Fabio Marroni

Fabio Marroni
University of Udine | UNIUD · Department of Agricultural and Environmental Sciences

PhD

About

120
Publications
21,554
Reads
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9,241
Citations
Additional affiliations
September 2019 - October 2020
University of Udine
Position
  • Professor (Assistant)
December 2017 - April 2019
IGA Technology
IGA Technology
Position
  • Bioinformatician
December 2012 - December 2017
University of Udine
Position
  • Researcher
Education
January 2002 - April 2005
Università di Pisa
Field of study
  • Experimental and Molecular Oncology
November 1992 - July 1999
Università di Pisa
Field of study
  • Biology

Publications

Publications (120)
Article
Full-text available
Background Brown trout is one of the most widespread fresh-water fish species in Europe. The evolutionary history of and phylogenetic relationships between brown trout populations are complex, and this is especially true for Italian populations, which are heavily influenced in different ways by stocking practices. The characterization of the geneti...
Article
Since 2012 Kiwifruit Vine Decline Syndrome (KVDS) has severely compromised all major kiwifruit growing areas in Italy. So far, aetiological studies were mainly focused on waterlogging effects or on the isolation of microorganisms from diseased plants, thus an all-encompassing picture on KVDS microbiota is still missing. This work aims to describe o...
Article
Full-text available
The western honey bee (Apis mellifera) is of major economic and ecological importance, with elevated rates of colony losses in temperate regions over the last two decades thought to be largely caused by the exotic ectoparasitic mite Varroa destructor and deformed wing virus (DWV), which the mite transmits. DWV currently exists as two main genotypes...
Article
Full-text available
Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Eu...
Article
Phytoplasmas are sieve-elements restricted wall-less, pleomorphic pathogenic microorganisms causing devastating damage to over 700 plant species worldwide. The invasion of sieve elements by phytoplasmas has several consequences on nutrient transport and metabolism, anyway studies about changes of the mineral-nutrient profile following phytoplasma i...
Article
Roots of the European hazelnut (Corylus avellana), i.e., one of the most economically important nut species, form symbiosis with ectomycorrhizal (ECM) fungi, including truffles. Although physical interactions only occur in roots, the presence of mycorrhizal fungi can lead to metabolic changes at systemic level, i.e., in leaves. However, how root co...
Article
Full-text available
In order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all analyses support a single domestication event that occurred in Western Asia and was followed by numerous and pervasive introgressions from European wild populations. T...
Article
Full-text available
Objective Allelic imbalance (AI) is the differential expression of the two alleles in a diploid. AI can vary between tissues, treatments, and environments. Methods for testing AI exist, but methods are needed to estimate type I error and power for detecting AI and difference of AI between conditions. As the costs of the technology plummet, what is...
Article
Virus detection is a crucial step for the implementation of clean stock programs that preserve healthy crop species. Viral infections in grapevine, a vegetatively propagated perennial crop, cannot be eradicated from the vineyards by the application of agrochemicals and must be curtailed at the stage of nursery production during the propagation of p...
Preprint
Full-text available
Allelic imbalance (AI) is the differential expression of the two alleles in a diploid. AI can vary between tissues, treatments, and environments. Statistical methods for testing in this area exist, with impacts of explosive type I error in the presence of bias well understood. However, for study design, the more important and understudied problem i...
Article
Full-text available
Vitis vinifera is an economically important crop and a useful model in which to study chromatin dynamics. In contrast to the small and relatively simple genome of Arabidopsis thaliana, grapevine contains a complex genome of 487 Mb that exhibits extensive colonization by transposable elements. We used Hi‐C, ChIP‐seq and ATAC‐seq to measure how chrom...
Article
Full-text available
The simultaneous presence of different N-forms in the rhizosphere leads to beneficial effects on nitrogen (N) nutrition in plants. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants. Maize fed with a mixture of urea and ammonium displayed a better N-uptake...
Article
Full-text available
The characterization of the genetic basis of maize leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and MAGIC maize recombinant inbred lines (RILs) were measured for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the t...
Article
Full-text available
Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? The approach described applies to any technology generating allele specific sequence c...
Article
Full-text available
The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of Limodorum abortivum, a terrestrial mixotrophic orchid that associates with ectomycorrhizal fun...
Article
Methane generation from seagrass contributes to green-house gases emissions but can also be a potential controlled biogas source. Understanding the natural fluctuations of emissions and the biotic and abiotic factors underlying such variations is essential. In this work, CH4 emission from beach-cast seagrass from the High-Adriatic coast was analyse...
Article
Full-text available
The ectoparasite protozoan Amyloodinium ocellatum (AO) is the etiological agent of amyloodiniosis in European seabass (Dicentrarchus labrax) (ESB). There is a lack of information about basic molecular data on AO biology and its interaction with the host. Therefore, de novo transcriptome sequencing of AO tomonts was performed. AO trophonts were deta...
Preprint
Full-text available
Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? Tests of allelic effect are performed by crossing individuals and comparing expression...
Article
Full-text available
In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan s...
Article
Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of th...
Article
Full-text available
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotg...
Article
Background and aims: The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genoty...
Article
Full-text available
Background: ‘Candidatus Phytoplasma solani’ is endemic in Europe and infects a wide range of weeds and cultivated plants. Phytoplasmas are prokaryotic plant pathogens that colonize the sieve elements of their host plant, causing severe alterations in phloem function and impairment of assimilate translocation. Typical symptoms of infected plants inc...
Article
Full-text available
Iron and phosphorus are abundant elements in soils but poorly available for plant nutrition. The availability of these two nutrients represents a major constraint for fruit tree cultivation such as apple (Malus × domestica) leading very often to a decrease of fruit productivity and quality worsening. Aim of this study was to characterize common and...
Article
Full-text available
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotg...
Article
In agricultural soil, the bioavailability of iron (Fe) and phosphorus (P) is often below the plant's requirement causing nutritional deficiency in crops. Under P-limiting conditions, white lupin (Lupinus albus L.) activates mechanisms that promote P solubility in the soil through morphological, physiological and molecular adaptations. Similar chang...
Article
Full-text available
This DIB article provides details about transcriptional and physiological response of Fe- and P-deficient white lupin roots, an extensive and complete description of plant response is shown in the research article "Physiological and transcriptomic data highlight common features between iron and phosphorus acquisition mechanisms in white lupin roots...
Article
The transcriptional regulatory structure of plant genomes is still relatively unexplored and little is known about factors that influence expression variation in plants. We used a genetic system consisting of 10 heterozygous grape varieties with high consanguinity and high haplotypic diversity to: (i) identify regions of haplotype sharing through w...
Article
Full-text available
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotg...
Article
The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and...
Article
Full-text available
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms in a single experiment, with the possibility of de novo reconstruction of the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metage...
Article
Full-text available
Allelic imbalance (AI) indicates the presence of functional variation in cis regulatory regions. Detecting cis regulatory differences using AI is widespread, yet there is no formal statistical methodology that tests whether AI differs between conditions. Here we present a novel model and formally test differences in AI across conditions using Bayes...
Article
Full-text available
Grapevine, cultivated for both fruit and beverage production, represents one of the most economically important fruit crops worldwide. With the aim of better understanding how grape roots respond to beneficial microbes, a transcriptome sequencing experiment has been performed to evaluate the impact of a single arbuscular mycorrhizal (AM) fungal spe...
Data
Figure S1 Representation of the algorithm implemented in χ‐scan. Figure S2 Performance of several tools in the detection of mosaic SV. Figure S3 Structural variation detected in V. vinifera chromosome 2 by different methods. Figure S4 Depth of Coverage analysis. Table S1 Simplified pseudocode to summarize the main steps of the algorithms. Meth...
Conference Paper
Full-text available
Taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated in Southwestern and Southern Asia, respectively, and spread over the world undergoing complex events of admixture. A recent work investigating genetic origin, admixture and population history of primitive European cattle highlighted, by using genome-wide single nucleotide polymorp...
Article
Full-text available
Structural variation (SV) is determined by genome rearrangements that affect large (> 1 kb) segments of DNA such as inversions and balanced translocations (balanced SV) or insertions, deletions and duplications (unbalanced SV) (Feuk et al., 2006). SV occurred in somatic cells originating from the same fertilized egg and affecting only a portion of...
Poster
Full-text available
The pan-genome describes all the genomic sequences present in a population of different varieties of the same species and it is commonly applied in bacterial genomics. The sequences present in all varieties represent the ”core” genome, while sequences present in some varieties and absent in others are named ”dispensable” genome and represent the va...
Article
Full-text available
Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species....
Article
Full-text available
Retrotransposons represent a major component of plant genomes; however, large-scale studies on their expression are rare. Massively parallel sequencing offers new analytical possibilities enabling a comprehensive study of retrotransposon RNA transcription. We evaluated the expression of long terminal repeat-retrotransposons in leaves of two sister...
Article
Full-text available
Merino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of...
Article
Full-text available
Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) substantially contribute to genetic variation and have an important effect on phenotypic diversity. Since unbalanced SVs are by definition sequences present only in some individuals, they have therefore been referred to as dispensable genome and are n...
Article
Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of i) characterizing the transcriptome through Illumina RNA-S...
Article
Full-text available
Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequenc...
Article
Next-generation (NG) sequencing in a natural population of Populus nigra revealed a mutant with a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis. The lignin composition of P. nigra trees homozygous for the defective allele was compared with...
Article
Biological plausibility and other prior information could help select genome-wide association (GWA) findings for further follow-up, but there is no consensus on which types of knowledge should be considered or how to weight them. We used experts' opinions and empirical evidence to estimate the relative importance of 15 types of information at the s...
Article
Prioritization is the process whereby a set of possible candidate genes or SNPs is ranked so that the most promising can be taken forward into further studies. In a genome-wide association study, prioritization is usually based on the P-values alone, but researchers sometimes take account of external annotation information about the SNPs such as wh...
Article
Restless legs syndrome (RLS) is a sleep-related movement disorder that affects up to 15 % of the population. Linkage studies have identified several genomic loci in single families (12q, 14q, 9p, 2q, 20p and 16p, respectively). However, confirmation of these loci has not always been achieved, and causative mutations have not yet been identified. Th...
Article
Full-text available
Next generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, few research groups worki...
Article
Anecdotal evidence suggests a high incidence in Trentino, Italy, of head and neck paragangliomas (HNPGL), a rare autosomal dominant disease called paraganglioma type 1 syndrome and caused by germ-line mutations of the SDHD gene. The aim of this study was to investigate the origin, spread, and clinical expression of the disease in this geographic re...
Article
Full-text available
Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic di...