GEM, una proteína con dominio GRAM, es un regulador negativo de la señalización por ABA durante la germinación en Arabidopsis thaliana

Tesis doctoral inédita, leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 22-03-201

Genomic variation and clone genotyping in Vitis vinifera L. Malbec

Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. The later is the case of grapevines used in the wine industry. Even though clonal propagation is a normal practice in this industry, a remarkable phenotypic variation has been reported at the intra-cultivar level. However, less is known about the genetic variability among clones. Malbec is the main cultivar for the Argentinean viticulture, showing a notorious phenotypic variation on many traits of technological interest, for example the biochemical composition of berries. Therefore, it turns relevant to develop a formal protocol to discriminate among clones exhibiting different properties. Here we performed a genomic analysis in order to test if the genetic variability is in agreement with the phenotypic variability, and also to develop a genetic-based protocol for clones? discrimination. For this aim we obtained Illumina reads at a 35x depth for four different Malbec clones (MB53, MB59, Cot143 and Cot225). Bioinformatic tools were employed to align these reads to the Pinot noir reference genome (PN40024) and to perform variant calling analysis for single nucleotide variants (SNVs) discovery. Afterwards, strict quality and frequency filters were applied to obtain a set of reliable SNVs. We discovered 2 million of shared SNVs (i.e. all clones shared the same allele); these variants allow distinguishing Malbec from the reference genome. On the other hand, we identified 458 non-shared SNVs (i.e. at least one of the clones has the same allele than the reference); these were of particular interest to us because they allow for clone discrimination. From the latter set we picked 48 SNVs to validate them through Sanger sequencing. After validation these same 48 SNVs were employ to build a chip for the high throughput genotyping platform FLUIDIGM. We genotyped 221 plants, including clones of known origin as well as plants belonging to five different mass selections. We were able to classify all genotyped plants in 10 different haplo-groups; showing that with a small but informative number of SNVs it is possible to discriminate among clones of the same cultivar in an efficient manner.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. Instituto de Ciencias de la Vid y el 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. Instituto de Ciencias de la Vid y el Vino; EspañaFil: Carbonell Bejerano, Pablo. No especifíca;Fil: Royo, Carolina. Instituto de Ciencias de la Vid y el Vino; EspañaFil: Sola, Cristobal. No especifíca;Fil: Martínez Zapater, José M.. Instituto de Ciencias de la Vid y el 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; Argentina63rd Italian Society of Agricultural Genetics Annual CongressNapoliItaliaItalian Society of Agricultural Genetic

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