Search results for " genotyping"
showing 10 items of 52 documents
Parentage Atlas of Italian Grapevine Varieties as Inferred From SNP Genotyping.
2021
The Italian grape germplasm is characterized by a high level of richness in terms of varieties number, with nearly 600 wine grape varieties listed in the Italian National Register of Grapevine Varieties and with a plethora of autochthonous grapes. In the present study an extended SNP genotyping has been carried out on Italian germplasm of cultivated Vitis vinifera subsp. sativa and Vitis hybrids. Several hundred Italian varieties maintained in the repositories of scientific Institutions and about one thousand additional varieties derived from previous studies on European, Southern Italy, Magna Graecia and Georgian germplasm were considered. The large genotyping data obtained were used to ch…
High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily
2016
The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars by using morphological and microsatellite markers. In this study, simple sequence repeat (SSR) were utilized to verify the true-to-typeness of a large clone collection (101) belonging to 21 biotypes of the most 10 cultivated Sicilian cultivars. Afterwards, 42 Organization Internationale de la Vigne…
A genomic map of climate adaptation in Mediterranean cattle breeds
2019
International audience; Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate sub-types. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional…
Morphological and molecular variability within the fig cultivar 'Dottato' in the Italian protected designation origin area "fichi di Cosenza"
2017
The morphological and molecular diversity among fig accessions of 'Dottato', found in the PDO "Fichi di Cosenza" area was studied by evaluating 24 morphological traits and by genotyping with 18 microsatellite markers. The microsatellite allelic profiles among the putative clones of 'Dottato' indicated a moderate genetic variability, discriminating unambiguously most of the accessions. Only two groups of identity were found. The average expected and observed heterozygosity were 0.43 and 0.62, respectively. The mean polymorphic information content (PIC) was 0.4, varying from 0.08 (LMFC26) to 0.067 (FCUP 38-6). The morphological clustering allowed the distinction of all genotypes. Some genotyp…
Genotyping and Antifungal Susceptibility of Dipodascus capitatus Isolated in a Neonatal Intensive Care Unit of a Sicilian Hospital
2017
In August 2015, Dipodascus capitatus was isolated from two patients admitted to the neonatal intensive care unit. Nosocomial acquisition of the fungus was suspected and epidemiological studies were undertaken. The patients were simultaneously hospitalized, and the comparison of the two isolates by two independent molecular typing methods have confirmed clonal dissemination of a single strain of D. capitatus. Antimicrobial susceptibility testing was useful for identifying the appropriated antifungal therapy in micafungin. To our knowledge these are the first described cases of neonatal D. capitatus infection and also the first report of successful treatment by micafungin.
Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochth…
2018
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and …
Measles in Italy: Viral strains and crossing borders
2019
In 2017, Italy experienced one of the largest outbreaks of measles in recent years, with 5404 notified cases and 4347 confirmed cases. A further 2029 cases were notified during the first 6 months of 2018, and 1516 of them were laboratory-confirmed. The B3 and D8 genotypes were identified as those responsible for the outbreak. Possible transmission routes can be established by monitoring the circulating measles virus strains in support of the national health authorities to warn people and travellers. Keywords: Outbreak, Measles, Genotype identification, Surveillance
Case-based surveillance of measles in Sicily during 2012-2017: The changing molecular epidemiology and implications for vaccine strategies.
2018
Following the indication of the World Health Organization, a national plan for the elimination of measles was approved in Italy and this included the improvement of the molecular surveil- lance of measles viruses and the interruption of indigenous transmission of the disease. Nevertheless, large outbreaks continue to occur in almost all regions of the country, includ- ing Sicily. Here we describe the epidemiology and molecular dynamics of measles viruses as a result of the measles surveillance activity carried out by the “Reference Laboratory for Measles and Rubella” in Sicily over a 5-year period. Biological samples of 259 suspected measles cases were tested for viral RNA detection and a t…
Ancient and recent admixture layers in Sicily and Southern Italy trace multiple migration routes along the Mediterranean
2017
The Mediterranean shores stretching between Sicily, Southern Italy and the Southern Balkans witnessed a long series of migration processes and cultural exchanges. Accordingly, present-day population diversity is composed by multiple genetic layers, which make the deciphering of different ancestral and historical contributes particularly challenging. We address this issue by genotyping 511 samples from 23 populations of Sicily, Southern Italy, Greece and Albania with the Illumina GenoChip Array, also including new samples from Albanian-and Greek-speaking ethno-linguistic minorities of Southern Italy. Our results reveal a shared Mediterranean genetic continuity, extending from Sicily to Cypru…
Sterol 27-hydroxylase polymorphism significantly associates with shorter telomere, higher cardiovascular and type-2 diabetes risk in obese subjects
2018
Background/objectivesThe pathologic relationship linking obesity and lipid dismetabolism with earlier onset of aging-related disorders, including cardiovascular disease (CVD) and type-2 diabetes (T2D), is not fully elucidate. Chronic inflammatory state, in obese individuals, may accelerate cellular aging. However, leukocyte telomere length (LTL), the cellular biological aging indicator, is elusively linked with obesity. Recent studies indicate that sterol 27-hydroxylase (CYP27A1) is an emerging antiatherogenic enzyme, that, by converting extrahepatic cholesterol to 27-hydroxycholesterol, facilitates cholesterol removal via high-density lipoprotein-cholesterol (HDL-C). We tested the hypothes…