Brassica oleracea is a representative species of the cruciferous family, which includes a remarkable variety of types used as vegetables. Numerous studies on B. oleracea have demonstrated its high nutraceutical value thanks to the production of numerous bioactive compounds beneficial to human health. The genotyping-by-sequencing (GBS) approach allows highthroughput, robust and cost-effective characterization of single nucleotide polymorphism (SNP) markers in germplasm collections. Within the frame of the projects BiodiverSO and BiodiverSO VEG" (PSR Puglia 2014-2020, Mis. 10.2), several landraces of B. oleracea have been collected in the Puglia region, of which the subspecific taxonomic identification is not certain. GBS can be a useful tool to evaluate the genetic relationships between local varieties and known commercial cultivars. In this study, GBS was applied to a collection of 84 B. oleracea genotypes including broccoli (var. italica), cauliflowers (var. botrytis), cabbages (var. capitata), kales (var. alboglabra), and Brussel sprouts (var. gemmifera). A representative portion of the B. oleracea collection consisted of local material from Puglia. The genetic structure of the germplasm collection was studied and the genetic relationships between the different taxa, landraces, and commercial cultivars of B. oleracea from Italy and other countries were evaluated. The results of this research showed that the SNP markers obtained through GBS were able to discriminate between the varieties and allowed the attribution of a taxonomic ranking of the local germplasm analysed.

The risk of colorectal cancer (CRC) depends on environmental and genetic factors. Among environmental factors, an imbalance in the gut microbiota can increase CRC risk. Also, microbiota is influenced by host genetics. However, it is not known if germline variants influence CRC development by modulating microbiota composition. We investigated germline variants associated with the abundance of bacterial populations in the normal (non-involved) colorectal mucosa of 93 CRC patients and evaluated their possible role in disease. Using a multivariable linear regression, we assessed the association between germline variants identified by genome wide genotyping and bacteria abundances determined by 16S rRNA gene sequencing. We identified 37 germline variants associated with the abundance of the genera Bacteroides, Ruminococcus, Akkermansia, Faecalibacterium and Gemmiger and with alpha diversity. These variants are correlated with the expression of 58 genes involved in inflammatory responses, cell adhesion, apoptosis and barrier integrity. Genes and bacteria appear to be involved in the same processes. In fact, expression of the pro-inflammatory genes GAL, GSDMD and LY6H was correlated with the abundance of Bacteroides, which has pro-inflammatory properties; abundance of the anti-inflammatory genus Faecalibacterium correlated with expression of KAZN, with barrier-enhancing functions. Both the microbiota composition and local inflammation are regulated, at least partially, by the same germline variants. These variants may regulate the microenvironment in which bacteria grow and predispose to the development of cancer. Identification of these variants is the first step to identifying higher-risk individuals and proposing tailored preventive treatments that increase beneficial bacterial populations.

'Nebbiolo' is a well-known grapevine variety used to produce prestigious monovarietal Italian red wines. Genetic traceability is an important tool used to protect the authenticity of high-quality wines. SNP-based assays are an effective method to reach this aim in wines, but several issues have been reported for the authentication of commercial wines. In this study, the impact of the most common commercial additives and processing aids used in winemaking was analysed in 'Nebbiolo' wine using SNP-based traceability. Gelatine and bentonite had the strongest impact on the turbidity, colour and phenolic composition of wines and on residual grapevine DNA. The DNA reduction associated with the use of bentonite and gelatine (> 99% compared to the untreated control) caused issues in the SNP-based assay, especially when the DNA concentration was below 0.5 pg/mL of wine. This study contributed to explaining the causes of the reduced varietal identification efficiency in commercial wines.

The identification of high-risk factors for the infection by SARS-CoV-2 and the negative outcome of COVID-19 is crucial. The genetic background of the host might account for individual responses to SARS-CoV-2 infection besides age and comorbidities. A list of candidate polymorphisms is needed to drive targeted screens, given the existence of frequent polymorphisms in the general population. We carried out text mining in the scientific literature to draw up a list of genes referable to the term "SARS-CoV*". We looked for frequent mutations that are likely to affect protein function in these genes. Ten genes, mostly involved in innate immunity, and thirteen common variants were identified, for some of these the involvement in COVID-19 is supported by publicly available epidemiological data. We looked for available data on the population distribution of these variants and we demonstrated that the prevalence of five of them, Arg52Cys (rs5030737), Gly54Asp (rs1800450) and Gly57Glu (rs1800451) in MBL2, Ala59Thr (rs25680) in CD27, and Val197Met (rs12329760) in TMPRSS2, correlates with the number of cases and/or deaths of COVID-19 observed in different countries. The association of the TMPRSS2 variant provides epidemiological evidence of the usefulness of transmembrane protease serine 2 inhibitors for the cure of COVID-19. The identified genetic variants represent a basis for the design of a cost-effective assay for population screening of genetic risk factors in the COVID-19 pandemic.

Germline variants in genes involved in SARS-CoV-2 cell entry and in host innate immune responses to viruses may influence the susceptibility to infection. This study used whole-genome analyses of lung tissue to identify polymorphisms acting as expression quantitative trait loci (eQTLs) for 60 genes of relevance to SARS-CoV-2 infection susceptibility. The expression of genes with confirmed or possible roles in viral entry-replication and in host antiviral responses was studied in the non-diseased lung tissue of 408 lung adenocarcinoma patients. No gene was differently expressed by sex, but APOBEC3H levels were higher and PARP12 levels lower in older individuals. A total of 125 cis-eQTLs (false discovery rate < 0.05) was found to modulate mRNA expression of 15 genes (ABO, ANPEP, AP2A2, APOBEC3D, APOBEC3G, BSG, CLEC4G, DDX58, DPP4, FURIN, FYCO1, RAB14, SERINC3, TRIM5, ZCRB1). eQTLs regulating ABO and FYCO1 were found in COVID-19 susceptibility loci. No trans-eQTLs were identified. Genetic control of the expression of these 15 genes, which encode putative virus receptors, proteins required for vesicle trafficking, enzymes that interfere with viral replication, and other restriction factors, may underlie interindividual differences in risk or severity of infection with SARS-CoV-2 or other viruses.

Wheat is one of the main crops bred worldwide. Durum wheat, specifically, is a key element of the Mediterranean diet, representing an elite crop grown in Italy. Durum wheat nutritional and technological values are largely due to the grain protein content (GPC), a complex genetic trait strongly affected by environmental factors and management practices. In the last decades, several breeding programs have been focused on improving GPC by both traditional and innovative approaches. Among seed storage proteins, prolamins, including both gliadins and glutenins, represent the major component. These two classes of proteins are indeed responsible of gluten formation and confer the extensibility and elasticity to the dough. Besides being of crucial importance for both technological properties and rheological characteristics, prolamins, and especially gliadins, have been found to be major triggers for human health, as involved in a number of wheat consumption-related conditions, such as the celiac disease, non-celiac gluten sensitivity, defined as the onset of a variety of manifestations related to wheat, rye and barley ingestion, and wheat allergies, both due to wheat ingestion or inhalation (of flour or pollen). The identification of loci responsible for the gliadin expression, and particularly of polymorphism in the aforementioned genes, which could result in a lower immunogenic/toxic potential, could be of great importance in breeding programs. For this purpose, we screened a collection of tetraploid wheat genotypes for allelic variants of annotated gliadin genes in the durum wheat genome, in order to identify genetic resources available to breeders to improve wheat nutritional and technological properties. Phylogenetic analysis among different species ofTriticumgenus and an in silico expression data analysis may also be useful in the exploitation of the complex scenario of gliadin-glutenin interaction and gluten role in the adverse reactions due to wheat consumption.

Plant populations are able to undergo very localized adaptive processes, that allow continuous populations to adapt to divergent habitats in spite of recurrent gene flow. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a nested sampling design, to evaluate microgeographic adaptation in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae). A high-coverage genomic resource of ~250 Mb was assembled de novo and annotated, leading to 32 789 predicted genes. 97 062 bi-allelic SNPs were detected in 25 803 contigs were detected, and a custom Bayesian model we implemented to uncover candidate genomic targets of divergent selection. A set of 290 'divergence' outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. These genes possibly underlie ecologically important phenotypes and tend to indicate that adaptation to microgeographic habitat patchiness would affect genomic regions involved in a variety of physiological processes, among which plant response to stress (for e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Identification of genomic targets of microgeographic adaptation in the Neotropics supports the hypothesis - frequently raised at the community level - that local adaptation would be a key driver of ecological diversification, probably operating across multiple spatial scales, from large- (i.e. regional) to microgeographic- (i.e. landscape) scales.

Extra virgin olive oil (EVOO) has elevated commercial value due to its health appeal, desirable characteristics and quantitatively limited production, and thus it has become an object of intentional adulteration. As EVOOs on the market might consist of a blend of olive varieties or sometimes even of a mixture of oils from different botanical species, an array of DNA-fingerprinting methods have been developed to check the varietal composition of the blend. Starting from a comparison between publicly available DNA extraction protocols, we set up a timely, low-cost, reproducible and effective DNA isolation protocol, which allows an adequate amount of DNA to be recovered even from commercial filtered EVOOs. Then, in order to verify the effectiveness of the DNA extraction protocol herein proposed, we applied PCR-based fingerprinting methods starting from the DNA extracted from three EVOO samples of unknown composition. In particular, genomic regions harboring nine simple sequence repeats (SSRs) and eight genotyping-by-sequencing-derived single nucleotide polymorphism (SNP) markers were amplified for authentication and traceability of the three EVOO samples. The whole investigation strategy herein described might favor producers in terms of higher revenues and consumers in terms of price transparency and food safety.

Background: Parkinson's disease (PD) is the second most common neurodegenerative disorder, affecting millions of people. Genome-wide association studies (GWAS) have found >25 genetic risk factors and at least 15 loci directly associated with PD. Recent advances in Next-Generation DNA Sequencing technologies, such as the semiconductor-based Ion Torrent platform, make multigene sequencing cheaper, faster, and more reliable. Objectives: Our objective was to test the power of the Next-Generation Sequencing technology to analyze large cohort samples of PD patients from Southern Italy by screening the majority of the most relevant PD-related genes known for single and compound mutations. Methods: To achive a rapid,robust, and cost-effective genetic analysis of a PD cohort, we designed a multiplex, amplicon based gene panel made by XXX genes. We conducted parallel sequencing using the Ion Torrent Personal Genome Machine (PGM)(®) system to detect mutations in 42 blood DNA samples from PD patients. To process data from PGM Ion Torrent runs, Ion Torrent Suite (TS) software v. 5.10 was used. The annotation was made using annovar and the variants where priorized using a standard filtering pipeline. Results: After bioinformatics analysis and filtering, 98% coverage of the targeted regions was obtained with at least >200-fold mean depth. We detected 50 coding nonsynonymous variants (indels, single-nucleotide variations (SNVs) and frameshift variants with a MAF<0.01. Of these 50 variations, 9 were identified in PARK2, 12 in LRRK2 and 1 in PINK1. The remaining variations were found in the other genes sequenced, most of which are strongly involved in the pathogenesis of PD. We are able to find a total of 154 CNVs (52 amplifications and 102 deletions). Out of these SNCA1 amplification, PRKN 1 deletion, PARK7 2 deletions, LRRK2 1 amplification and 7 deletions. Conclusions: Benchtop next-generation sequencing is a powerful method for genetic screening for PD. Our results indicated that it yielded a high frequency of discovery of SNV e CNV variants in carriers from an enriched Southern-Italy PD sample.

Asthma and rhino-conjunctivitis are common chronic diseases in childhood. In this cross-sectional study, we performed a gene association analysis with current asthma and rhino-conjunctivitis in a cohort of Sicilian children aged 10-15 years. Overall, our findings reveal the importance of different genetic variants at 4p14, 16p12.1, 17q12, 6p12.2 and 17q21.1, identifying possible candidate genes responsible for susceptibility to asthma and rhino-conjunctivitis.

[object ObjRhizomania is one of the most devastating biotic stresses affecting sugar beet (Beta vulgaris L.). It is caused by Beet necrotic yellow vein virus (BNYVV) vectored by the plasmodiophorid Polymyxa betae K. The only means available to control the disease is the use of genetically resistant varieties. "Rizor" or "Holly" (Rz1) and WB42 (Rz2) have been the most widely used resistance sources in the commercial varieties. Recently, naturally occurring resistance-breaking (RB) rhizomania strains have been identified causing major concerns. The aim of this study was to identify SNP mutations that show associations with resistance to rhizomania in sugar beet plants grown under resistance-breaking (RB)-BNYVV soils. Rhizomania virus content was evaluated by indirect triple-antibody sandwich-ELISA within two F2 segregating populations respectively grown on an AYPR and IV-BNYVV strain infected soils. Bulked segregant analysis (BSA) was performed. The resistant and susceptible plants were genotyped with a 384-SNPs panel. Of the 384 SNPs, SNP249 was found to associate with the resistance both to the AYPR strain (R² = 0.37; P = 0.0004) and to the IV-BNYVV (R² = 0.09; P = 0.0074). Our results suggested that the SNP249 could be readily applicable for marker-assisted breeding of resistance to AYPR strain of rhizomania.ect]

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8M and 56.4M of 30-150bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC.

The paper describes ?-scan, a tool developed to identify mosaic structural variation.

Longidorus piceicola, a new geographical and host record from Romania, was described and illustrated on the basis of two populations originating from a coniferous and a deciduous forest. The main morphological characters of specimens from Romania correspond very well with the type material collected from the soil around Picea abies L. (Slovakia) except for the shorter body and tail. The D2-D3 fragment of 28S rDNA from both populations was amplified and sequenced, and the sequences were identical to L. piceicola sequence from Slovakia. The partial 18S-ITS1-5.8S-ITS2 rDNA regions from one of the populations were sequenced for the first time. The evolutionary relationships between L. piceicola and the closest species L. intermedius based on D2-D3 sequence divergence and single-nucleotide polymorphisms are discussed. Although having very low sequence dissimilarity (0.3-0.9 %) both species have distinct morphology and biology. Longidorus piceicola differs from L. intermedius in having a much longer odontostyle, body, distance anterior end -guide ring, a wider lip region, more ventromedian supplements (11 vs 5-7) in the male, and develops through four rather than three juvenile stages. Furthermore, L. piceicola occurs more frequently in association with conifers, while L. intermedius is found mainly in oak forests.

Although common bean has a good content in essential minerals, it also accumulates significant amounts of compounds that reduce its nutritional value by lowering nutrient bioavailability. Phytic acid, which is the major form of phosphorus stored in the seed, is one of such compounds, as, during gastro-intestinal passage, it binds trace elements and reduces their absorption, leading, under certain dietary circumstances, to mineral (mostly Fe, Zn, Ca) deficiencies. A major goal for grain crop improvement is the reduction of phytic acid content in the seed to improve micronutrient bioavailability, through the identification of low phytic acid (lpa) mutants. In common bean only one of such mutants has been described so far. Genes involved in phytic acid pathway and transport have been described in different species, including common bean. Recently, new genomic resources have become available for the common bean research community, thanks to the release of two whole genome sequences: the Andean G19833 and the Mesoamerican BAT93 genotypes. In this chapter we use the two common bean reference genomes to compare the sequences of genes involved or putatively involved in phytic acid synthesis and transport, some of them never reported in this species. Moreover, we discuss transcriptomic data of these genes, reported in different organs at different developmental stages for the Mesoamerican genotype. Finally, we discuss alternatives on how to exploit these new genomic resources to study and eventually manipulate phytic acid pathway and transport.

Phenolic acids are major components of cell walls in wheat and have important implications on human health as antioxidants with anti-tumor activity. Our objectives were to identify phenolic acid genes in wheat by single nucleotide polymorphisms (SNPs) detected within the coding sequences of candidate genes, and to identify chromosomal regions associated with single phenolic acids and total soluble phenolic compounds. A set of candidate genes involved in the biosynthesis of hydroxycinnamic acid derivatives were identified by comparative genomics. SNPs found in the coding sequences of six genes (PAL1, PAL2, C4H, C3H, COMT1 and COMT2) were used to determine their chromosomal location and accurate map position on two reference consensus linkage maps. The genome-wide association study (GWAS), based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs, detected 22 quantitative trait loci (QTL) distributed on almost all durum wheat chromosomes. Two QTL for p-coumaric acid were coincident with the phenylalanine ammonia-lyase (PAL2) and p-coumarate 3-hydroxylase (C3H) genes on chromosome arms 2AL and 1AL, respectively. The availability of candidate gene-based markers can allow elucidating the mechanism of phenolic acids accumulation in wheat kernels and exploiting the genetic variability of phenolic acids content for the nutritional improvement of wheat end-products.

We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.

Nell'ampia gamma delle cultivar di vite il Nebbiolo riveste un ruolo di particolare rilevanza. Le eccellenti caratteristiche qualitative di questo vitigno derivano dall'interazione tra la sua nota variabilità intravarietale (cloni) e le differenti caratteristiche pedoclimatiche degli ambienti in cui esso è coltivato (terroir). A fronte dell'interesse anche economico, erano disponibili poche informazioni a livello genomico per il Nebbiolo e mancavano dati fondamentali per comprendere in modo organico vari aspetti patologici e qualitativi della cultivar. Per colmare questa lacuna, nel 2012 è stato avviato il progetto triennale "Nebbiolo Genomics: genomica strutturale e funzionale su aspetti patologici e qualitativi", finanziato dalla Fondazione Cassa di Risparmio di Cuneo e finalizzato alla caratterizzazione genetica approfondita del Nebbiolo. Il progetto prevedeva in primo luogo il sequenziamento del genoma di 3 cloni di Nebbiolo; tale sequenziamento ha rappresentato la base di partenza per l'approfondimento di alcune importanti tematiche: 1) lo studio delle interazioni tra la biodiversità genetica esistente e l'ambiente di coltivazione (clima, microclima e terreno); 2) lo studio dei meccanismi di interazione vite/fitoplasma attraverso la caratterizzazione del trascrittoma; 3) l'individuazione di marcatori genetici clone-specifici. In questa sede vengono riportati i risultati ottenuti in particolare per quanto riguarda quest'ultima tematica.

Since involved in synaptic transmission and located on X-chromosome, neuroligins 3 and 4X have been studied as good positional and functional candidate genes for autism spectrum disorder pathogenesis, although contradictory results have been reported. Here, we performed a case-control study to assess the association between noncoding genetic variants in NLGN3 and NLGN4X genes and autism, in an Italian cohort of 202 autistic children analyzed by high-resolution melting. The results were first compared with data from 379 European healthy controls (1000 Genomes Project) and then with those from 1061 Italian controls genotyped by Illumina single nucleotide polymorphism (SNP) array 1M-duo. Statistical evaluations were performed using Plink v1.07, with the Omnibus multiple loci approach. According to both the European and the Italian control groups, a 6-marker haplotype on NLGN4X (rs6638575(G), rs3810688(T), rs3810687(G), rs3810686(C), rs5916269(G), rs1882260(T)) was associated with autism (odd ratio = 3.58, p-value = 2.58 ? 10-6 for the European controls; odds ratio = 2.42, p-value = 6.33 ? 10-3 for the Italian controls). Furthermore, several haplotype blocks at 5-, 4-, 3-, and 2-, including the first 5, 4, 3, and 2 SNPs, respectively, showed a similar association with autism. We provide evidence that noncoding polymorphisms on NLGN4X may be associated to autism, suggesting the key role of NLGN4X in autism pathophysiology and in its male prevalence