Genetic variants of Grapevine leafroll-associated virus 2 infecting Portuguese grapevine cultivars

Genetic variability of 19 isolates of Grapevine leafroll-associated virus 2 (GLRaV-2) from Portuguese grapevine cultivars was characterized by sequencing the entire capsid protein (CP) gene of the virus. Global phylogenetic analysis of the CP gene, which included nucleotide sequences obtained in this study and complete homologous sequences from GenBank, showed segregation of GLRaV-2 variants from Portuguese isolates into three major phylogroups (PN, 93/955 and H4). The novelty of these phylogenetic results is the evidence of well-supported subdivision within H4 as well as within PN, with subgroup PN3 composed exclusively of variants from a Portuguese isolate. These findings and the genetic analysis of global phylogroups indicate demographic expansion, mainly within PN and 93/955. Because the existence of a mixture of variants from different phylogroups was detected in some of the isolates, a typification assay based on reverse transcription reaction followed by polymerase chain reaction and restriction fragment length polymorphism analysis, was developed to complement molecular detection assay of the virus. This protocol discriminates variants from the phylogroups identified in this study, and is appropriate for routine testing for GLRaV-2

Effect of the variety on the rooting of grapevine softwood cuttings

From the massal and clonal selection of grapevine developed in Portugal for the last 30 years, clones of several varieties with high genetic potential were obtained, which are currently used for multiplication to produce base and certified materials. In order to allow the rapid multiplication of selected clones of grapevine, this work evaluate the effect of the variety (Arinto, Malvasia Fina, Aragonez, and Trincadeira) on the rooting of softwood cuttings, treated with and without naphthaleneacetic acid (NAA, 0 and 50 μM). The experimental design used was randomized in a 4 x 2 factorial arrangement (4 varieties x 2 NAA concentrations). Each treatment was composed by 40 softwood cuttings. Thirty days after planting the cuttings, the following variables were evaluated: percentage of rooted cuttings, percentage of sprouted cuttings, number of roots per cutting, total root length, longer root and dry root weight. The results obtained so far allowed to verify that the above variables were not affected by auxin, although a significant effect of the variety was identified on all the parameters but root dry weigh

Pedigree analysis of the Spanish grapevine cultivar 'Hebén'

The use of Single Nucleotide Polymorphism (SNP) markers allows genetic identification and parentage analysis of grapevine cultivars. Ancient cultivars like 'Hebén' were widely cultivated in the Iberian Peninsula along its history and likely contributed to the origin of varieties which are still cultivated today. The goal of our study was to search for possible first-degree relationships between the female variety 'Hebén' and other Iberian and Mediterranean cultivars. For this purpose, we used a set of 261 SNP markers which allowed identifying 23 trios and 37 parent-offspring relationships supported by high overall likelihood ratios (LOD scores). The results shed light on the relationships among several cultivars from Spain and Portugal, and demonstrated that 'Hebén' is a major founder of current varieties in the Iberian Peninsula viticulture, and contributed to spread the chlorotype A in this region.L. H. ZINELABIDINE was supported by a fellowship from the Agencia Española de Cooperación Internacional. J. CUNHA was supported by a Post-doctoral fellowship “Fundação para a Ciência e Tecnologia” (SFRH/BPD/ 74895/2010). LHZ and JC were supported by COST action FA1003 “East-West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding”, from European Cooperation in the Field of Scientific and Technical Research, through the funding of short scientific missions at the ICVV.Peer Reviewe

Pedigree analysis of the Spanish grapevine cultivar Heben

Trabajo presentado en la Final Conference Progress in Vitis Vinifera diversity evaluation and use, celebrada en Lisboa del 7 al 9 de octubre de 2014.Cost action FA1003 - GRAPENET. East-West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding.Several studies have shown that some varieties have had a large contribution in the production of varieties in certain regions, like ‘Pinot’ and ‘Heunisch Weiss’ in France. Previous results had pointed out that the old Spanish female variety ‘Hebén’, known as ‘Mourisco Branco’ in Portugal, could be one of those varieties with a remarkable role in the Iberian Peninsula. This ancient winegrape cultivar was already described in Spain in the 16th century as a white variety of grapevine producing large and sparse bunches of grape with big seeds.Peer Reviewe

Using rapid chlorophyll fluorescence transients to classify vitis genotypes

Silva, J. M. da, Figueiredo, A., Cunha, J., Eiras-Dias, J. E., Silva, S., Vanneschi, L., & Mariano, P. (2020). Using rapid chlorophyll fluorescence transients to classify vitis genotypes. Plants, 9(2), 1-19. [174]. https://doi.org/10.3390/plants9020174When a dark-adapted leaf is illuminated with saturating light, a fast polyphasic rise of fluorescence emission (Kautsky effect) is observed. The shape of the curve is dependent on the molecular organization of the photochemical apparatus, which in turn is a function of the interaction between genotype and environment. In this paper, we evaluate the potential of rapid fluorescence transients, aided by machine learning techniques, to classify plant genotypes. We present results of the application of several machine learning algorithms (k-nearest neighbors, decision trees, artificial neural networks, genetic programming) to rapid induction curves recorded in different species and cultivars of vine grown in the same environmental conditions. The phylogenetic relations between the selected Vitis species and Vitis vinifera cultivars were established with molecular markers. Both neural networks (71.8%) and genetic programming (75.3%) presented much higher global classification success rates than k-nearest neighbors (58.5%) or decision trees (51.6%), genetic programming performing slightly better than neural networks. However, compared with a random classifier (success rate = 14%), even the less successful algorithms were good at the task of classifying. The use of rapid fluorescence transients, handled by genetic programming, for rapid preliminary classification of Vitis genotypes is foreseen as feasible.publishersversionpublishe

The first insight into the metabolite profiling of grapes from three vitis vinifera L. cultivars of two controlled appellation (DOC) regions

The characterization of the metabolites accumulated in the grapes of specific cultivars grown in different climates is of particular importance for viticulturists and enologists. In the present study, the metabolite profiling of grapes from the cultivars, Alvarinho, Arinto and Padeiro de Basto, of two Portuguese Controlled Denomination of Origin (DOC) regions (Vinho Verde and Lisboa) was investigated by gas chromatography-coupled time-of-flight mass spectrometry (GC-TOF-MS) and an amino acid analyzer. Primary metabolites, including sugars, organic acids and amino acids, and some secondary metabolites were identified. Tartaric and malic acids and free amino acids accumulated more in grapes from vines of the DOC region of Vinho Verde than DOC Lisboa, but a principal component analysis (PCA) plot showed that besides the DOC region, the grape cultivar also accounted for the variance in the relative abundance of metabolites. Grapes from the cultivar, Alvarinho, were particularly rich in malic acid and tartaric acids in both DOC regions, but sucrose accumulated more in the DOC region of Vinho Verde.This work was supported by European Union Funds (FEDER/COMPETE-Operational Competitiveness Programme) and by the Portuguese national funds (FCT—Portuguese Foundation for Science and Technology) under the project FCOMP-01-0124-FEDER-022692, the research project FCOMP-010124-FEDER-008760 (ref. FCT PTDC/AGR-ALI/100636/2008), and the PhD grants, no. SFRH/BD/ 64587/2009 to VM and SFRH/BD/74257/2010 to HN This work also benefited from the networking activities within the European project, INNOVINE (ref. 311775), and the European COST action (FA1106 “QualityFruit” and FA1003 “East-West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding”).info:eu-repo/semantics/publishedVersio

Grapevine cultivar "Alfrocheiro" or "Bruñal" plays a primary role in the relationship among iberian grapevines

The grapevine cultivar known in Portugal as 'Alfrocheiro', and in Spain as 'Bastardo Negro', 'Bruñal' or 'Baboso Negro', plays a central role in the genetic network of the Iberian Peninsula grapevine cultivars. Three sets of different molecular markers, SNPs, nSSRs and cpSSRs, revealed more than twenty parent-offspring links with this cultivar. 'Alfrocheiro' chlorotype is definitely Western European but their parents are still unknown. The distribution of the cultivar, their offspring as well as the two main co-parents direct to a geographic origin around the Portuguese and Spanish border. This cultivar and their progenies represent about 15 % of the total grapevine acreage in Portugal, stressing the importance of 'Alfrocheiro' in the Portuguese wine character.This research was supported by: IVV – Instituto da Vinha e do Vinho (Ministério da Agricultura e do Mar-MAM); Programa de Desenvolvimento Rural (PRODER - Ação 2.2.3.1. - PA 18621 - MAM) and J. CUNHA was supported by a Post-doctoral fellowship >Fundação para a Ciência e Tecnologia> (SFRH/BPD/74895/2010) and a short scientific mission in the ICVV was part of COST action, FA 1003 from European Cooperation in the Field of Scientific and Technical Research. L. H. ZINELABIDINE was supported by a fellowship from the Agencia Española de Cooperación Internacional and a short-term scientific mission from COST FA1003 >East-West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding>.Peer Reviewe

Grapevine cultivar “Alfrocheiro” or “Bastardo Negro" plays a primary role in Iberian grapevine diversity

Trabajo presentado en la Final Conference Progress in Vitis Vinifera diversity evaluation and use, celebrada en Lisboa del 7 al 9 de octubre de 2014.Cost action FA1003 - GRAPENET. East-West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding.The grapevine cultivar known in Portugal as ‘Alfrocheiro’, and in Spain as ’Bastardo Negro’, ’Bruñal’ or ’Baboso Negro’, plays a central role in the genetic network of the Iberian Peninsula grapevine cultivars. ‘Alfrocheiro’ was already identified as a progenitor of several cultivars either by SSRs or by SNPs but until now it progenitors are unknown.Peer Reviewe

Integrating metabolomics and targeted gene expression to uncover potential biomarkers of fungal/oomycetes-associated disease susceptibility in grapevine

Vitis vinifera, one of the most cultivated fruit crops, is susceptible to several diseases particularly caused by fungus and oomycete pathogens. In contrast, other Vitis species (American, Asian) display different degrees of tolerance/resistance to these pathogens, being widely used in breeding programs to introgress resistance traits in elite V. vinifera cultivars. Secondary metabolites are important players in plant defence responses. Therefore, the characterization of the metabolic profiles associated with disease resistance and susceptibility traits in grapevine is a promising approach to identify trait-related biomarkers. In this work, the leaf metabolic composition of eleven Vitis genotypes was analysed using an untargeted metabolomics approach. A total of 190 putative metabolites were found to discriminate resistant/partial resistant from susceptible genotypes. The biological relevance of discriminative compounds was assessed by pathway analysis. Several compounds were selected as promising biomarkers and the expression of genes coding for enzymes associated with their metabolic pathways was analysed. Reference genes for these grapevine genotypes were established for normalisation of candidate gene expression. The leucoanthocyanidin reductase 2 gene (LAR2) presented a significant increase of expression in susceptible genotypes, in accordance with catechin accumulation in this analysis group. Up to our knowledge this is the first time that metabolic constitutive biomarkers are proposed, opening new insights into plant selection on breeding programsinfo:eu-repo/semantics/publishedVersio