1,720,976 research outputs found
Scouting downy and powdery mildew susceptibility genes: a diversity study in Vitis spp.
No full textWorld viticulture is continually threatened by both known and emerging pathogens. Until now, the investigation on resistance loci/genes has been the main trend to understand the interaction between grapevine (Vitis spp.) and mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, not to confer total immunity and to be potentially overcome within a few years. Recently, on the footprint of research conducted on Arabidopsis and barley, genes associated to downy (DM) and powdery (PM) mildew susceptibility have been discovered also in the grapevine genome.
In the present work, in order to find new sources of broad-spectrum recessively inherited resistance against pathogens five susceptibility genes were re-sequenced (Illumina, 1000X depth) in 96 grapevine accessions including wild, vinifera and hybrid individuals. The scouted genes were VvDMR6-1, VvDMR6-2, VvDLO1, VvDLO2 involved in susceptibility to DM and VvMLO7 associated with susceptibility to PM. These genes were mapped on the reference genome and analysed to identify polymorphisms and haplotypes using dedicated software to study the mutation impact. Preliminary results showed 10 mutations affecting the VvMLO7 protein structure (high-medium impact) dispersed in 75% of accessions; in particular, one Single Nucleotide Polymorphisms (SNPs) led to premature stop codons. Moreover, 70% of the accessions showed a total of 13 SNPs in VvDMR6-1 and 11 in VvDMR6-2 impacting their coding and amino acid sequences. Finally, 12 mutations were detected in the VvDLO1 coding sequence in 37 individuals, whereas the VvDLO2 sequence appeared much more conserved with only one SNP identified in four accessions. These findings will be validated taking advantage of several reliable parentages. Prior haplotype function confirmation, the final results will corroborate genomic-assisted breeding programs for resistance to biotic stresses
Generation of mildew-resistant grapevine clones via genome editing
Get PDFPesticides-mostly fungicides- are massively used in viticulture to contain spreading of fungal and
fungal-like diseases such as powdery mildew (PM) and downy mildew (DM), towards which
cultivated grapevine (Vitis vinifera) is highly susceptible. Such consumption of fungicides is costly
and deleterious both for human health and the environment.
Alternatively, the successful control of such diseases was obtained by inactivation of plant
susceptibility genes in other crops: in fact, knocking out of DMR6 genes was demonstrated very
effective in controlling DM in Arabidopsis thaliana and other species. However their efficacy
toward DM resistance has yet to be demonstrated in grapevine. In addition, silencing of a group
of MLO genes resulted in resistance to PM in grapevine.
Selection of non-functional copies of susceptibility genes can be achieved via traditional breeding;
however crossing is not always desirable in grapevine, since maintenance of clonal genetic
integrity is commercially important (i.e. in wine grapes).
The revolutionary advent of genome editing now offers tools to edit and completely knock out
susceptibility genes in many crops while maintaining their cultivar and clonal genetic
backgrounds. CRISPR /Cas 9 technology was used in this work to edit DM and PM
susceptibility genes in different grapevine clones. Several plants edited in DMR6 and MLO genes
were obtained and are currently being screened for DM and PM resistance. This work will
establish whether DMR6 is determinant in controlling resistance to DM in grapevine, whether a
full knock-out of DMR6 and MLO genes provides resistance to DM and PM respectively, and
will hopefully deliver mildew resistant grapevine plants
Exploring genetic variability of susceptibility genes in grapevine: a recent frontier to dissect disease resistance
Get PDFGrapevine is one the most important and studied tree crops worldwide. Obtaining resistance to pathogens as Plasmopara viticola (the causal agent of downy mildew, DM) has always been a main goal in Europe since spreading of these pathogens at the end of the 19th century. In the last decades, due to the need to reduce environmentally-impacting fungicides, breeders focused on crossing Eurasian Vitis vinifera with wild American and Asian species to obtain resistant individuals. Unfortunately, dominantly inherited gene-based resistance has shown to be racespecific in some cases, to confer partial immunity and to be potentially overcome within a few years from the introduction of the resistance trait. Recently, the identification of susceptibility genes in herbaceous and tree crops, as factors required by the pathogen to infect the host-tissue, has opened up a chance for their exploitation as an alternative to breed for resistant plants. On the footprint of the research conducted on Arabidopsis, genes associated with DM susceptibility have been discovered also in the grapevine genome. Four susceptibility genes were re-sequenced (Illumina, 1,000X depth) in 190 grapevine accessions including 23 wild, 28 vinifera and 139 hybrid individuals to discover new sources of broad-spectrum recessively inherited resistance against P. viticola. The scouted genes were VvDMR6-1, VvDMR6-2, VvDLO1, VvDLO2 involved in susceptibility to DM. These genes were mapped on the reference genome and analysed to identify polymorphisms and haplotypes using dedicated software to study the mutation effect. Regarding those mutations with putative impact on gene function, within the 190 accessions we observed ~14% accessions mutated in VvDMR6-1 and ~18% mutated in VvDMR6-2, only a handful of accessions that were mutated in both genes. ~21% and ~16% accessions showed mutations in VvDLO1 and VvDLO2 respectively, and again only a few accessions were mutated in both genes. 86% of the total impacting mutations were SNPs (in the strict sense) while 14% were substitutions. Out of the 129 accessions carrying selected mutations ~83% were hybrids whereas 7% and 10% were respectively wild species and vinifera varieties. When taking into account haplotype frequencies, highly shared haplotypes (in ~40% of the mutation-carrying accessions) were observed for VvDMR6-2 and VvDLO1, whereas for VvDMR6-1 and VvDLO2 almost every accession showed a specific haplotype. Moreover, a validation of Illumina results was carried out with a Sanger sequencing on 25 selected accessions as informative for interesting non-synonymous or synonymous substitutions in one or more of the genes under investigation. Basing on these findings, the VvDMR6-1 and VvDLO1 protein model based on confirmed mutations-carrying haplotypes was drafted with the aim to investigate the impact of amino acids substitution on protein folding and function. These results will inform grapevine genetics and corroborate genomic-assisted breeding programs for resistance to biotic stresse
Mining grapevine downy mildew susceptibility genes: A resource for genomics-based breeding and tailored gene editing
Get PDFSeveral pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes—namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2—in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses
Generation of mildew-resistant grapevine clones via genome editing
No full textCultivated grapevine (Vitis vinifera) is highly susceptible to several fungal and fungal-like diseases such as powdery mildew (PM) and downy mildew (DM), which require large use of pesticides for their containment. In other crops, knock-out mutations of host genes controlling susceptibility to such diseases have proven a successful strategy to obtain resistant plants. Recent works demonstrated the importance of the MLO family as susceptibility genes for PM resistance also in grapevine, whereas DMR6 has been identified as DM susceptibility gene in Arabidopsis thaliana, and its involvement in DM susceptibility is yet to be demonstrated in grapevine. Today, emerging new breeding technologies such as CRISPR/Cas9, recently applied also to grapevine, allow to generate knock-out mutants in specific DNA targets while maintaining the varietal and clonal identity as by traditional breeding.
In this work we aim to knock-out specific grapevine susceptibility genes, such as MLO and DMR6 genes via CRISPR/Cas9 technology, to generate PM and DM resistant clones of grapevine. Embryogenic callus of Chardonnay and microvine varieties were transformed via Agrobacterium tumefaciens with CRISPR/Cas9 vectors designed to specifically edit these genes. In vitro plants regenerated form these embryogenic calli were sequenced confirming the presence of small insertion and deletions or single nucleotide polymorphisms at the target sites
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
- …
