Gabriele di Gaspero

Istituto di Genomica Applicata | IGA

Background Croatia is a geographically small country with a remarkable diversity of cultivated and spontaneous grapevines. Local germplasm has been characterised by microsatellite markers, but a detailed analysis based on single nucleotide polymorphisms (SNPs) is still lacking. Here we characterize the genetic diversity of 149 accessions from three...

Understanding ripening patterns and governing ripening speed are central aspects of grapevine ( Vitis vinifera ) berry biology owing to the importance of grape ripeness in winemaking. Despite this, the genetic control of ripening is largely unknown. Here, we report a major quantitative trait locus that controls ripening speed, expressed as speed of...

Background Croatia is a geographically small country, but it has a remarkable genetic diversity of cultivated and wild grapevines. Local germplasm has been characterised by microsatellite markers, but a detailed analysis based on single nucleotide polymorphisms (SNPs) is still lacking. Here we characterize the genetic diversity of 149 accessions fr...

In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing d...

Minor varieties represent a significant part of the grapevine germplasm (Vitis vinifera L. subsp. vinifera) in Croatia. During the long history of grape cultivation in insular, coastal and continental Croatia, numerous local varieties were cultivated, many of which are still used today. There are also several populations of wild grapevine (Vitis vi...

Broomcorn millet (Panicum miliaceum L.) is a prehistorical cereal, today cultivated as a minor crop with low yields but with a renewed interest for its high water use efficiency and gluten-free grains. To reverse the downward trend in broomcorn millet cultivation, the crop needs genetic improvement and creation of novel genetic variation to increas...

Over the past two centuries, introgression through repeated backcrossing has introduced disease resistance from wild grape species into the domesticated lineage Vitis vinifera subsp. sativa. Introgression lines are being cultivated over increasing vineyard surface areas, as their wines now rival in quality those obtained from preexisting varieties....

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...

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...

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-...

The necessity to adapt to climate change is even stronger for grapevine than for other crops, because grape berry composition—a key determinant of fruit and wine quality, typicity and market value— highly depends on “terroir” (complete natural environment), on vintage (annual climate variability), and on their interactions. In the same time, there...

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the specie...

The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Inter-varietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), suggesting a simple Mendelian inheritance of the trait. A double digest restriction associated DNA (ddRAD) sequencing of a biparental population segregating for incompa...

A wild grape haplotype (Rpv3‐1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR‐NB‐LRR (TNL) gene pair that originated 1.6‐2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen‐induced necrosis...

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...

In the middle of the 20th century, varieties of Vitis vinifera locally grown in the Balkans were crossed with varieties from Western Europe with the aim of improving wine quality. The variety 'Probus' originated from the crossing of 'Kadarka' and 'Cabernet Sauvignon' and was released in 1983. The acreage of 'Probus' has recently increased in Serbia...

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-...

Since 1998 at University of Udine started a breeding program with the purpose of introgressing resistance genes into elite wine cultivars. The first ten varieties were released in collaboration with the Institute of Applied Genomics and introduced into the market by Vivai Cooperativi Rauscedo, one of the leading grape nurseries. Here we present the...

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 va...

Changes in the performance of genotypes in different environments are defined as genotype x environment (GxE) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil, and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect...

Downy mildew (Plasmopara viticola) is one of the most destructive diseases of the cultivated species Vitis vinifera. The use of resistant varieties, originally derived from backcrosses of North American Vitis spp., is a promising solution to reduce disease damage in the vineyards. To shed light on the type and the timing of pathogen-triggered resis...

A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

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...

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...

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study...

In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without gen...

Autochthonous cultivars are a resource for viticulture linked to territory. However they are prone to diseases like all V. vinifera cultivars. A breeding program has been set up in 1998 at the University of Udine, region Friuli, north-eastern Italy to obtain new grapevine resistant selections with high quality of grapes and wine. Up to date more th...

Grapevine is a major horticulture crop grown on ~7.6 million hectares that secure a yearly production of ~70 million tons of grapes. A significant part of the crop (65 %) annually fuels a worldwide wine industry of ~27 billion liters. In 2007, 2.8 billion liters in wine sales in the United States alone were worth US$ 30 billion. Grapevines and wine...

The current chromosome assembly of the grapevine reference genome is under improvement using two strategies. First several maps have been densified using SNP markers developed both from a classic Sanger re-sequencing of the parents and from the re-sequencing of a panel of diversity in the Vitaceae genome to develop a 18K genotyping chip (http://urg...

Grapevine (. Vitis vinifera L.) encompasses a staggering complexity of biochemical variation in the fruit of varieties that individually differ by nuances of colour, taste and aroma. A deep understanding of the underlying DNA variation unlocks the evolutionary relationships between varieties, their somatic mutants and their living wild relatives, a...

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 grape...

Microsatellite and SNP markers on chr14. (JPG)

Validation of the Rpv12 genetic interval in progeny derived from the cross ‘Kunbaràt’ x ‘Sarfeher’. (PDF)

Description of the Rpv12 region in the reference genome, in the Rpv12+ resistant haplotype, and diversity among grapevines: (panel A) recombination in custom-made populations; (panel B) variable sites between Rpv12+ and V. vinifera haplotypes in six single-copy genes at symmetrical positions with respect to Rpv12 (the analysis was extended to addit...

Introgression of the Rpv12+ region in grapevine varieties and the surrounding chromosomal landscape. Genetic (panel A) and physical (panels D,H) distance of mapped markers; density of exons, class I and II TEs, unclassified high-copy sequences, and low-copy DNA (panel C); density of NB-LRR genes (panels E,I) and their phylogenetic relationships (pa...

DNA fingerprinting and kinship of six accessions claimed to belong to the first filial generation of V. amurensis x V. vinifera crosses. (JPG)

Pedigrees of custom-made populations for genetic mapping, and varieties containing the resistant haplotype of Rpv12. (JPG)

Genetic maps and QTL plots for downy mildew foliar resistance (OIV452 parameter) in an Rpv12+/Rpv12− Rpv3−/Rpv3− resistant parent (panels A and C) and in an Rpv12+/Rpv12− Rpv3+/Rpv3− resistant parent (panels B and D). For the sake of simplicity, cosegregating markers are shown only once on the x-axis of the QTL plots. (JPG)

List of 200 grapevine accessions and their genotypes at the Rpv12 locus. DNA typing was performed by Sanger sequencing of the gene fragments GSVIVT00036207001 and GSVIVT00023546001 and by scoring nucleotide variants at the chromosomal positions chr14:9036110 and chr14: 9882587, flanking the Rpv12 NB-LRR cluster. (JPG)

DNA fingerprinting and kinship of 48 accessions of V. amurensis, descendents of V. amurensis x V. vinifera crosses with unknown pedigree, and introgression lines in the first two generations of descent with known pedigree. (JPG)

The mature berry of Vitis vinifera 'Alicante Bouschet' is entirely red, but anthocyanin metabolism discloses elements of histological discontinuity. This provides an experimental system amenable to studies of compartmentalised secondary metabolism in a fleshly fruit. We compared microscopy of fixed berry sections and chemical composition of anthocy...

Heavy alcohol consumption is associated with increased overall mortality, cancer, liver, and cardiovascular diseases; but low doses of alcohol (up to one drink per day) are not associated with the risk of any cancer site with the exception of breast cancer and possibly of oral and pharyngeal cancers. Moreover, recent evidence indicates that moderat...

The Rpv3 locus is a major determinant of downy mildew resistance in grapevine (Vitis spp.). A selective sweep at this locus was revealed by the DNA genotyping of 580 grapevines, which include a highly diverse set of 265 European varieties that predated the spread of North American mildews, 82 accessions of wild species, and 233 registered breeding...

The Rpv3 locus determines the ability to operate an isolate-specific hypersensitive response (HR) against Plasmopara viticola in grapevines that carry a resistant Rpv3 (+) haplotype. Artificial infection was performed on leaf discs of Rpv3 (+) and Rpv3 (-) grapevines with two distinct isolates of the pathogen (avrRpv3 (+) and avrRpv3 (-)). The plan...

A collection of 1005 grapevine accessions was genotyped at 34 microsatellite loci (SSR) with the aim of analysing genetic diversity and exploring parentages. The comparison of molecular profiles revealed 200 groups of synonymy. The removal of perfect synonyms reduced the database to 745 unique genotypes, on which population genetic parameters were...

Multiple alignments of non-coding DNA in 10-kb surrounding duplicate F3'5'H genes. In the panel on top of each page, F3'5'H exons are indicated as thick blue bars, introns are thin blue connectors. Coloured boxes indicate annotated TEs. Plots of sequence identity range from 50 to 100% on the y-axis in the LAGAN multi-panels.

Evolutionary relationships among grapevine F3'5'Hs. Phylogenetic trees are inferred using the Maximum Parsimony method and are based on (a) mRNA sequence alignments of all grapevine F3'5'Hs and (b) intron sequences of F3'5'Hs that reside in duplicate blocks on chr6. The most parsimonious tree was obtained using the Close-Neighbor-Interchange algori...

Amino acid alignment of substrate recognition sites (SRS) and functional domains for hydroxylation activity (CR1) in plant F3'5'Hs. Amino acid positions crucial for 3' vs. 3'5'-hydroxylation in CR1 and SRS6 are indicated by black arrows; significant amino acid substitutions in grapevine F3'5'Hs are in green background. Relevant amino acid substitut...

Transcripts of duplicate F3'5'Hs detected in various organs of two grape cultivars by semiquantitative PCR. Bold + indicates high expression of PCR amplicons visualised on agarose gel stained with ethidium bromide (see Figure 7), regular + indicates weak expression detected only by the more sensitive silver staining, - indicates lack of detectable...

Expression of duplicate F3'5'Hs in berry skin of four cultivars accumulating 3'5'-OH anthocyanins detected by semiquantitative PCR. Berry skin was sampled at four developmental stages. cDNA was normalised using the housekeeping Ubiquitin gene. UFGT was used as a marker for anthocyanin gene expression. Even though the pre-veraison berries were sampl...

Chromosomal positions of F3'Hs and F3'5'Hs in the grapevine genome.

Lack of gene collinearity around the isolated F3'5'Hp on chr8 and the F3'5'H multi-copy array on chr6. The positions of F3'5'Hs are shown as cyan ticks, gene models are shown in blue, and partial peptides are shown in grey, above and below the corresponding GEvo diagrams. Regions of sequence similarity were identified by comparing both DNA strands...

Genome landscape in a 10-kb window around F3'5'Hs in the chr6 array. Exons are indicated as thick blue bars, introns are thin blue connectors. Coloured models indicate annotated TEs. Sequence gaps (Ns) in the PN40024 genome assembly are indicated by dotted red lines.

Genomic organisation and transcription of two copies of F3'Hs present in the grapevine genome. In section a, exon/intron structure of F3'Hs is shown as blue boxes (exons) connected by blue lines (introns); TEs are shown as coloured boxes. In section b and c, selective amplification of exon junctions astride the terminal intron and expression of eac...

Multiple alignments of non-coding DNA within each of 9 tandemly duplicated blocks in the F3'5'H locus on chr6. On top of each page, coloured bars indicate annotated TEs in the PN40024 genome; sequence gaps (Ns) in the genome assembly are indicated by dotted red lines. Plots of sequence identity range from 50 to 100% on the y-axis in the LAGAN multi...

Analysis of variance of duplicate F3'5'H expression in berry skin of four cultivars along eight developmental stages.

Berry sampling in four red-skinned cultivars and a green-skinned cultivar (Tocai) across eight developmental stages.

Conservation and SSCP polymorphisms of duplicate F3'5'Hs in the family Vitaceae. PCR amplicons were obtained from genomic DNA using copy-specific primers. DNA samples included the ornamental grapevines Virginia creeper Parthenocissus quinquefolia, native to Northeastern-America, and the porcelain berry Ampelopsis brevipedunculata, native to tempera...

Primer sequences for grapevine F3'Hs and F3'5'Hs.

Flavonoid 3',5'-hydroxylases (F3'5'Hs) and flavonoid 3'-hydroxylases (F3'Hs) competitively control the synthesis of delphinidin and cyanidin, the precursors of blue and red anthocyanins. In most plants, F3'5'H genes are present in low-copy number, but in grapevine they are highly redundant. The first increase in F3'5'H copy number occurred in the p...

In the context of the sequencing project for the grapevine reference genome sequence, two genetic maps were completed with SSR markers in order to align the sequence contigs of the Vv12X.0 version of the genome assembly along the chromosomes. For this purpose, two full-sib families, 'Syrah' x 'Grenache' (SxG, 192 individuals) and 'Chardonnay' x 'Bi...

Natural disease resistance is a cost-effective and environmentally friendly way of controlling plant disease. Breeding programmes need to make sure that the resistance deployed is effective and durable. Grapevine downy mildew, caused by the Oomycete Plasmopara viticola, affects viticulture and it is controlled with pesticides. Downy mildew resistan...