoLA Klasse I Typ scheint nicht den Prozentsatz der positiven Zellen der Klasse II und der Leukozyten der PBM signifikant zu beeinflussen. Resumen Polimorfismo de BoLA clase I y immunidad a los antigenos del M. bovis Se escojeron 47 novillos dentro de un grupo de 119 animales que segun analisis previamente hecha tenian BoLA de clase I. Estos 47 novillos fueron escojidos de manera que tuvieran 9 distintos tipos de MHC (A6, A6.9, A10, A11, A14, A15, A30, W16, M103), la misma edad, las mismas condiciones de cria. Estos animales fueron inoculados subcutaneo con M. bovis matados en una suspension oleosa y la misma inoculacion fue repetida una secunda vez despues de dos dias. Por cada animal se tomaron muestras de sangre antes y 21 dias despues de la inoculacion de arriba. Las muestras de sangre fueron pruebaoas con: 1. Stimulacion Lymhocitaria con PPD bovina y avicola. 2. Actividad phagocitaria a M. bovis. 3. Expresion sobre la superficie celular de moleculas de clase II. 4. Porcentaje de poblaciones y de subpob-laciones de leucocitos. Todos los animales y todos los tipos de MHC dieron respuestas positivas en las pruebas de Stimulacion Lymphocitaria. Los animales que tenian la BoLA A10 presentaron valores de c.p.m. y indices mas altos de los demas animales. Estos valores se encontraron significativamente y positivamente relacionados sea a la PPD bovina que a la PPD avicola. Por medio de la analisis de varianzas se encontro que el tipo BoLA A14 muestraba una correlacion significativa y algo positiva con una mejor actividad fagocitaria. Los tipos de clase BoLA I no parecieron que influenzaran de manera appreciable el porcentaje de positividad por la clase II y el porcentaje de leucocitos en la sangre PBM.

Autosomal-dominant polycystic kidney disease (AD-PKD) is common in Persians and Persians-related breeds. The aims of this study were to evaluate the sensitivity and specificity of early ultrasound examination and to compare ultrasound and genetic testing for early diagnosis. Sixty-three Persians and seven Exotic Shorthairs were considered. All underwent ultrasonographic and genetic testing (polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) assay) between 2.5 and 3.5 months of age (10–14 weeks). With ultrasound, 41.4% showed renal cysts, while 37.1% were PKD positive by genetic testing and DNA sequencing. Six cats with at least one renal cyst were negative by genetic testing, while only one cat negative at ultrasound resulted positive at genetic test. DNA sequencing of three polycystic cats, negative by genetic test, revealed they were heterozygous for the mutation. Agreement was described by Cohen's kappa that resulted 0.85, considering genetic test and DNA sequencing. Sensitivity and specificity of ultrasound were 96.2% and 91%, respectively. Sensitivity was higher and specificity lower than reported previously. The higher sensitivity could be due to improved technical capabilities of ultrasound machines and transducers. Other causes of PKD could explain the lower specificity. In conclusion, ultrasound resulted in a reliable diagnostic method for feline AD-PKD1 at early age and it should always be used with genetic testing, in order to reach a complete screening programme and eventually to identify other genetic mutations.

Made available in DSpace on 2016-10-10T03:52:47Z (GMT). No. of bitstreams: 5 An international parentage and identification panel for the domestic cat Felis catus.pdf: 509557 bytes, checksum: e4cd9a3f2e792036d13d81fa70d95dbf (MD5) license_url: 52 bytes, checksum: 3d480ae6c91e310daba2020f8787d6f9 (MD5) license_text: 23851 bytes, checksum: 294cb7010cc40c47642971e073de3dba (MD5) license_rdf: 23892 bytes, checksum: afd5dad10b1d1e6dc10c8c5d25222c7a (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2007 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 ¼ 261) from the USA, Europe and Brazil and eight breeds (n ¼ 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 genderspecific 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. Publicado

Background The cat has one common blood group with two major serotypes, blood type A that is dominant to type B. A rare type AB may also be allelic and is suspected to be recessive to A and dominant to B. Cat blood type antigens are defined, N-glycolylneuraminic acid (NeuGc) is associated with type A and N-acetylneuraminic acid (NeuAc) with type B. The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) determines the sugar bound to the red cell by converting NeuAc to NeuGc. Thus, mutations in CMAH may cause the A and B blood types. Results Genomic sequence of CMAH from eight cats and the cDNA of four cats representing all blood types were analyzed to identify causative mutations. DNA variants consistent with the blood types were genotyped in over 200 cats. Five SNPs and an indel formed haplotypes that were consistent with each blood type. Conclusion Mutations in type B cats likely disrupt the gene function of CMAH, leading to a predominance of NeuAc. Type AB concordant variants were not identified, however, cDNA species suggest an alternative allele that activates a downstream start site, leading to a CMAH protein that would be altered at the 5' region. The cat AB blood group system is proposed to be designated by three alleles, A > a ab > b. The A and b CMAH alleles described herein can distinguish type A and type B cats without blood sample collections. CMAH represents the first blood group gene identified outside of non-human primates and humans.

The oral mucosae of the lips and muzzle appeared histologically normal. Mitotic chromosomes were visualised with conventional staining and RBA-banding from non-synchronised cultures of peripheral blood lymphocytes of the affected calves and their relatives (De Grouchy and others 1964, Dutrillaux and others 1973). No abnormality was detected in either the structure or the number of chromosomes. Genealogical data from the Chianina Breed Stud Book, from the Associazione Nazionale Allevatori Bovini Italiani da Carne (ANABIC), were collected to analyse the pedigrees of the two affected animals and of nine other newborn Chianina calves showing the same condition (Fig 3). Wherever possible, blood samples were collected from the affected animals and their sires, dams and siblings. Parentage relationships were verified by microsatellite analysis with StockMarks for Cattle Paternity PCR typing kits (Applied Biosystems). Forty-nine animals of the familial group were evaluated. Analysis of the pedigree information revealed that all clinical cases were generated by consanguineous matings. In particular, three bulls were acknowledged as being disease carriers: bulls 23, 30 and 34 (Fig 3). Bull 23 sired three affected male calves (26, 28 and 48) and two healthy female calves (31 and 35); bull 30 sired two affected male calves (27 and 49) and two healthy calves, one male (34) and one female (46); and bull 34 sired six affected calves, four males (38, 40, 41 and 47) and two females (43 and 44) and four healthy calves, three males (37, 42 and 45) and one female (39). None of the carIchthyosis in Chianina cattle

EPIDERMOLYSIS bullosa (EB) is a genetic disease involving the skin and mucous membranes in human beings, horses, cattle, sheep, cats and dogs ([Bruckner-Tuderman and others 1991][1], [Olivry and others 1999][2], [Jiang and Uitto 2005][3], [Magnol and others 2005][4], [Fine and others 2008][5], [

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2)) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2) was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2) ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2) ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

International audience; The term arthrogryposis refers to a symptom complex that is characterised by congenital limb contractures. Arthrogryposis has been reported in man, in farm animals and in pets. Several forms have been reported to have a genetic origin in man. In Brown Swiss and Holstein Friesian cattle, congenital contractures have been recorded and classified as spinal muscular atrophy (SMA). The survival motor neuron gene (SMN) has been suggested as a candidate gene for SMA. In the last 20 years, the National Association of Piedmont Cattle have recorded arthrogryposis cases. We cloned and sequenced SMN cDNA extracted from the spinal cord samples of two animals: one Piedmont calf showing a severe clinical form of arthrogryposis and one normal Piedmont calf. In the affected calf, more than 50% of the 5$'$end clones showed a ATG $>$ TTG single nucleotide polymorphism (SNP) in exon 1 that should determine a Met $>$ Leu aminoacid change (single point mutation M3L). This mutation is associated with a 9 bp increase length of 5$'$UTR and to a TTC $\rightarrow$ TTT silent mutation in exon 1. No single point mutation or 5$'$end polymorphism was shown in healthy animals and in the remaining 50% of the clones from the affected calf. We hypothesise a possible pathogenic effect of the 5$'$end-exon 1 polymorphism.

Mitochondrial D-loop hypervariable region was analysed in 20 Sanfratellano and two other Sicilian autochthonous horse breeds (20 Sicilian Oriental Purebred and 20 Sicilian Indigenous) in order to investigate matrilineal genetic diversity. A total of 20 different haplotypes were identified sequencing a fragment of 397 bp; overall, haplotypes showed 31 polymorphic sites (7.8%). High diversity was detected in Sanfratellano (11 haplotypes) and Sicilian Indigenous (13 haplotypes), whereas only one haplotype was found in Sicilian Oriental Purebred. Sanfratellano sequences were compared with those belonging to the other Sicilian autochthonous horses and 118 sequences selected from the GenBank database in order to calculate the statistics of molecular diversity. Six haplotypes were exclusive of Sanfratellano which shares haplotype C, D, H, and O with the Sicilian Indigenous and haplotype U with the Sicilian Oriental Purebred; not significant differentiation was found between Sanfratellano and Sicilian Indigenous. BLAST search showed Sicilian haplotypes overlap with the database sequences but for three. Phylogenetic analysis did not show monophyletic group for Sanfratellano samples or the other breeds included in this analysis.