Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics

Novel loci associated with resistance to downy and powdery mildew in grapevine

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.

Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r² was between 0.45 and 0.2 and became flat when r² was 0.05. The average LD decay for the entire genome was 30 kb when r^2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.

VaAPRT3 Gene is Associated With Sex Determination in Vitis amurensis

In the past decade, progress has been made in sex determination mechanism in Vitis. However, genes responsible for sexual differentiation and its mechanism in V. amurensis remain unknown. Here, we identify a sex determination candidate gene coding adenine phosphoribosyl transferase 3 (VaAPRT3) in V. amurensis. Cloning and sequencing of the VaAPRT3 gene allowed us to develop a molecular marker able to discriminate female individuals from males or hermaphrodites based on a 22-bp InDel. Gene expression and endogenous cytokinin content analysis revealed that the VaAPRT3 gene is involved in sex determination or, to be precise, in female organ differentiation, through regulating cytokinin metabolism in V. amurensis. This study enlarged the understanding of sex determination mechanism in the genus Vitis, and the sex marker could be used as a helpful tool for sexual identification in breeding programs as well as in investigation and collection of V. amurensis germplasms.

Fine Mapping of Leaf Trichome Density Revealed a 747-kb Region on Chromosome 1 in Cold-Hardy Hybrid Wine Grape Populations

Segregation for leaf trichome density was observed in a cold-hardy hybrid grape population GE1025 (N = ∼125, MN1264 × MN1246) that was previously used to detect a quantitative trait locus (QTL) underlying foliar phylloxera resistance on chromosome 14. Our hypothesis was that high trichome density was associated with resistance to phylloxera. Existing literature found trichome density QTL on chromosomes 1 and 15 using a hybrid grape population of "Horizon" × Illinois 547-1 and suggested a few candidate genes. To validate the reported QTL and our hypothesis, interval mapping was conducted in GE1025 with previous genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) genotype data and phenotypic scores collected using a 0-6 trichome density scale at several leaf positions. Evaluations were done on replicated forced dormant cuttings in 2 years and on field-grown leaves in 1 year. There was no strong relationship between trichome density and phylloxera resistance except for a Pearson's correlation (r) of about -0.2 between a few trichome density traits and phylloxera severity traits at 2 and 3 weeks after infestation. Two genetic regions were repeatedly detected for multiple trichome density traits: from 10 to 20.7 Mbp (∼10 Mbp) on chromosome 1 for ribbon and simple density traits and from 2.4 to 8.9 Mbp on chromosome 10 for ribbon density traits, explaining 12.1-48.2 and 12.6-27.5% of phenotypic variation, respectively. To fine map, we genotyped a larger population, GE1783 (N = ∼1,023, MN1264 × MN1246), with conserved rhAmpSeq haplotype markers across multiple Vitis species and phenotyped 233 selected potential recombinants. Evaluations were conducted on field-grown leaves in a single year. The QTL for ribbon trichome density on adaxial vein and adaxial leaf and simple density on abaxial vein was fine mapped to 12.63-13.38 Mbp (747 kb) on chromosome 1. We found variations of MN1264 and MN1246 at candidate genes NAC transcription factor 29, EF-hand protein, and MYB140 in this region and three other surrounding candidate genes proposed previously. Even though no strong relationship between foliar phylloxera resistance and trichome density was found, this study validated and fine mapped a major QTL for trichome density using a cold-hardy hybrid grape population and shed light on a few candidate genes that have implications for different breeding programs.

Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs

The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.

New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

BACKGROUND

Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera 'Red Globe' × 'Muscat Hamburg' was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes.

RESULTS

A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs.

CONCLUSION

These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.

Ecology and Genetics of Natural Populations of North American Vitis Species Used as Rootstocks in European Grapevine Breeding Programs

Three North American Vitis species (V. riparia, V. berlandieri, V. rupestris) became widely used in rootstock breeding programs following the expansion of North American pests and diseases introduced in vineyards of the world during the 19th century. When they escape, they become feral in the most dynamic parts of Mediterranean floodplains. To better understand this ongoing process, we studied the ecology of Vitis species in their native sympatric range. We analyzed in deep 61 plots of 710 m2 containing Vitaceae species along 216 km of the Buffalo River and adjacent plateaus (Arkansas, United States). We investigated the populations structure and genetics of the Vitis complex (i.e., possible hybrids and the Vitis species) and the sharing of habitats with other Vitaceae (Muscadinia rotundifolia and Parthenocissus quinquefolia). Vitaceae share space according to their life strategies and microhabitat along ecological gradients. The plateau niche seems optimal for V. berlandieri and V. aestivalis. V. berlandieri is also found in alluvial zones. The most erosive parts of the river are colonized by V. rupestris, whereas the first terraces include most of the M. rotundifolia populations. Vitis riparia and Parthenocissus live in the largest range of forest habitats, from plateaus to alluvial forests, and from the forest floor to the canopy, with the highest densities along the river. Interestingly, natural hybridization can occur, but establishment success is rare and limited to alluvial forests. In their native range, these populations are controlled by biotic and abiotic conditions. In Europe, the biotic relations among species are different. Our study shows that V. riparia and its hybrids could be the best candidates for a large scale invasion.

Characterization of genetic determinants of the resistance to phylloxera, Daktulosphaira vitifoliae, and the dagger nematode Xiphinema index from muscadine background

BACKGROUND

Muscadine (Muscadinia rotundifolia) is known as a resistance source to many pests and diseases in grapevine. The genetics of its resistance to two major grapevine pests, the phylloxera D. vitifoliae and the dagger nematode X. index, vector of the Grapevine fanleaf virus (GFLV), was investigated in a backcross progeny between the F1 resistant hybrid material VRH8771 (Vitis-Muscadinia) derived from the muscadine R source 'NC184-4' and V. vinifera cv. 'Cabernet-Sauvignon' (CS).

RESULTS

In this pseudo-testcross, parental maps were constructed using simple-sequence repeats markers and single nucleotide polymorphism markers from a GBS approach. For the VRH8771 map, 2271 SNP and 135 SSR markers were assembled, resulting in 19 linkage groups (LG) and an average distance between markers of 0.98 cM. Phylloxera resistance was assessed by monitoring root nodosity number in an in planta experiment and larval development in a root in vitro assay. Nematode resistance was studied using 10-12 month long tests for the selection of durable resistance and rating criteria based on nematode reproduction factor and gall index. A major QTL for phylloxera larval development, explaining more than 70% of the total variance and co-localizing with a QTL for nodosity number, was identified on LG 7 and designated RDV6. Additional QTLs were detected on LG 3 (RDV7) and LG 10 (RDV8), depending on the in planta or in vitro experiments, suggesting that various loci may influence or modulate nodosity formation and larval development. Using a Bulked Segregant Analysis approach and a proportion test, markers clustered in three regions on LG 9, LG 10 and LG 18 were shown to be associated to the nematode resistant phenotype. QTL analysis confirmed the results and QTLs were thus designated respectively XiR2, XiR3 and XiR4, although a LOD-score below the significant threshold value was obtained for the QTL on LG 18.

CONCLUSIONS

Based on a high-resolution linkage map and a segregating grapevine backcross progeny, the first QTLs for resistance to D. vitifoliae and to X. index were identified from a muscadine source. All together these results open the way to the development of marker-assisted selection in grapevine rootstock breeding programs based on muscadine derived resistance to phylloxera and to X. index in order to delay GFLV transmission.

High-density genetic linkage-map construction of hawthorn and QTL mapping for important fruit traits

Few reports exist on QTL mapping of the important economic traits of hawthorn. We hybridized the cultivars ‘Shandongdamianqiu’ (female parent) and ‘Xinbinruanzi’ (male parent), and 130 F₁ individuals and the two parents were used for RAD-seq, SNP development, and high-density linkage map construction. Three genetic maps were obtained, one for each of the parents and an integrated one. In these three maps, 17 linkage groups were constructed. The female and male parent maps contained 2657 and 4088 SNP markers, respectively, and had genetic distances of 2689.65 and 2558.41 cM, respectively, whereas the integrated map was 2470.02 cM, and contained 6,384 SNP markers. QTL mapping based on six agronomic traits, namely fruit transverse diameter, vertical diameter, single fruit weight, pericarp brittleness, pericarp puncture hardness, and average sarcocarp firmness were conducted, and 25 QTLs were detected in seven linkage groups. Explained phenotypic variation rate ranged from 17.7% to 35%. This genetic map contains the largest number of molecular markers ever obtained from hawthorn and will provide an important future reference for fine QTL mapping of economic traits and molecular assisted selection of hawthorn.

Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators

BACKGROUND

Grapevine is a crop of major economic importance, yet little is known about the regulation of shoot development in grapevine or other perennial fruits crops. Here we combine genetic and genomic tools to identify candidate genes regulating shoot development in Vitis spp.

RESULTS

An F2 population from an interspecific cross between V. vinifera and V. riparia was phenotyped for shoot development traits, and three Quantitative Trait Loci (QTLs) were identified on linkage groups (LGs) 7, 14 and 18. Around 17% of the individuals exhibited a dwarfed phenotype. A transcriptomic study identified four candidate genes that were not expressed in dwarfed individuals and located within the confidence interval of the QTL on LG7. A deletion of 84,482 bp was identified in the genome of dwarfed plants, which included these four not expressed genes. One of these genes was VviCURLY LEAF (VviCLF), an orthologue of CLF, a regulator of shoot development in Arabidopsis thaliana.

CONCLUSIONS

The phenotype of the dwarfed grapevine plants was similar to that of clf mutants of A. thaliana and orthologues of the known targets of CLF in A. thaliana were differentially expressed in the dwarfed plants. This suggests that CLF, a major developmental regulator in A. thaliana, also controls shoot development in grapevine.

Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops

The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.

Introgression reshapes recombination distribution in grapevine interspecific hybrids

In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous. Vitis rotundifolia, an American species related to the cultivated European grapevine Vitis vinifera, has a high level of resistance to several grapevine major diseases and is consequently a valuable resource for grape breeding. However, crosses between both species most often lead to very few poorly fertile hybrids. In this context, identifying genetic and genomic features that make cross-breeding between both species difficult is essential. To this end, three mapping populations were generated by pseudo-backcrosses using V. rotundifolia as the donor parent and several V. vinifera cultivars as the recurrent parents. Genotyping-by-sequencing was used to establish high-density genetic linkage maps and to determine the genetic composition of the chromosomes of each individual. A good collinearity of the SNP positions was observed between parental maps, confirming the synteny between both species, except on lower arm of chromosome 7. Interestingly, recombination rate in V. rotundifolia × V. vinifera interspecific hybrids depends on the length of the introgressed region. It is similar to grapevine for chromosome pairs entirely homeologous. Conversely, for chromosome pairs partly homeologous, recombination is suppressed in the homeologous regions, whereas it is enhanced in the homologous ones. This balance leads to the conservation of the total genetic length of each chromosome between V. vinifera and hybrid maps, whatever the backcross level and the proportion of homeologous region. Altogether, these results provide new insight to optimize the use of V. rotundifolia in grape breeding and, more generally, to improve the introgression of gene of interest from wild species related to crops.

The Rpv3-3 Haplotype and Stilbenoid Induction Mediate Downy Mildew Resistance in a Grapevine Interspecific Population

The development of new resistant varieties to the oomycete Plasmopara viticola (Berk.& Curt) is a promising way to combat downy mildew (DM), one of the major diseases threatening the cultivated grapevine (Vitis vinifera L.). Taking advantage of a segregating population derived from "Merzling" (a mid-resistant hybrid) and "Teroldego" (a susceptible landrace), 136 F1 individuals were characterized by combining genetic, phenotypic, and gene expression data to elucidate the genetic basis of DM resistance and polyphenol biosynthesis upon P. viticola infection. An improved consensus linkage map was obtained by scoring 192 microsatellite markers. The progeny were screened for DM resistance and production of 42 polyphenols. QTL mapping showed that DM resistance is associated with the herein named Rpv3-3 specific haplotype and it identified 46 novel metabolic QTLs linked to 30 phenolics-related parameters. A list of the 95 most relevant candidate genes was generated by specifically exploring the stilbenoid-associated QTLs. Expression analysis of 11 genes in Rpv3-3 +/- genotypes displaying disparity in DM resistance level and stilbenoid accumulation revealed significant new candidates for the genetic control of stilbenoid biosynthesis and oligomerization. These overall findings emphasized that DM resistance is likely mediated by the major Rpv3-3 haplotype and stilbenoid induction.

Armenian national grapevine collection: Conservation, characterization and prospects

The general strategy for grapevine genetic resources conservation in Armenia encompasses the collection of the still existing diversity and the use of protection techniques to minimize the losses over time. Being studied mainly by ampelography, the genetic diversity of Armenian grapevine needs to be re-investigated in accordance with modern requirements and international scales. The purpose of the presented research was the first large-scale molecular characterization of Armenian grape varieties by molecular methods using a set of 24 simple sequence repeat (SSR) markers encompassing the nine SSR markers recommended by the European project GrapeGen06. The obtained results indicate the uniqueness of the major part of the investigated varieties and reveal a substantial level of genetic variation within the Armenian grapevine. Based on the realized large-scale investigation a true-to-type inventory of Armenian grape germplasm will be realized and documented in theVitis International Variety Catalogue and in the European Vitisdatabase. The next step having strategic importance in terms of conservation of grape genetic resources in Armenia will be establishment of the first ArmenianVitis database with multi-crop passport description of all varieties preserved in grape collection.

Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing

BACKGROUND

High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding. Development of a large set of single nucleotide polymorphisms (SNPs) via next-generation sequencing (NGS)-based methods, restriction-site associated DNA sequencing (RAD-seq), and the generation of a highly saturated genetic map help improve fine mapping of quantitative trait loci (QTL).

RESULTS

We generated a highly saturated genetic map to identify significant traits in two elite grape cultivars and 176 F₁ plants. In total, 1,426,967 high-quality restriction site-associated DNA tags were detected; 51,365, 23,683, and 70,061 markers were assessed in 19 linkage groups (LGs) for the maternal, paternal, and integrated maps, respectively. Our map was highly saturated in terms of marker density and average "Gap ≤ 5 cM" percentage.

CONCLUSIONS

In this study, RAD-seq of 176 F₁ plants and their parents yielded 8,481,484 SNPs and 1,646,131 InDel markers, of which 65,229 and 4832, respectively, were used to construct a highly saturated genetic map for grapevine. This map is expected to facilitate genetic studies on grapevine, including an evaluation of grapevine and deciphering the genetic basis of economically and agronomically important traits. Our findings provide basic essential genetic data the grapevine genetic research community, which will lead to improvements in grapevine breeding.

Mutation rate analysis via parent-progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent–offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination–heterozygozity correlation in peach, we caution against such an interpretation.

The table grape 'Victoria' with a long shaped berry: a potential mutation with attractive characteristics for consumers

BACKGROUND

Puglia is the most important region in Italy for table grape production. Since consumers look for new products, the number of table grape varieties has greatly increased in recent years.

RESULTS

In a survey in the Puglia region, we identified several years ago a potential mutation of the cv. Victoria. We described this accession in comparison with the standard Victoria for some amphelographic traits. All the characteristics were very similar to the standard Victoria except for the berry shape, which was significantly more elongated. Moreover, the berry of the mutated Victoria showed higher firmness, lightness and chroma than the standard one, with a more intense yellow colour of the skin (appreciated by consumers). The molecular characterisation with 25 SSR markers showed that normal and mutant Victoria were genetically identical at all the analysed loci, thus suggesting that the two accessions could be considered as clones with the difference in berry shape probably due to a somatic mutation.

CONCLUSIONS

This mutation of the cv. Victoria may have interesting perspective for the market since consumers are always attracted by different shape and colour of the fruits (consumers buy with eyes). This accession can be an alternative clone of the already known standard Victoria. © 2017 Society of Chemical Industry.

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F₁ families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from 'Seyval blanc', through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.

Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.

The Tubulin-Based-Polymorphism Method Provides a Simple and Effective Alternative to the Genomic Profiling of Grape

The TBP (Tubulin-Based-Polymorphism) method, based on a nuclear ILP (Intron-Length-Polymorphism) molecular marker, has been used for genotyping 37 accessions of the genus Vitis inclusive of different species, rootstocks, wild and cultivated subspecies. A distinct DNA barcode made up by a different number of amplicons, was attributed to each of the different accessions. TBP data were compared with those obtained, with the use of an internationally validated set of six SSR markers. Genetic relationships among the different accessions, dendrogram distributions, correlation values and polymorphic index values (PICs) were definitively comparable when not in favor of TBP. Such an experimental consistency is based upon a genomic organization of the multiple members of the β-tubulin gene family, the targets of TBP-mediated amplification, that is conserved in Vitis as in any other plant species. The TBP amplicons can actually be used as a useful source of sequence polymorphisms for generating primer pairs capable of identifying specific cultivars in a simple assay. An example for the identification of the ‘Sangiovese’ cv. is reported. More generally, these data are discussed in terms of the actual advantages that the introduction of the TBP method in the field of grape characterization and genotyping can provide.

Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family

In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F₁ families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing (GBS) technology in an F₂ mapping family of 424 progeny derived from a cross between the wild species V. riparia Michx. and the interspecific hybrid winegrape cultivar, ‘Seyval’. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, covering 95% of the genome with an average distance between markers of 1.67 cM. Compared to an SSR map previously developed for this F₂ family, these results represent an improved map covering a greater portion of the genome with higher marker density. The accuracy of the map was validated using the well-studied trait berry color. QTL affecting YAN, MA and SS related traits were detected. A joint MA and SS QTL spans a region with candidate genes involved in the malate metabolism pathway. We present an analytical pipeline for calling intercross GBS markers and a high-density linkage map for a large F₂ family of the highly heterozygous Vitis genus. This study serves as a model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and to enhance the breeding process by marker-assisted selection. The GBS protocols for identifying intercross markers developed in this study can be adapted for other heterozygous species.

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

BACKGROUND

Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis.

RESULTS

We first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number.

CONCLUSION

Slow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials.

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine

Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.

Genetic diversity of wild and cultivated grapevine accessions from southeast Turkey

Wild grapevine genetic diversity in southeast Turkey has not been documented to date. In the present work, in order to clarify the relationships between wild and cultivated grape accessions from southeastern Turkey, 22 nuclear and three chloroplast microsatellite loci were used on 21 wild grapevine Vitis vinifera L. ssp. sylvestris (Gmelin) and 13 cultivated grapevine Vitis vinifera ssp. sativa accessions. The number of alleles per SSR locus ranged from 4 (VVIn16) to 20 (VVIv67) and the mean allele number per locus was 10.09. Expected locus heterozygosity ranged from 0.586 (locus VVIb01) to 0.898 (locus (VVIv67)). The three cpSSR molecular markers presented variation in size both in cultivars and in wild Turkish accessions. Two size variants were detected for cpSSR3 (106 and 107 bp) for cpSSR5 (104 and 105 bp), and for cpSSR10 (115 and 116 bp). The six alleles in wild grapevines fell into three haplotypes B, C and D. A genetic structure according to accessions taxonomic status (wild or cultivated) was revealed by UPGMA analysis. This highlighted a clear separation between domesticated and wild accessions in Turkish germplasm. The results pointed out the need to further collect and characterize this wild and cultivated grapevine germplasm.

Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries

BACKGROUND

QTLs controlling individual sugars and acids (fructose, glucose, malic acid and tartaric acid) in grape berries have not yet been identified. The present study aimed to construct a high-density, high-quality genetic map of a winemaking grape cross with a complex parentage (V. vinifera × V. amurensis) × ((V. labrusca × V. riparia) × V. vinifera), using next-generation restriction site-associated DNA sequencing, and then to identify loci related to phenotypic variability over three years.

RESULTS

In total, 1 826 SNP-based markers were developed. Of these, 621 markers were assembled into 19 linkage groups (LGs) for the maternal map, 696 for the paternal map, and 1 254 for the integrated map. Markers showed good linear agreement on most chromosomes between our genetic maps and the previously published V. vinifera reference sequence. However marker order was different in some chromosome regions, indicating both conservation and variation within the genome. Despite the identification of a range of QTLs controlling the traits of interest, these QTLs explained a relatively small percentage of the observed phenotypic variance. Although they exhibited a large degree of instability from year to year, QTLs were identified for all traits but tartaric acid and titratable acidity in the three years of the study; however only the QTLs for malic acid and β ratio (tartaric acid-to-malic acid ratio) were stable in two years. QTLs related to sugars were located within ten LGs (01, 02, 03, 04, 07, 09, 11, 14, 17, 18), and those related to acids within three LGs (06, 13, 18). Overlapping QTLs in LG14 were observed for fructose, glucose and total sugar. Malic acid, total acid and β ratio each had several QTLs in LG18, and malic acid also had a QTL in LG06. A set of 10 genes underlying these QTLs may be involved in determining the malic acid content of berries.

CONCLUSION

The genetic map constructed in this study is potentially a high-density, high-quality map, which could be used for QTL detection, genome comparison, and sequence assembly. It may also serve to broaden our understanding of the grape genome.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.)

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

Genetic variation in a grapevine progeny (Vitis vinifera L. cvs Grenache×Syrah) reveals inconsistencies between maintenance of daytime leaf water potential and response of transpiration rate under drought

In the face of water stress, plants evolved with different abilities to limit the decrease in leaf water potential, notably in the daytime (ΨM). So-called isohydric species efficiently maintain high ΨM, whereas anisohydric species cannot prevent ΨM from dropping as soil water deficit develops. The genetic and physiological origins of these differences in (an)isohydric behaviours remain to be clarified. This is of particular interest within species such as Vitis vinifera L. where continuous variation in the level of isohydry has been observed among cultivars. With this objective, a 2 year experiment was conducted on the pseudo-F1 progeny from a cross between the two widespread cultivars Syrah and Grenache using a phenotyping platform coupled to a controlled-environment chamber. Potted plants of all the progeny were analysed for ΨM, transpiration rate, and soil-to-leaf hydraulic conductance, under both well-watered and water deficit conditions. A high genetic variability was found for all the above traits. Four quantitative trait loci (QTLs) were detected for ΨM under water deficit conditions, and 28 other QTLs were detected for the different traits in either condition. Genetic variation in ΨM maintenance under water deficit weakly correlated with drought-induced reduction in transpiration rate in the progeny, and QTLs for both traits did not completely co-localize. This indicates that genetic variation in the control of ΨM under water deficit was not due simply to variation in transpiration sensitivity to soil drying. Possible origins of the diversity in (an)isohydric behaviours in grapevine are discussed on the basis of concurrent variations in soil-to-leaf hydraulic conductance and stomatal control of transpiration.

QTL analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in Vitis

In the recent past, genetic analyses of grapevine focused mainly on the identification of resistance loci for major diseases such as powdery and downy mildew. Currently, breeding programs make intensive use of these results by applying molecular markers linked to the resistance traits. However, modern genetics also allows to address additional agronomic traits that have considerable impact on the selection of grapevine cultivars. In this study, we have used linkage mapping for the identification and characterization of flowering time and ripening traits in a mapping population from a cross of V3125 ('Schiava Grossa' × 'Riesling') and the interspecific rootstock cultivar 'Börner' (Vitis riparia × Vitis cinerea). Comparison of the flowering time QTL mapping with data derived from a second independent segregating population identified several common QTLs. Especially a large region on linkage group 1 proved to be of special interest given the genetic divergence of the parents of the two populations. The proximity of the QTL region contains two CONSTANS-like genes. In accordance with data from other plants such as Arabidopsis thaliana and Oryza sativa, we hypothesize that these genes are major contributors to control the time of flowering in Vitis.

Haplotype diversity of VvTFL1A gene and association with cluster traits in grapevine (V. vinifera)

BACKGROUND

Interaction between TERMINAL FLOWER 1 (TFL1) and LEAFY (LFY) seem to determine the inflorescence architecture in Arabidopsis. In a parallel way, overexpression of VvTFL1A, a grapevine TFL1 homolog, causes delayed flowering and production of a ramose cluster in the reiterated reproductive meristem (RRM) somatic variant of cultivar Carignan. To analyze the possible contribution of this gene to cluster phenotypic variation in a diversity panel of cultivated grapevine (Vitis vinifera L. subsp. vinifera) its nucleotide diversity was characterized and association analyses among detected sequence polymorphisms and phenology and cluster traits was carried out.

RESULTS

A total of 3.6 kb of the VvTFL1A gene, including its promoter, was sequenced in a core collection of 140 individuals designed to maximize phenotypic variation at agronomical relevant traits. Nucleotide variation for VvTFL1A within this collection was higher in the promoter and intron sequences than in the exon regions; where few polymorphisms were located in agreement with a high conservation of coding sequence. Characterization of the VvTFL1A haplotype network identified three major haplogroups, consistent with the geographic origins and the use of the cultivars that could correspond to three major ancestral alleles or evolutionary branches, based on the existence of mutations in linkage disequilibrium. Genetic association studies with cluster traits revealed the presence of major INDEL polymorphisms, explaining 16%, 13% and 25% of flowering time, cluster width and berry weight, respectively, and also structuring the three haplogroups.

CONCLUSIONS

At least three major VvTFL1A haplogroups are present in cultivated grapevines, which are defined by the presence of three main polymorphism LD blocks and associated to characteristic phenotypic values for flowering time, cluster width and berry size. Phenotypic differences between haplogroups are consistent with differences observed between Eastern and Western grapevine cultivars and could result from the use of different genetic pools in the domestication process as well as different selection pressures on the development of table and wine cultivars, respectively. Altogether, these results are coherent with previous classifications of grapevine phenotypic diversity mainly based on cluster and berry morphotypes as well as with recent results on the structure of genetic diversity in cultivated grapevine.

SSR and SRAP marker-based linkage map of Vitis vinifera L

An F1 population was created by the cross ‘87-1’ × ‘9-22’. The female parent ‘87-1’ was an extremely early maturing cultivar with strong flavour. The male parent was an excellent breeding line producing large berries maturing late. The mapping population included 149 randomly chosen individuals. Molecular genetic map for each parent and the consensus map were constructed using simple sequence repeat and sequence-related amplified polymorphism markers by software JoinMap 3.0. The ‘87-1’ map covers a total length of 1272.9 cM distributed in 21 linkage groups and consists of 163 molecular markers with an average distance between adjacent markers of 8.9 cM. The ‘9-22’ map covers a total length of 1267.4 cM distributed in 20 linkage groups and consists of 158 molecular markers with an average distance between adjacent markers of 9.1 cM. The consensus map covers a total length of 1537.1 cM distributed in 21 linkage groups and one doublet and consists of 217 molecular markers with an average distance of 7.8 cM between adjacent markers. The length of the linkage groups is 69.8 cM on average. The map covers the 19 chromosomes of the Vitis genome and can lay a solid foundation for further studies such as quantative trait loci (QTL) mapping of correlated traits and marker-assisted selection.

QTL mapping of black rot (Guignardia bidwellii) resistance in the grapevine rootstock 'Börner' (V. riparia Gm183 × V. cinerea Arnold)

In the grapevine cultivar 'Börner' QTLs for black rot resistance were detected consistently in several independent experiments. For one QTL on chromosome 14 closely linked markers were developed and a detailed map provided. Black rot is a serious grapevine disease that causes substantial yield loss under unfavourable conditions. All traditional European grapevine cultivars are susceptible to the causative fungus Guignardia bidwellii which is native to North America. The cultivar 'Börner', an interspecific hybrid of V. riparia and V. cinerea, shows a high resistance to black rot. Therefore, a mapping population derived from the cross of the susceptible breeding line V3125 ('Schiava grossa' × 'Riesling') with 'Börner' was used to carry out QTL analysis. A resistance test was established based on potted plants which were artificially inoculated in a climate chamber with in vitro produced G. bidwellii spores. Several rating systems were developed and tested. Finally, a five class scheme was applied for scoring the level of resistance. A major QTL was detected based on a previously constructed genetic map and data from six independent resistance tests in the climate chamber and one rating of natural infections in the field. The QTL is located on linkage group 14 (Rgb1) and explained up to 21.8 % of the phenotypic variation (LOD 10.5). A second stable QTL mapped on linkage group 16 (Rgb2; LOD 4.2) and explained 8.5 % of the phenotypic variation. These two QTLs together with several minor QTLs observed on the integrated map indicate a polygenic nature of the black rot resistance in 'Börner'. A detailed genetic map is presented for the locus Rgb1 with tightly linked markers valuable for the development for marker-assisted selection for black rot resistance in grapevine breeding.

Detection of new genetic profiles and allelic variants in improperly classified grapevine accessions

Thirty-seven grapevine accessions, collected in Central Italy, were characterized by morphological and genetic analysis, according to guidelines developed by European Union programs of grapevine research and standardization. Traditional denominations of some sampled varieties were revealed to be incorrect; moreover, 10 synonymies and 12 homonymies were recognized. Ampelographic and ampelometric measurements of leaf characters were performed. These data generated a phenotypic similarity matrix and a relative diagram showing morphological differences between specimens. Many samples presented different morphology even in the presence of the same genotype, probably as a result of various environmental pressures. Grapevines were typed by 12 microsatellite loci and then compared with the CRA-VIT genetic resource database. Twenty-five SSR profiles were clearly identified as well-known cultivars, while nine genotypes did not find a direct correspondence: these samples could represent putative new autochthonous Latial Vitis vinifera cultivars or hybrid varieties. The genetic approach also detected three new (169 and 173 in VVMD27 locus; 179 in ISV2 locus) and seven rare allelic variants. Plant sample classification by oral history, morphological observations, and molecular results were compared and discussed. Scions of samples were planted in the Botanic Garden of the University of Rome “Tor Vergata”, to preserve grapevine biodiversity and to protect possible new autochthonous varieties.

Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map

Improved efficacy and durability of powdery mildew resistance can be enhanced via knowledge of the genetics of resistance and susceptibility coupled with the development of high-resolution maps to facilitate the stacking of multiple resistance genes and other desirable traits. We studied the inheritance of powdery mildew (Erysiphe necator) resistance and susceptibility of wild Vitis rupestris B38 and cultivated V. vinifera 'Chardonnay', finding evidence for quantitative variation. Molecular markers were identified using genotyping-by-sequencing, resulting in 16,833 single nucleotide polymorphisms (SNPs) based on alignment to the V. vinifera 'PN40024' reference genome sequence. With an average density of 36 SNPs/Mbp and uniform coverage of the genome, this 17K set was used to identify 11 SNPs on chromosome 7 associated with a resistance locus from V. rupestris B38 and ten SNPs on chromosome 9 associated with a locus for susceptibility from 'Chardonnay' using single marker association and linkage disequilibrium analysis. Linkage maps for V. rupestris B38 (1,146 SNPs) and 'Chardonnay' (1,215 SNPs) were constructed and used to corroborate the 'Chardonnay' locus named Sen1 (Susceptibility to Erysiphe necator 1), providing the first insight into the genetics of susceptibility to powdery mildew from V. vinifera. The identification of markers associated with a susceptibility locus in a V. vinifera background can be used for negative selection among breeding progenies. This work improves our understanding of the nature of powdery mildew resistance in V. rupestris B38 and 'Chardonnay', while applying next-generation sequencing tools to advance grapevine genomics and breeding.

Selection of candidate genes for grape proanthocyanidin pathway by an integrative approach

Proanthocyanidins (PA) play a major role in plant protection against biotic and abiotic stresses. Moreover these molecules are known to be beneficial for human health and are responsible for astringency of foods and beverages such as wine and thus have a great impact on the final quality of the product. Genes playing a role in the PA pathway are only partially known. The amount of available transcriptomic and genetic data to select candidate genes without a priori knowledge from orthologous function increases every day. However, the methods used so far generate so many candidate genes that it is impossible to validate all of them. In this study, we used an integrative strategy based on different screening methods to select a reduced list of candidate genes. We have crossed results from different screening methods including QTL mapping and three transcriptomic studies to select 20 candidate genes, located in QTL intervals and fulfilling at least two transcriptomic screenings. This list includes three glucosyltransferases, already suspected to have a role in the PA biosynthetic pathway. Among the 17 remaining genes, we selected three genes to perform further analysis by association genetic studies. For each of these genes, we found a polymorphism linked to PA variation. The three genes (VvMybC2-L1, VvGAT-like and VvCob-like), not previously known to play a role in PA synthesis, are promising candidates for further molecular physiology studies.

Evaluating the Polyphenol Profile in Three Segregating Grape (Vitis vinifera L.) Populations

This paper explores the characteristics of the anthocyanin and flavonol composition and content in grapes from plants resulting from intraspecific crosses of Vitis vinifera varieties Monastrell × Cabernet Sauvignon, Monastrell × Syrah, and Monastrell × Barbera, in order to acquire information for future breeding programs. The anthocyanin and flavonol compositions of twenty-seven hybrids bearing red grapes and 15 hybrids bearing white grapes from Monastrell × Syrah, 32 red and 6 white from Monastrell × Cabernet Sauvignon, and 13 red from Monastrell × Barbera have been studied. Among the intraspecific crosses, plants with grapes presenting very high concentrations of anthocyanins and flavonols were found, indicating a transgressive segregation for this character, and this could lead to highly colored wines with an increased benefits for human health. As regards the qualitative composition of anthocyanins and flavonols, the hydroxylation pattern of the hybrids that also may influence wine color hue and stability presented intermediate values to those of the parentals, indicating that values higher than that showed by the best parental in this respect will be difficult to obtain. The results presented here can be helpful to acquire information for future breeding efforts, aimed at improving fruit quality through the effects of flavonoids.

Mapping genetic loci for tolerance to lime-induced iron deficiency chlorosis in grapevine rootstocks (Vitis sp.)

Iron is essential to plants for chlorophyll formation as well as for the functioning of various iron-containing enzymes. Iron deficiency chlorosis is a wide-spread disorder of plants, in particular, of those growing on calcareous soils. Among the different ways to control iron deficiency problems for crops, plant material and especially rootstock breeding is a suitable and reliable method, especially for fruit trees and grapes. The aim of the experiment was to characterize the genetic basis of grapevine chlorosis tolerance under lime stress conditions. A segregating population of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera Cabernet Sauvignon (tolerant) × V. riparia Gloire de Montpellier (sensitive) was developed and phenotyped both as cuttings and as rootstock grafted with Cabernet Sauvignon scions in pots containing non-chlorosing and chlorosing soils. Tolerance was evaluated by chlorosis score, leaf chlorophyll content and growth parameters of the shoots and roots. The experiments were performed in 2001, 2003 and 2006. The plants analysed in 2006 were reassessed in 2007. The most significant findings of the trial were: (a) the soil properties strongly affect plant development, (b) there are differences in tolerance among segregating genotypes when grown as cuttings or as rootstocks on calcareous soil, (c) calcareous conditions induced chlorosis and revealed quantitative trait loci (QTLs) implicated in polygenic control of tolerance, (d) rootstock strongly contributes to lime-induced chlorosis response, and (e) a QTL with strong effect (from 10 to 25 % of the chlorotic symptom variance) was identified on chromosome 13. This QTL colocalized with a QTL for chlorophyll content (R (2) = 22 %) and a major QTL for plant development that explains about 50 % of both aerial and root system biomass variation. These findings were supported by stable results among the different years of experiment. These results open new insights into the genetic control of chlorosis tolerance and could aid the development of iron chlorosis-tolerant rootstocks.

A reference genetic map of Muscadinia rotundifolia and identification of Ren5, a new major locus for resistance to grapevine powdery mildew

Muscadinia rotundifolia, a species closely related to cultivated grapevine Vitis vinifera, is a major source of resistance to grapevine downy and powdery mildew, two major threats to cultivated traditional cultivars of V. vinifera respectively caused by the oomycete Plasmopara viticola and the ascomycete Erisyphe necator. The aim of the present work was to develop a reference genetic linkage map based on simple sequence repeat (SSR) markers for M. rotundifolia. This map was created using S1 M. rotundifolia cv. Regale progeny, and covers 948 cM on 20 linkage groups, which corresponds to the expected chromosome number for muscadine. The comparison of the genetic maps of V. vinifera and M. rotundifolia revealed a high macrosynteny between the genomes of both species. The S1 progeny was used to assess the general level of resistance of M. rotundifolia to P. viticola and E. necator, by scoring different parameters of pathogen development. A quantitative trait locus (QTL) analysis allowed us to highlight a major QTL on linkage group 14 controlling resistance to powdery mildew, which explained up to 58 % of the total phenotypic variance. This QTL was named 'Resistance to Erysiphe Necator 5' (Ren5). A microscopic evaluation E. necator mycelium development on resistant and susceptible genotypes of the S1 progeny showed that Ren5 exerts its action after the formation of the first appressorium, and acts by delaying, and then stopping, mycelium development.

Mapping of crown gall resistance locus Rcg1 in grapevine

Agrobacteria are efficient plant pathogens. They are able to transform plant cells genetically resulting in abnormal cell proliferation. Cultivars of Vitis vinifera are highly susceptible to many virulent Agrobacterium strains but certain wild Vitis species, including Vitis amurensis have resistant genotypes. Studies of the molecular background of such natural resistance are of special importance, not only for practical benefits in agricultural practice but also for understanding the role of plant genes in the transformation process. Earlier, crown gall resistance from V. amurensis was introgressed into V. vinifera through interspecific breeding and it was shown to be inherited as a single and dominant Mendelian trait. To develop this research further, towards understanding underlying molecular mechanisms, a mapping population was established, and resistance-coupled molecular DNA markers were identified by three different approaches. First, RAPD makers linked to the resistance locus (Rcg1) were identified, and on the basis of their DNA sequences, we developed resistance-coupled SCAR markers. However, localization of these markers in the grapevine genome sequence failed due to their similarity to many repetitive regions. Next, using SSR markers of the grapevine reference linkage map, location of the resistance locus was established on linkage group 15 (LG15). Finally, this position was supported further by developing new chromosome-specific markers and by the construction of the genetic map of the region including nine loci in 29.1 cM. Our results show that the closest marker is located 3.3 cM from the Rcg1 locus that may correspond to 576 kb.

A framework genetic map of Muscadinia rotundifolia

This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n = 20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879 cM on 18 chromosomes. The average distance between the markers was 4.1 cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841 cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088 cM, which represented 66 % of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

BACKGROUND

Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs.

RESULTS

Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel.

CONCLUSIONS

This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.