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Different approaches to identify genetic traits responsible for susceptibility and resistance to Flavescence dorée in grapevine
Get PDFFlavescence dorée (FD) is one of the most destructive grapevine yellows (GY) disease that caused huge losses in grape and wine industries. It is causes by phytoplasmas, which are bacteria living in the phloem and transmitted in vineyard by the leafhopper Scaphoideus titanus Ball. Grapevine varieties completely resistant to FD have not been uncovered yet, however inter and intraspecific differences in susceptibility have already been observed, such as poor presence of the disease in vineyard, no severe symptoms and recovery ability of the plant. The different behavior among the grapevine varieties suggests the presence of genetic traits in grapevine germplasm related to high or low susceptibility to FD. The aim of this work is to uncover the low susceptibility mechanisms, and also identify the genetic traits responsible for different phenotypes.
The first work presented here, newly accepted, concerns the study of some mechanisms occurring during FD infection in ‘Tocai friulano’ plants, a scarcely susceptible variety. The surveys, performed in a highly FD-infected vineyard, showed a different response against the pathogen in symptomatic ‘Tocai friulano’ plants compared to ‘Pinot gris’ symptomatic ones, a variety highly susceptible. Compartmentalization of FDp in symptomatic portions of ‘Tocai friulano’, its absence in asymptomatic vegetative parts and the absence of the pathogen in permanent tissues (i.e. trunk) were observed. The ability of this cultivar to block and avoid the spread of the symptoms and the pathogen into the whole canopy suggested the possibility of recovery starting events; thus, metabolic analyses and gene expression studies were performed in the phloem tissues to investigate the possible defense mechanisms involved.
The second PhD work concerns the study of a population obtained by a cross between ‘Tocai friulano’ and ‘Chardonnay’ (a highly susceptible cultivar) at CREA Viticulture and Enology in Conegliano (Treviso, Italy). Genotyping by sequencing (GBS) analysis was performed on the parentals and on 184 individuals of the progeny, and the resulting single nucleotide polymorphism (SNP) dataset was used both to construct a linkage map and to identify polymorphisms putatively involved in gene
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regulation. In this work GBS was coupled with a in silico study to identify SNPs modifying transcription factor binding motifs (TFBM) in the proximal regulatory region of genes. Target genes were selected among constitutive differentially expressed genes (DEGs) between ‘Tocai friulano’ and ‘Chardonnay’, previously identified. Parallelly, the observation and the analysis of different FD symptoms in more than 100 infected plants belonging to the progeny led to the identification of valuable phenotypic traits that could be used during phenotype evaluation aimed to QTL identifications.
Finally, the existence of differences in FD susceptibility among three ‘Chardonnay’ clones observed in vineyard suggested a further study focused on the transcriptomic and genomic differences among them. The genomes of the three clones were fully sequenced by PacBio HiFi on Sequel II, de novo assembled, and then compared each other to identify structural variants and SNPs. In addition, a transcriptomic study during the early stage of FD infection on two of the three clones showing different phenotype was performed. A dataset of the structural variants distinguishing the less susceptible clone from the other two was defined and it will be used to further investigation on the genes involved in FD infection and susceptibility. During the PhD course this third work was designed and partially performed, however further analyses are required to achieve more complete results.Flavescence dorée (FD) is one of the most destructive grapevine yellows (GY) disease that caused huge losses in grape and wine industries. It is causes by phytoplasmas, which are bacteria living in the phloem and transmitted in vineyard by the leafhopper Scaphoideus titanus Ball. Grapevine varieties completely resistant to FD have not been uncovered yet, however inter and intraspecific differences in susceptibility have already been observed, such as poor presence of the disease in vineyard, no severe symptoms and recovery ability of the plant. The different behavior among the grapevine varieties suggests the presence of genetic traits in grapevine germplasm related to high or low susceptibility to FD. The aim of this work is to uncover the low susceptibility mechanisms, and also identify the genetic traits responsible for different phenotypes.
The first work presented here, newly accepted, concerns the study of some mechanisms occurring during FD infection in ‘Tocai friulano’ plants, a scarcely susceptible variety. The surveys, performed in a highly FD-infected vineyard, showed a different response against the pathogen in symptomatic ‘Tocai friulano’ plants compared to ‘Pinot gris’ symptomatic ones, a variety highly susceptible. Compartmentalization of FDp in symptomatic portions of ‘Tocai friulano’, its absence in asymptomatic vegetative parts and the absence of the pathogen in permanent tissues (i.e. trunk) were observed. The ability of this cultivar to block and avoid the spread of the symptoms and the pathogen into the whole canopy suggested the possibility of recovery starting events; thus, metabolic analyses and gene expression studies were performed in the phloem tissues to investigate the possible defense mechanisms involved.
The second PhD work concerns the study of a population obtained by a cross between ‘Tocai friulano’ and ‘Chardonnay’ (a highly susceptible cultivar) at CREA Viticulture and Enology in Conegliano (Treviso, Italy). Genotyping by sequencing (GBS) analysis was performed on the parentals and on 184 individuals of the progeny, and the resulting single nucleotide polymorphism (SNP) dataset was used both to construct a linkage map and to identify polymorphisms putatively involved in gene
2
regulation. In this work GBS was coupled with a in silico study to identify SNPs modifying transcription factor binding motifs (TFBM) in the proximal regulatory region of genes. Target genes were selected among constitutive differentially expressed genes (DEGs) between ‘Tocai friulano’ and ‘Chardonnay’, previously identified. Parallelly, the observation and the analysis of different FD symptoms in more than 100 infected plants belonging to the progeny led to the identification of valuable phenotypic traits that could be used during phenotype evaluation aimed to QTL identifications.
Finally, the existence of differences in FD susceptibility among three ‘Chardonnay’ clones observed in vineyard suggested a further study focused on the transcriptomic and genomic differences among them. The genomes of the three clones were fully sequenced by PacBio HiFi on Sequel II, de novo assembled, and then compared each other to identify structural variants and SNPs. In addition, a transcriptomic study during the early stage of FD infection on two of the three clones showing different phenotype was performed. A dataset of the structural variants distinguishing the less susceptible clone from the other two was defined and it will be used to further investigation on the genes involved in FD infection and susceptibility. During the PhD course this third work was designed and partially performed, however further analyses are required to achieve more complete results
A successful defence strategy in grapevine cultivar 'Tocai friulano' provides compartmentation of grapevine Flavescence dorée phytoplasma
Get PDFBackgroundFlavescence doree (FD) is a grapevine disease caused by phytoplasma and it is one of the most destructive pathologies in Europe. Nowadays, the only strategies used to control the epidemics are insecticides against vector, but more sustainable techniques are required. Completely resistant Vitis vinifera varieties have not been uncovered yet, but differences in susceptibility among cultivars and spontaneous recovery from FD symptoms have been observed. The grapevine cultivar 'Tocai friulano' shows very low susceptibility to FD but its defence strategy to counteract the phytoplasma spread has not been deciphered yet. In this work, the mechanisms occurring within 'Tocai friulano' FD-infected plants were examined in depth to identify the phytoplasma distribution and the defence pathways involved.ResultsIn 'Tocai friulano' symptoms of FD-infection remained confined near the area where they appeared during all the vegetative season. Analyses of secondary phloem showed a total absence of FD phytoplasma (FDp) in the trunk and its disappearance in 2-year-old arms from July to November, which was different from 'Pinot gris', a highly susceptible variety.Diverse modulations of defence genes and accumulation of metabolites were revealed in 1-year-old canes of 'Tocai friulano' FD-infected plants, depending on the sanitary status. Symptomatic portions showed high activation of both jasmonate- and salicylate-mediated responses, together with a great accumulation of resveratrol. Whereas activation of jasmonate-mediated response and high content of epsilon-viniferin were identified in asymptomatic 1-year-old cane portions close to the symptomatic ones.ConclusionSuccessful defence mechanisms activated near the symptomatic areas allowed the compartmentation of FD symptoms and phytoplasmas within the infected 'Tocai friulano' plants. These results could suggest specific agronomical practices to be adopted during FD management of this variety, and drive research of resistance genes against FD
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Grapevine red blotch virus is sporadically present in a germplasm collection in Northern Italy
No full textLimited information is available on the distribution of grapevine red blotch virus (GRBV) in grape-growing regions outside
North America. In this study, the presence of GRBV was investigated in 596 grapevine samples coming from different
sources in Northern Italy, including rootstock and table grape accessions from ampelographic collections, and commercial
varieties with red blotch-like symptoms. Only ‘Queen’ and ‘Incrocio Dalmasso VIII-5’ accessions, collected from the
CREA-Viticulture and Enology repository of table grape varieties, tested positive for GRBV. Sequencing of fragments from
replication and coat protein genes revealed that the two accessions were infected with GRBV isolates belonging to two distinct
lineages. While the American origin of ‘Queen’ could explain the GRBV presence in this accession, the viral infection
of the Italian ‘Incrocio Dalmasso VIII-5’ remains an unsolved mystery
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