Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12-mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins

Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip

UMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne[b]Background[/b] [br/]The increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci). [br/][b]Results[/b] [br/]Ten stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered. [br/][b]Conclusions[/b] [br/]This study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variatio

The genetic background modulates the intensity of Rpv3-dependent downy mildew resistance in grapevine

Grape varieties with resistance to downy mildew (DM) carry alien chromosome segments in Vitis vinifera backgrounds. We previously showed that the largest descent group shares a non-vinifera haplotype at the locus Rpv3. Here, we performed a common garden experiment with 76 varieties to evaluate the level of field resistance across four years. All varieties exhibited effector-triggered immunity (ETI)-associated necrosis. On a scale of 1–9, the median OIV452 value for foliar resistance was 7.1 in the resistant lineage vs. 3.2 in vinifera controls. Genotype, year and their interaction significantly affected the level of resistance. Some resistant genotypes showed high mean values of OIV452 and low variance among years. Other resistant genotypes showed lower mean OIV452 and higher variance. They were capable of activating ETI, but the intensity was inadequate to restrict pathogen growth under highly conducive conditions. Rpv3-dependent responses were stronger in highly native genetic backgrounds and tended to attenuate in late backcross generations. Genetic backgrounds donated by European winegrapes of the convarietas occidentalis provided on average higher levels of Rpv3 resistance than backgrounds of orientalis table grapes

Immunohistochemical analysis of the antiapoptotic Mcl-1 and Bcl-2 proteins in follicular lymphoma

In the present study, we investigated the expression of Mcl-1 and Bcl-2 by immunohistochemistry in 85 patients of grades 1–3 and transformed follicular lymphoma (FL). In lymphoma tissue, centroblasts uniformly expressed high levels of Mcl-1 (Mcl-1hi) whereas centrocytes demonstrated low Mcl-1 expression (Mcl-1lo). Bcl-2 expression in centroblasts/centrocytes was reciprocal to Mcl-1 staining in most cases. A high number of Mcl-1hi centroblasts in tissue sections (?200/high-power field) correlated with poor overall survival (P < 0·001), independent of the International Prognostic Index and FL grade. This suggests that the number of centroblasts with strong Mcl-1 staining is associated with clinical outcome in FL patients

InDel markers for monitoring the introgression of downy mildew resistance from wild relatives into grape varieties

We identified haplotype-tagging insertion/deletions (InDels) for downy mildew resistance (Rpv3-1) in grapevine and converted them into InDel markers. InDel-25,941 and InDel-26,032 were validated by fragment analysis via capillary electrophoresis in 174 varieties of Vitis vinifera, 50 resistant varieties of the ‘Seibel 4614’ lineage that share Rpv3-1 by descent, and in 83 Vitis accessions. Amplicon sequencing of ancestral and derived alleles revealed that both mutations were caused by deletions. The 25,941-deletion is most likely recent. The derived allele is present only in resistant varieties obtained from ‘Seibel 4614’ and has originated in North American populations through two successive deletions within a predicted multiple stem-loop ssDNA structure, consisting of three nearby short inverted repeats, which shortened the ancestral DNA stepwise. The 26,032-deletion is more ancient. The derived allele is always present in resistant varieties of the ‘Seibel 4614’ lineage, completely absent from V. vinifera, not found in other North American accessions, and rarely present in Asian species. It may have originated in a common ancestral population before the continental disjunction, followed by incomplete lineage sorting, or in either lineage followed by introgression via secondary contacts. Genotyping with these markers does not require special instruments or chemistry for routine screening in breeding practice. Differences in amplicon size between grapes that carry or do not carry Rpv3-1 are detectable via standard agarose gel electrophoresis, or classical melting curve analysis using nonsaturating fluorescent dyes. The recombination rate between each marker and the trait locus is 0.118% for InDel-25,941 and 0.071% for InDel-26,032

Landslide Early Warning Systems as Climate Change Adaptation Measures for Rail Infrastructure

Railways represent a significant asset for Italy, with more than 16,000 km of rail lines distributed all over the country. The impacts of extreme weather events can be particularly severe on rail infrastructure because of the highly integrated nature of the rail system. Historical failure of rail infrastructure due to extreme weather events is well documented. In addition, it is to be expected that climate change affects the stability of engineered slopes and have consequences on landslides. Failure of a single asset can result in potential fatalities, large replacement costs, and loss of service. Consequently, Rete Ferroviaria Italiana (RFI), the Italian public limited company for railway transportation, is moving towards risk assessment methods as part of holistic asset management. In this context, ETS Srl has been developing a methodology called MIRETS (Management and Identification of the Risk - ETS), a workflow to connect survey-inspection data for geology, digitalization, diagnostics, and design. Within this framework, a three-phase methodological approach has been developed for the design and the implementation of a landslide early warning system (LEWS) along a strategic railway infrastructure. This study describes the first preliminary results, focusing on the collection and the processing of the input data

Historical introgression of the downy mildew resistance gene Rpv12 from the Asian species Vitis amurensis into grapevine varieties.

The Amur grape (Vitis amurensis Rupr.) thrives naturally in cool climates of Northeast Asia. Resistance against the introduced pathogen Plasmopara viticola is common among wild ecotypes that were propagated from Manchuria into Chinese vineyards or collected by Soviet botanists in Siberia, and used for the introgression of resistance into wine grapes (Vitis vinifera L.). A QTL analysis revealed a dominant gene Rpv12 that explained 79% of the phenotypic variance for downy mildew resistance and was inherited independently of other resistance genes. A Mendelian component of resistance–a hypersensitive response in leaves challenged with P. viticola–was mapped in an interval of 0.2 cM containing an array of coiled-coil NB-LRR genes on chromosome 14. We sequenced 10-kb genic regions in the Rpv12+ haplotype and identified polymorphisms in 12 varieties of V. vinifera using next-generation sequencing. The combination of two SNPs in single-copy genes flanking the NB-LRR cluster distinguished the resistant haplotype from all others found in 200 accessions of V. vinifera, V. amurensis, and V. amurensis x V. vinifera crosses. The Rpv12+ haplotype is shared by 15 varieties, the most ancestral of which are the century-old ‘Zarja severa’ and ‘Michurinets’. Before this knowledge, the chromosome segment around Rpv12+ became introgressed, shortened, and pyramided with another downy mildew resistance gene from North American grapevines (Rpv3) only by phenotypic selection. Rpv12+ has an additive effect with Rpv3+ to protect vines against natural infections, and confers foliar resistance to strains that are virulent on Rpv3+ plants