Genome- wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi- arid area

Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunis ia n sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of Europe an gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58–49.61 Mbp). These results were confirmed using FST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds

Maedi Visna virus infection and TMEM154 genotypes in Valle del Belìce sheep breed

Maedi Visna (MV) is a viral infection in sheep caused by Lentivirus and characterised by a long incubation period, slow progression, weight loss and eventually death. TMEM154 was reported in the ovine as major candidate gene associated with host susceptibility/resistance. The aim of this study was to verify the prevalence of MV infection within Sicilian herds of Valle del Belìce breed using an ELISA serological test and to estimate the frequencies of the resistant/susceptible genotypes to the TMEM154 gene. Finally, we investigated the association between TMEM154 E/K genotype and MV infectious status. A total of 1,083 animals from different flocks were tested. The ELISA method showed 15.33% (n = 166) of infected individuals. Analyses of the sequences showed the presence of both K and E alleles with frequencies of 0.151 and 0.849, respectively. On the total individuals, only 23 carried KK genotype while 280 were heterozigous EK, and 780 homozygous EE. The locus was in Hardy-Weinberg equilibrium in the breed (p-value <0.05) and observed and expected heterozygosity values were 0.258 and 0.256, respectively. Moreover, a significant association (p-value < 0.001) between TMEM154 genotypes and seroprevalence status (positive vs. negative) was found. This study allowed us to know the prevalence of MV infection in Sicilian flocks of Valle del Belìce breed and could be helpful in establishing selection programs aimed at controlling and eradicating this virus

Age estimation by tooth/pulp ratio in canines by peri-apical X-rays: reliability in age determination of Spanish and Italian medieval skeletal remains

Estimation of age at death is an unavoidable step in the process of human identification, both in forensic practice and in the anthropological and palaeopathological study of skeletal remains. In several cases, in which medical or demographic records are completely lacking, a reliable estimation of the age at death becomes very important. Skeletal remains from archaeological contexts suffer from several biasing factors such as post-mortem changes, taphonomy and various burial practices depending on age, sex and social status of the deceased persons. Currently, anthropological methods of age determination reveal several possibilities of inaccuracy. Of all the body parts used in age estimation, teeth are the least affected by any taphonomic process. Although there are many dental methods for age at death estimation, some of them are very complex and/or destructive and they are not normally used in anthropology. However, study of the apposition of secondary dentine by examining peri-apical X-rays of canines is beginning to supply very interesting results. The aim of this work was to test Cameriere\u2019s method on a large sample of historical subjects from several cemeteries in Spain and Italy. The Spanish sample belongs to the Medieval cemetery of La Torrecilla (Arenas del Rey, Granada) and is housed in the Laboratory of Anthropology, Faculty of Medicine, University of Granada. The Italian samples come from the Medieval cemeteries of Comacchio (Ferrara) and Castel S. Pietro (Bologna). In order to test the reliability of Cameriere\u2019s method, age estimations of canines were compared with the mean ranges of age of the most commonly applied anthropological methods such as tooth wear changes in the pubic symphysis or the metamorphosis of the auricular surface of the ilium. Tests on these Middle Ages cemeteries produced satisfactory results, indicating that Cameriere\u2019s method is a reliable tool in determining age at death in skeletal remains of archaeological context

Dental implants with locking taper connection versus screwed connection: microbiologic and scanning electron microscope study.

The aim of this study is to carry out an analysis of the Fixture-Abutment Interfaces (FAI), comparing different connection systems, to evaluate the role of geometric discrepancy, which is present between the abutment and the fixture, in favoring the permeability to bacterial colonization. Two types of commercially available FAI were studied, 16 screwed FAI (Sweden-Martina Italia) (4 of Ø 3.8 mm, 4 of Ø 4.7 mm, 4 of Ø 5.7 mm and 4 of Ø 6.7 mm) and 4 FAI (Bicon) (Ø 3.5mm). The assays were carried out in vitro, placing the different dental implants in contact with broth culture of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Streptococcus pyogenes to test the infiltration inside the FAI. Furthermore, scanning electron microscope (SEM) analysis was carried out to evaluate the gap at the fixture-abutment interface. In all the locking taper FAI and in the screwed FAI with a diameter of 3.8 mm there was no trace of bacterial infiltration of the species examined. In the screwed FAI with a diameter of 4.7 mm, 5.7 mm and 6.7 mm there was an increasing level of bacterial infiltration in relationship to the diameter. Therefore, this paper shows that there exists an important correlation between the diameter of the screwed implant and the permeability to microbic infiltration that is directly proportional to the diameter of the implant

How polymer additives reduce the pour point of hydrocarbon solvents containing wax crystals

We have investigated how four different pour point depressant (PPD) polymers affect the pour point transition in mixtures of a single pure wax in a solvent. We used either n-eicosane (C20), CH3(CH2)18CH3, n-tetracosane (C24), CH3(CH2)22CH3 or n-hexatriacontane (C36), CH3(CH2)34CH3 as the wax component with either n-heptane or toluene as the solvent component. For all wax–solvent combinations, the measured variation of wax solubility with temperature is well predicted by ideal solution theory. The variation of pour point temperature as a function of the overall wax concentration is quantitatively modelled using the idea that, for each overall wax concentration, the pour point occurs at a temperature at which a critical volume fraction ϕ* of wax crystals has precipitated. Close to the pour point temperature, extraction and examination of the wax crystals show they consist of polydisperse, irregularly-shaped platelets with axial ratios (h/d, where h is the plate thickness and d is the plate long dimension) in the range 0.005–0.05. It is found that the measured ϕ* values corresponding to the pour point transitions are weakly correlated with the wax crystal axial ratios (h/d) for all wax–solvent–PPD polymer combinations. These results indicate that the pour point transition occurs at a volume fraction larger than the value at which the volumes of rotation of the platelet crystals overlap, i.e., 2.5(h/d) < ϕ* < 11(h/d). PPD polymers work, in part, by increasing the wax crystal axial ratio (h/d), thereby increasing ϕ* and reducing the pour point temperature. Since the PPD's ability to modify the wax crystal shape relies on its adsorption to the crystal-solution surface, it is anticipated and observed experimentally that optimum PPD efficacy is correlated with the difference between the wax and the polymer solubility boundary temperatures. This finding and the mechanistic insight gained here provide the basis for a simple and rapid screening test to identify candidate species likely to be effective PPDs for particular wax systems

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome

Mapping adaptation of barley to droughted environments

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectivel

QTL Mapping of Stem Rust Resistance in Populations of Durum Wheat

Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. 'Svevo'

Genome wide analyses reveal the population distinctiveness of the ‘Nera del Mela’ sheep

Italy has a long history of sheep breeding and counts several local populations that may represent a unique source of genetic diversity. Among these, Nera del Mela is a sheep genetic resource historically reared in Sicily but not officially recognised as a breed. In this study, we genotyped 36 individuals of Nera del Mela using the OvineSNP50K array, in order to estimate the genetic diversity and evaluate the population structure and relatedness with other Italian sheep breeds. Genetic diversity indices, and inbreeding estimated from runs of homozygosity (FROH) revealed a moderate level of variability. Runs of homozygosity islands mapped candidate genes involved in the adaptation to local environment and immune response. Population genetic analyses using different approaches highlighted the hypothesis that this sheep possesses a defined genetic structure, especially if compared with other recognised breeds, despite the influence of other populations such as the Sicilian breeds. Overall, our findings represent a starting point for the possible official acknowledgement of this population, for the creation of a conservation plan, and thus for preserving this genomic heritage.HIGHLIGHTS Nera de Mela sheep can be considered as a reservoir of genetic diversity. The results indicated a clear genetic differentiation from other populations and moderate level of genetic variability. Our findings represent a starting point for the creation of conservation plans