Caracterización de los virus asociados a la enfermedad enrollado de la hoja de la vid en la Argentina

In the present study, we investigate the evolutive forces shaping the genetic diversity of grapevine leafroll-associated viruses obtained from leafroll-infected grapevine plants in Argentina. An evolutionary analysis was performed and a new recombination event was inferred in the considered dataset. The N- and C-terminal regions of CP appeared to be under purifying selection, but the N-terminal region presented twelve sites under positive selection and a dN/dS ratio 6-fold greater than that of the C-terminal region. These sites under diversifying selection correspond to the previously reported as most variable sites in the CP and also to the most prone to be linear epitopes.Facultad de Ciencias Exacta

Incidence of grapevine leafroll associated viruses -1, -2, and -3 in Mendoza vineyards

Indexación: ScieloViticulture is important in Argentina's economy, especially in the province of Mendoza, which is responsible for more than 75% of the crop cultivated area. In this work, we evaluated the incidence of Grapevine leafroll-associated viruses (GLRaV) -1, -2, and -3 in Vitis vinifera clones of cultivars Cabernet Sauvignon, Cabernet Franc, and Sauvignon Blanc, planted in different zones of Mendoza. The selected clones were previously reported as putatively infected by GLRaV-2. All selected samples were analyzed by DAS-ELISA for GLRaV-1,-2 and -3. GLRaV-2 was the only virus identified in all the analyzed clones. The overall infection rates were 0.6%, 18.8% and 1.2 % for GLRaV-1, 2 and 3 respectively. For the clone Cabernet Sauvignon 337, the infection rate was very high (68.3%).http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1982-56762010000600007&nrm=is

Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem

In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNAseq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.Fil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carvajal, Sofia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Ellison, Shelby. University of Wisconsin; Estados UnidosFil: Senalik, Douglas A.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. University of Wisconsin; Estados UnidosFil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Simon, Philipp W.. University of Wisconsin; Estados UnidosFil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; Argentin

Grapevine virus L: a novel vitivirus in grapevine

Vitiviruses are ssRNA(+) viruses in the family Betaflexiviridae (subfamily Trivirinae). There are currently 10 ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and official recognition of six more have been proposed recently. Here, we present the characterization of a novel virus from grapevine, which fits the genomic architecture and evolutionary constraints to be classified within the Vitivirus genus. The detected virus sequence is 7607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Phylogenetic analyses based on the predicted RP and CP proteins unequivocally place the new virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. Additionally, we detected, confirmed, and assembled virus sequences from grapevine samples of distinct cultivars from America, Europe, Asia and Oceania, sharing 74.4%–97.8% nt identity, suggesting that the identified virus is widely distributed and diverse. We propose the name grapevine virus L (GVL) to the detected Vitivirus.Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Soltero Brisbane, Reid. Foundation Plant Services; Estados UnidosFil: Voncina, Darko. University of Zagreb; CroaciaFil: Almeida, Rodrigo P.. University of California at Berkeley; Estados UnidosFil: Blouin, Arnaud G.. No especifíca;Fil: Al Rwahnih, Maher. University of California at Berkeley; Estados UnidosFil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentin

Differences on the transcriptomic profiles explain clonal phenotypic variation in Vitis vinifera L. 'Malbec'

Resumen del trabajo presentado en el XIII International Symposium on Grapevine Breeding and Genetics, celebrado en Landau in der Pfalz (Alemania), del 10 al 17 de julio de 2022Cultivated grapevines are clonally propagated, mainly to maintain phenotypic traits of productiveinterest; this practice turns particularly relevant in the wine industry to preserve the varietal typicity.Nonetheless, a wide clonal phenotypic diversity has been reported for several cultivars. Malbec isappreciated for producing high-quality red wines and recognized world-wide as the flag cultivar ofthe Argentine viticulture. Previous analyses demonstrated a notorious clonal phenotypic diversity forMalbec, in technologically relevant traits. On the other hand, clonal genetic diversity was shown tobe scarce, affecting mostly the intergenic regions. Aiming to dissect the molecular bases of thereported phenotypic diversity, we studied 27 clonal accessions grown under the same environmentaland cultural conditions at Vivero Mercier Argentina experimental vineyard. Phenotypic analyses wereperformed on berries at technological maturity (∼23º Brix), during two consecutive seasons (2017-2019). More precisely, we meassured: i) phenolic composition, ii) analytical profile and iii) skinweight. Afterwards, we chose the six accessions exhibiting extreme contrasting values for theevaluated features. Whole RNA extractions were performed from veraison berries (75% colored),from the six selected clones. Illumina stranded paired-end reads (150 bp in length) were obtained,totaling ∼122 Gb of transcriptomic data for 18 samples (6 clones x 3 biological replicates). In order toperform differential gene expression (DEG) and gene ontology (GO) enrichment analyses, theobtained transcriptomic data was aligned to a Malbec reference genome, assembled de novo in atruly-phased fashion and annotated by our group. After performing a discriminant analysis includingall RNA-seq data, clone Cot-595 exhibited a highly differentiated transcriptomic profile. Moreover,this clone showed the highest total polyphenols and anthocyanins concentration, while clones Mb-506 and Cot-596 showed the lowest concentrations. Therefore, we focused the fore coming DEG andGO analyses to pairwise comparisons among the three mentioned accessions. Consistently, Cot-595exhibited GO enrichment for genes involved in the anthocyanins biosynthesis pathways, while Mb-506 and Cot-596 showed enrichment for genes involved in metabolic pathways that regulatevegetative growth. These results suggest that phenotypic diversity observed among Malbec clones,might have solid ground on the described differences at the transcriptomic level

A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)

Most grapevine cultivars originated from the outcrossing of two genetically diverse parents, and are clonally propagated to preserve phenotypes of productive interest. Hence, cultivars are first filial generations (F1) with highly heterozygous diploid genomes, that turn challenging to assemble. "Malbec" is the main cultivar for the Argentine wine industry and it originated in France, from the outcrossing of Magdeleine Noir des Charentes and Prunelard cultivars. Based on that mother-father-offspring relationship, here we followed the algorithm implemented in the software CanuTrio to produce a phased assembly of Malbec genome. For this aim, parental cultivars? Illumina short-reads were used to sort ?Malbec? PacBio long-reads into its haploid complements, to be assembled separately. Post- assembly, bioinformatic procedures were employed to reduce the number of duplicated regions and perform sequence error corrections (using Malbec Illumina short-reads). We obtained two highly complete and contiguous haploid assemblies for Malbec, Haplotype- Prunelard (482.4 Mb size; contig N50=7.7 Mb) and Haplotype-Magdeleine (479.4 Mb size; contig N50=6.6 Mb), with 96.1 and 95.8% of BUSCO genes, respectively. We tested for the composition of both haplophases with the tool Merqury, and observed 15% of both assemblies affected by structural variations, along with 3.2 million SNPs and 0.6 million InDels. Our results indicate that this is a valid approach to assemble highly heterozygous and complex diploid genomes in a completely-phased way.Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Carbonell Bejerano, P.. Max Planck Institute for Developmental Biology; AlemaniaFil: Mauri, N. Instituto de Ciencias de la Vid y del Vino; EspañaFil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Bree, Laura. No especifíca;Fil: Sola, C. No especifíca;Fil: Bergamin, D. No especifíca;Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Ibañez, J. Instituto de Ciencias de la Vid y del Vino; EspañaFil: Martinez-Zapater, JM. Instituto de Ciencias de la Vid y del Vino; EspañaFil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaXVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética HumanaChileSociedad Argentina de Genétic

Clonal propagation history shapes the intra-cultivar genetic diversity in Malbec grapevines

Grapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal 26 attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming 27 to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic 28 diversity, we have focused on ‘Malbec’. This cultivar is appreciated for red wines elaboration, 29 it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, 30 we generated whole-genome resequencing data for four ‘Malbec’ clones with different 31 historical backgrounds. A stringent variant calling procedure was established to identify reliable 32 clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 33 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of 34 validated SNVs, a genotyping experiment was custom-designed to survey ‘Malbec’ genetic 35 diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, 36 that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long 37 history of clonal propagation in Argentina, while Group-Fr was driven by clones that have 38 longer remained in Europe. Findings show the ability of such approaches for clonal genotypes 39 identification in grapevines. In particular, we provide evidence on how human actions may have 40 shaped ‘Malbec’ extant genetic diversity pattern.Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Mauri, Nuria. Consejo Superior de Investigaciones Científicas; EspañaFil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Carbonell Bejerano, Pablo. Max Planck Institute for Biology of Ageing; AlemaniaFil: Bree, Laura. No especifíca;Fil: Sola, Cristobal. No especifíca;Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Royo, Carolina. Consejo Superior de Investigaciones Científicas; EspañaFil: Ibañez, Javier. Consejo Superior de Investigaciones Científicas; EspañaFil: Martinez-Zapater, José Miguel. Consejo Superior de Investigaciones Científicas; EspañaFil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentin

Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Mauri Panadero, Nuria. Consejo Superior de Investigaciones Científicas; EspañaFil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Carbonell Bejerano, Pablo. Max Planck Institute for Developmental Biology; AlemaniaFil: Bree, Laura. No especifíca;Fil: Bergamin, Daniel. No especifíca;Fil: Sola, Cristobal. No especifíca;Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Royo, Carolina. Consejo Superior de Investigaciones Científicas; EspañaFil: Ibáñez, Javier. Consejo Superior de Investigaciones Científicas; EspañaFil: Martínez Zapater, José Miguel. Consejo Superior de Investigaciones Científicas; EspañaFil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentin

First description of Grapevine leafroll-associated virus 5 in Argentina and partial genome sequence

An accession of Vitis vinifera cv. Red Globe from Argentina, was found to be infected with Grapevine leafroll-associated virus-5 by ELISA. It was partially sequenced, and three ORFs, corresponding to HSP70h, HSP90h, and CP, were found. This isolate shares a high aminoacid identity with the previously reported sequence of the virus, and identities between 80% and 90% with previously reported GLRaV-9 and GLRaV-4 isolates. The analysis of the sequence supports the clustering together with GLRaV-4 and GLRV-9 inside the Ampelovirus genus.Instituto de Biotecnología y Biología Molecula

Genetic characterization of grapevine-infecting Botrytis cinerea isolates from Argentina

Botrytis cinereaes un ascomiceto con una gran diversidad gene ́tica y una complejaestructura poblacional cuya presencia ha sido descrita en diversos lugares y hue ́spedes distintos, pero nadase sabe acerca de su diversidad gene ́tica en Argentina.Objetivos:El objetivo de este trabajo fue estimar la diversidad gene ́tica de una poblacio ́n local deaislamientos deB. cinereaobtenidos de vid en Argentina.Me ́todos:En este trabajo, 35 cepas aisladas de vides fueron genotipadas mediante marcadores molecularesbasados en PCR-RFLP y segu ́n la presencia de elementos transposables. Estos resultados fueron comparadoscon los de una gran poblacio ́n francesa del hongo, y utilizados para realizar un ana ́lisis de gene ́ticapoblacional utilizando el software Genepop.Resultados:Todos los aislamientos analizados fueron clasificados como grupo II (de acuerdo ala clasificacio ́nma ́s recientemente propuesta) y mostraron un alto grado de diversidad gene ́tica, con14 haplotipos distintos en el nu ́mero de muestras involucradas. Se observo ́una notable diferencia en lafrecuencia ale ́lica entre ambas poblaciones.Conclusiones:Estas diferencias entre las poblaciones comparadas condujeron a la deteccio ́n de un altonivel de diversidad y diferenciacio ́n poblacional entre los aislamientos locales y los franceses. Esto fueconfirmado por un valor Fst de 0,3332, superior al previamente reportado para otras comparaciones deeste tipo. Este trabajo es el primero en documentar la diversidad gene ́tica de aislamientos deB. cinereaysuestructura poblacional en ArgentinaFil: Muñoz, Claudio Javier. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Gómez Talquenca, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Oriolani, Enrique. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Combina, Mariana. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentin