Preliminary study on MC1R polymorphism in some cattle breeds raised in Italy

Ricerche preliminari sul polimorfismo del gene MC1R in alcune razze bovine allevate in Italia – Il gene MC1R è stato analizzato in 193 soggetti appartenenti a 8 razze bovine, tramite PCR, per la presenza di due mutazioni ad effetto fenotipico noto sulla pigmentazione del mantello: la delezione G310 e la sostituzione T296C, associate rispettivamente al fenotipo feomelanico (e) ed eumelanico nero (Ed). Sessanta soggetti di razza Limousine e Pezzata Rossa Italiana presentano genotipo e/e; 27 soggetti di razza Frisona Italiana mostrano genotipo Ed/Ed mentre 2 genotipo Ed/e. Gli 84 soggetti appartenenti alle razze Cabannina, Chianina, Marchigiana e Piemontese non presentano tali mutazioni, analogamente a 18 soggetti di razza Romagnola, nella quale però si sono anche osservati 2 soggetti portatori dell’allele e allo stato eterozigote

Agonist antibodies activating the Met receptor protect cardiomyoblasts from cobalt chloride-induced apoptosis and autophagy

Met, the tyrosine kinase receptor for hepatocyte growth factor (HGF), mainly activates prosurvival pathways, including protection from apoptosis. In this work, we investigated the cardioprotective mechanisms of Met activation by agonist monoclonal antibodies (mAbs). Cobalt chloride (CoCl(2)), a chemical mimetic of hypoxia, was used to induce cardiac damage in H9c2 cardiomyoblasts, which resulted in reduction of cell viability by (i) caspase-dependent apoptosis and (ii) – surprisingly – autophagy. Blocking either apoptosis with the caspase inhibitor benzyloxycarbonyl-VAD-fluoromethylketone or autophagosome formation with 3-methyladenine prevented loss of cell viability, which suggests that both processes contribute to cardiomyoblast injury. Concomitant treatment with Met-activating antibodies or HGF prevented apoptosis and autophagy. Pro-autophagic Redd1, Bnip3 and phospho-AMPK proteins, which are known to promote autophagy through inactivation of the mTOR pathway, were induced by CoCl(2). Mechanistically, Met agonist antibodies or HGF prevented the inhibition of mTOR and reduced the flux of autophagosome formation. Accordingly, their anti-autophagic function was completely blunted by Temsirolimus, a specific mTOR inhibitor. Targeted Met activation was successful also in the setting of low oxygen conditions, in which Met agonist antibodies or HGF demonstrated anti-apoptotic and anti-autophagic effects. Activation of the Met pathway is thus a promising novel therapeutic tool for ischaemic injury

Genomic variability of Cirneco dell’Etna and the genetic distance with other dog breeds

Cirneco dell’Etna is an old Italian breed of scent hunting dogs. Commonly used genomic measures such as heterozygosity, fixation indexes, and runs of homozygosity can help to improve knowledge about its genetic diversity. This study aimed to: (i) investigate Cirneco’s genomic background, (ii) quantify its genomic inbreeding, and (iii) detect genomic regions differentiating the Cirneco’s two allowed coat colours, self-coloured fawn and tan and white. Canine 230K SNP BeadChips was used to investigate 24 Cirneco (19 self-coloured fawn, and 5 tan and white) and other 106 dogs from eight phylogenetically and historically related breeds. The genetic distance, ancestry, and relationship among breeds were explored by multidimensional scaling, Reynolds distances, phylogenetic tree, and admixture analysis. The genomic inbreeding (FROH) was calculated for each breed. Averaged Wright’s fixation index FST was used to identify the genes that most differentiated the two groups of Cirneco. All analyses highlighted that Segugio Italiano and Kelb tal Fenek are the closest breeds to Cirneco. Within the breed, tan and white subjects showed a more heterogeneous genetic background and a lower inbreeding in comparison with self-coloured fawn ones, even though more than half of the latter presented a superimposable admixture. The gene that most differentiated these two groups is Microphthalmia-Associated Transcription Factor (MITF), previously associated with white spotting in other breeds. Given the small size of the Cirneco population and its open registry, its management should carefully combine morphological and genealogical evaluations with genetic tools to identify the best breeders while maintaining an acceptable genetic pool.peer-reviewe

Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study,we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) andMessinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as formilk yield, reproduction, and immune response, and are consistentwith the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource

Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers

Background During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection. Methodology/Principal findings Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions, therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with the software MATSAM, based on a correlative approach (SAM), and with MCHEZA and BAYESCAN, two FST based software able to detect markers carrying signatures of natural selection. MATSAM identified four loci possibly under natural selection - also confirmed by FSToutlier methods - and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation. Conclusions/Significance These results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments

TRACEABILITY OF FOUR EUROPEAN PROTECTED GEOGRAPHIC INDICATION (PGI) BEEF PRODUCTS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNP) AND BAYESIAN STATISTICS

The use of SNPs in combination with Bayesian statistics for the geographic traceability of cattle were evaluated using a dataset comprising 24 breeds from Italy,France,Spain, Denmark, the Netherlands,Switzerland and UK genotyped with 90 polymorphic markers. The percentage of correct assignment of the individuals to their Country of origin was 90%, with an average assignment probability of 93% and an average specificity of 92%. The higher value was observed for UK breeds (97% of correct assignment) while Swiss animals were the most difficult to allocate (77% of correct assignment). Tracing of Protected Geographic Indication (PGI) products, the approach correctly assigned 100% of Guaranteed Pure Highland Beef; 97% of “Vitellone dell’Appennino Centrale” breeds; 84% of Ternera de Navarra, and 80% of Boeuf de Chalosse. Methods to verify Products of Designated Origin (PDO) and Protected Geographic Indication (PGI) products will help to protect regional foods and promote the economic growth of marginal rural areas by encouraging the product on of high quality niche market foods

Characterization of skin surface and dermal microbiota in dogs with mast cell tumor

The skin microbiota interacts with the host immune response to maintain the homeostasis. Changes in the skin microbiota are linked to the onset and the progression of several diseases, including tumors. We characterized the skin surface and dermal microbiota of 11 dogs affected by spontaneous mast cell tumor (MCT), using skin contralateral sites as intra-animal healthy controls. The microbial profile differed between healthy and tumor skin surfaces and dermis, demonstrating that the change in microbiota composition is related to the presence of MCT. The number of observed taxa between MCT and healthy skin surfaces was detected, showing a decrease in number and heterogeneity of taxa over the skin surface of MCT, at both inter- and intra-individual level. Preliminary data on bacterial population of MCT dermis, obtained only on three dogs, demonstrated an intra-individual reduction of taxa number when compared to the skin surface. Taxonomy reveals an increase of Firmicutes phylum and Corynebacteriaceae family in MCT skin surface when compared to the healthy contralateral. In conclusion, we demonstrate that microbial population of skin surface and dermis is related to mast cell tumor. Our study provides the basis for future investigations aiming to better define the interaction between mast cell tumors, microbiota and host immune response

Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds

The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been done to find the gene(s) that controls roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goats breeds that did not have the same coat color pattern (Group B). Run of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6 and 12 were considered unique among the group A versus B group comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats