High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology

Background: Single-nucleotide polymorphisms (SNPs) are the most abundant type of DNA sequence polymorphisms. Their higher availability and stability when compared to simple sequence repeats (SSRs) provide enhanced possibilities for genetic and breeding applications such as cultivar identification, construction of genetic maps, the assessment of genetic diversity, the detection of genotype/phenotype associations, or marker-assisted breeding. In addition, the efficiency of these activities can be improved thanks to the ease with which SNP genotyping can be automated. Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative sequence polymorphisms within and among a reduced number of cultivars. In parallel, the sequence of the grapevine cultivar Pinot Noir is also providing thousands of polymorphisms present in this highly heterozygous genome. Still the general application of those SNPs requires further validation since their use could be restricted to those specific genotypes. Results: In order to develop a large SNP set of wide application in grapevine we followed a systematic re-sequencing approach in a group of 11 grape genotypes corresponding to ancient unrelated cultivars as well as wild plants. Using this approach, we have sequenced 230 gene fragments, what represents the analysis of over 1 Mb of grape DNA sequence. This analysis has allowed the discovery of 1573 SNPs with an average of one SNP every 64 bp (one SNP every 47 bp in non-coding regions and every 69 bp in coding regions). Nucleotide diversity in grape ( = 0.0051) was found to be similar to values observed in highly polymorphic plant species such as maize. The average number of haplotypes per gene sequence was estimated as six, with three haplotypes representing over 83% of the analyzed sequences. Short-range linkage disequilibrium (LD) studies within the analyzed sequences indicate the existence of a rapid decay of LD within the selected grapevine genotypes. To validate the use of the detected polymorphisms in genetic mapping, cultivar identification and genetic diversity studies we have used the SNPlex genotyping technology in a sample of grapevine genotypes and segregating progenies. Conclusion: These results provide accurate values for nucleotide diversity in coding sequences and a first estimate of short-range LD in grapevine. Using SNPlex genotyping we have shown the application of a set of discovered SNPs as molecular markers for cultivar identification, linkage mapping and genetic diversity studies. Thus, the combination a highly efficient re-sequencing approach and the SNPlex high throughput genotyping technology provide a powerful tool for grapevine genetic analysis. © 2007 Lijavetzky et al; licensee BioMed Central Ltd

Solar ultraviolet radiation is necessary to enhance grapevine fruit ripening transcriptional and phenolic responses

Background: Ultraviolet (UV) radiation modulates secondary metabolism in the skin of Vitis vinifera L. berries, which affects the final composition of both grapes and wines. The expression of several phenylpropanoid biosynthesis-related genes is regulated by UV radiation in grape berries. However, the complete portion of transcriptome and ripening processes influenced by solar UV radiation in grapes remains unknown.Results: Whole genome arrays were used to identify the berry skin transcriptome modulated by the UV radiation received naturally in a mid-altitude Tempranillo vineyard. UV radiation-blocking and transmitting filters were used to generate the experimental conditions. The expression of 121 genes was significantly altered by solar UV radiation. Functional enrichment analysis of altered transcripts mainly pointed out that secondary metabolism-related transcripts were induced by UV radiation including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes and monoterpenoid biosynthetic genes. Berry skin phenolic composition was also analysed to search for correlation with gene expression changes and UV-increased flavonols accumulation was the most evident impact. Among regulatory genes, novel UV radiation-responsive transcription factors including VvMYB24 and three bHLH, together with known grapevine UV-responsive genes such as VvMYBF1, were identified. A transcriptomic meta-analysis revealed that genes up-regulated by UV radiation in the berry skin were also enriched in homologs of Arabidopsis UVR8 UV-B photoreceptor-dependent UV-B -responsive genes. Indeed, a search of the grapevine reference genomic sequence identified UV-B signalling pathway homologs and among them, VvHY5-1, VvHY5-2 and VvRUP were up-regulated by UV radiation in the berry skin.Conclusions: Results suggest that the UV-B radiation-specific signalling pathway is activated in the skin of grapes grown at mid-altitudes. The biosynthesis and accumulation of secondary metabolites, which are appreciated in winemaking and potentially confer cross-tolerance, were almost specifically triggered. This draws attention to viticultural practices that increase solar UV radiation on vineyards as they may improve grape features. © 2014 Carbonell-Bejerano et al.; licensee BioMed Central Ltd

Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15, 309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production

Challenges of viticulture adaptation to global change: tackling the issue from the roots

Viticulture is facing emerging challenges not only because of the effect of climate change on yield and composition of grapes, but also of a social demand for environmental‐friendly agricultural management. Adaptation to these challenges is essential to guarantee the sustainability of viticulture. The aim of this review is to present adaptation possibilities from the soil‐hidden, and often disregarded, part of the grapevine, the roots. The complexity of soil–root interactions makes necessary a comprehensive approach taking into account physiology, pathology and genetics, in order to outline strategies to improve viticulture adaptation to current and future threats. Rootstocks are the link between soil and scion in grafted crops, and they have played an essential role in viticulture since the introduction of phylloxera into Europe at the end of the 19th century. This review outlines current and future challenges that are threatening the sustainability of the wine sector and the relevant role that rootstocks can play to face these threats. We describe how rootstocks along with soil management can be exploited as an essential tool to deal with the effects of climate change and of emerging soil‐borne pests and pathogens. Moreover, we discuss the possibilities and limitations of diverse genetic strategies for rootstock breeding.info:eu-repo/semantics/publishedVersio

Challenges of viticulture adaptation to global change: tackling the issue from the roots

[EN] Viticulture is facing emerging challenges not only because of the effect of climate change on yield and composition of grapes, but also of a social demand for environmental-friendly agricultural management. Adaptation to these challenges is essential to guarantee the sustainability of viticulture. The aim of this review is to present adaptation possibilities from the soil-hidden, and often disregarded, part of the grapevine, the roots. The complexity of soil-root interactions makes necessary a comprehensive approach taking into account physiology, pathology and genetics, in order to outline strategies to improve viticulture adaptation to current and future threats. Rootstocks are the link between soil and scion in grafted crops, and they have played an essential role in viticulture since the introduction of phylloxera into Europe at the end of the 19th century. This review outlines current and future challenges that are threatening the sustainability of the wine sector and the relevant role that rootstocks can play to face these threats. We describe how rootstocks along with soil management can be exploited as an essential tool to deal with the effects of climate change and of emerging soil-borne pests and pathogens. Moreover, we discuss the possibilities and limitations of diverse genetic strategies for rootstock breeding.This work is framed in the networking activities of RedVitis (AGL2015-70931-REDT) and RedVitis 2.0 (AGL2017-90759-REDT), funded by the State Research Agency (AEI) of the Spanish Ministry of Science and Innovation. Ms Diana Marin is beneficiary of postgraduate scholarship funded by Universidad Publica de Navarra (FPI-UPNA-2016). Dr Juan Emilio Palomares-Rius acknowledges the State Research Agency (AEI) of the Spanish Ministry of Science and Innovation for the 'Ramon y Cajal' Fellowship RYC-2017-22228 and Dr David Gramaje acknowledges Spanish Ministry of Economy and Competitiveness for the 'Ramon y Cajal' Fellowship RYC-2017-23098.Marín, D.; Armengol Fortí, J.; Carbonell-Bejerano, P.; Escalona, J.; Gramaje Pérez, D.; Hernández-Montes, E.; Intrigliolo, DS.... (2021). Challenges of viticulture adaptation to global change: tackling the issue from the roots. Australian Journal of Grape and Wine Research. 27(1):8-25. https://doi.org/10.1111/ajgw.12463S825271AGÜERO, C. B., URATSU, S. L., GREVE, C., POWELL, A. L. T., LABAVITCH, J. M., MEREDITH, C. P., & DANDEKAR, A. M. (2005). Evaluation of tolerance to Pierce’s disease andBotrytisin transgenic plants ofVitis viniferaL. expressing the pear PGIP gene. 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Identifying populations of wild vines and grapevines trained on the facades of old farmhouses.

El presente trabajo se ha centrado sobre la Cuadrilla de Ayala (Álava), donde se han localizado ocho poblaciones relictas de vid silvestre en diversos hábitats. Se ha comprobado su carácter dioico durante el periodo de floración. Se han identificado las principales especies parásitas existentes sobre estas parras y las principales componentes de su vegetación acompañante. Por otro lado, se han estudiado quince vides cultivadas, con una edad superior a cincuenta años, situadas en la fachada principal de los caseríos. El análisis del ADN de ambos tipos de parras se ha realizado con 48 marcadores SNPs. Los resultados obtenidos han sido comparados con la base de datos disponible en el Instituto de Ciencias de la Vid y del Vino (Logroño), a fin de proceder a la caracterización genética de las muestras.This paper focuses on the Cuadrilla de Ayala (Álava province, Spain), where eight relic wild grapevine populations were located in different habitats. The dioecious nature of these lianas was determined at flowering time. The main parasitic species on these vines and also the most frequent taxa of their accompanying vegetation were identified. On the other hand, fifteen vines, aged in excess of fifty, and located in the main entrances of traditional farmhouses (caseríos), were also studied. The analysis of the DNA from both kinds of sampled vines was based on 48 SNPs markers. Results were compared with the available data base at the Instituto de Ciencias de la Vid y del Vino (Logroño, Spain) for the sample genetic characterization

Early life risk factors and their cumulative effects as predictors of overweight in Spanish children

Objectives: To explore early life risk factors of overweight/obesity at age 6 years and their cumulative effects on overweight/obesity at ages 2, 4 and 6 years. Methods: Altogether 1031 Spanish children were evaluated at birth and during a 6-year follow-up. Early life risk factors included: parental overweight/obesity, parental origin/ethnicity, maternal smoking during pregnancy, gestational weight gain, gestational age, birth weight, caesarean section, breastfeeding practices and rapid infant weight gain collected via hospital records. Cumulative effects were assessed by adding up those early risk factors that significantly increased the risk of overweight/obesity. We conducted binary logistic regression models. Results: Rapid infant weight gain (OR 2.29, 99% CI 1.54–3.42), maternal overweight/obesity (OR 1.93, 99% CI 1.27–2.92), paternal overweight/obesity (OR 2.17, 99% CI 1.44–3.28), Latin American/Roma origin (OR 3.20, 99% CI 1.60–6.39) and smoking during pregnancy (OR 1.61, 99% CI 1.01–2.59) remained significant after adjusting for confounders. A higher number of early life risk factors accumulated was associated with overweight/obesity at age 6 years but not at age 2 and 4 years. Conclusions: Rapid infant weight gain, parental overweight/obesity, maternal smoking and origin/ethnicity predict childhood overweight/obesity and present cumulative effects. Monitoring children with rapid weight gain and supporting a healthy parental weight are important for childhood obesity prevention

Development and characterization of new microsatellite markers for grape

Thirty five new grape microsatellite markers were developed under an international consortium involving AGROGENE. These loci were amplified in 41 Spanish cultivars of V. vinifera. Eleven of the markers were polymorphic and informative in V. vinifera. Twelve were monomorphic and of the remaining markers one was polymorphic but less useful because individuals amplified more than two bands and the rest had amplification problems. The number of alleles detected for the 11 informative markers ranged from 4 to 12, with heterozygosity values ranging from 0.6 to 0.8. Primer sequences are reported for these markers

The FT/TFL1 gene family in grapevine

The FT/TFL1 gene family encodes proteins with similarity to phosphatidylethanolamine binding proteins which function as flowering promoters and repressors. We show here that the FT/TFL1 gene family in Vitis vinifera is composed of at least five genes. Sequence comparisons with homologous genes identified in other dicot species group them in three major clades, the FT, MFT and TFL1 subfamilies, the latter including three of the Vitis sequences. Gene expression patterns are in agreement with a role of VvFT and VvMFT as flowering promoters; while VvTFL1A, VvTFL1B and VvTFL1C could be associated with vegetative development and maintenance of meristem indetermination. Overexpression of VvFT in transgenic Arabidopsis plants generates early flowering phenotypes similar to those produced by FT supporting a role for this gene in flowering promotion. Overexpression of VvTFL1A does not affect flowering time but the determination of flower meristems, strongly altering inflorescence structure, which is consistent with the biological roles assigned to similar genes in other species. © 2006 Springer Science+Business Media B.V

DNA methylation increases throughout Arabidopsis development

We used amplified fragment length polymorphisms (AFLP) to analyze the stability of DNA methylation throughout Arabidopsis development. AFLP can detect genome-wide changes in cytosine methylation produced by DNA demethylation agents, such as 5-azacytidine, or specific mutations at the DDM1 locus. In both cases, cytosine demethylation is associated with a general increase in the presence of amplified fragments. Using this approach, we followed DNA methylation at methylation sensitive restriction sites throughout Arabidopsis development. The results show a progressive DNA methylation trend from cotyledons to vegetative organs to reproductive organs. © Springer-Verlag 2005