Analysis of the origin of parthenocarpy in grapevine cultivar Corinto Bianco

Póster presentado en la 2nd Annual ConferenceFleshy Fruit Development & Ripening (COST Action FA1106 QualityFruit), celebrada en Chania (Grecia) del 22 al 25 de septiembre de 2013.Seedless fruits appear spontaneously in grapevine (Vitis vinifera L.) as a result of somatic variation. Stenospermocarpic and parthenocarpic seedlesness are known. The first type is widely used in table grapes production because seed development aborts after fertilization giving rise to seed traces and almost normal size berries. In contrast, small berries without seed traces develop in absence of fertilization in parthenocarpic cultivars that are appreciated for raisin production. The cultivar Corinto Bianco is a parthenocarpic somatic variant of the Spanish seeded cultivar Pedro Ximénez. Morphological and molecular comparison of flower development and gametogenesis between both genotypes were directed to understand the genetic and molecular basis of this parthenocarpic phenotype. Histological analyses showed that ovules developed similarly in both genotypes. However, macrogametogenesis was altered in Corinto Bianco showing disorders during mitosis after mother cell meiotic reduction. Microgametogenesis was also altered in Corinto Bianco, which pollen was 100% sterile in 2012 and 2013, compared with Pedro Ximénez pollen that showed only 8.47 and 21.64% of sterility in those years. The average number of seeds per berry was 1.35 in Pedro Ximénez berries, which weight was six times higher than in Corinto Bianco parthenocarpic berries with zero seeds. In addition, we observed partial phenotypic reversion in 2.6% of Corinto Bianco berries that carried one seed and displayed a comparable size to that of Pedro Ximénez berries. These seeds were unable to germinate in soil under normal conditions. Fortunately, following an in vitro germination protocol we were able to rescue 41 seedlings derived from revertant berries for further analyses. Gene expression alterations between Pedro Ximénez and Corinto Bianco, that could lead to the identification of candidate genes responsible for the phenotypic change, were analyzed by comparing closed flowers of both genotypes at 50% bloom time using the NimbleGen Vitis HX12 microarray. We identified 441 genes upregulated and 949 downregulated in the parthenocarpic mutant (¿2-fold change and 5% FDR). Interestingly, genes related with cell cycle and gametogenesis were downregulated in Corinto Bianco, including a cyclin (CYB1;2- like) and a MADS-box gene (AGL66-like), whose function in Arabidopsis is related with mitosis and pollen development, respectively. The expression of these genes could be related with defects in gametogenesis in Corinto Bianco. These preliminary results suggest the presence of defects in the meiotic mechanisms central to the process of gametogenesis in Corinto Bianco, providing clues for further characterization of the origin of parthenocarpy in this cultivar.Peer Reviewe

Chromosome reorganizations in the origin of Tempranillo Blanco and other white grape cultivars

Póster presentado en la 11th International Conference on Grapevine Breeding and Genetics, celebrada en Pekín del 29 de julio al 2 de agosto de 2014.Acknowledgmcnts: Projects 8102011-26229 and INNOVINE.Peer Reviewe

DNA methylation-based classification of central nervous system tumours.

Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology

Genetic characterization of raspberry cultivars using molecular markers

8 páginas.-- Trabajo presentado al "IX International Rubus and Ribes Symposium".Molecular (DNA) markers have some advantages over morphological markers for identification purposes and for estimating genetic diversity. In this study we have used two types of molecular markers to characterize a collection of 36 raspberry cultivars: Ten RAPD primers and seven microsatellite (SSR) loci were used. The collection included commercial cultivars, very closely related because some cultivars have been recurrently used in many breeding programs. Even though, both kind of markers (RAPD and SSR) could distinguish all cultivars, although SSR data showed higher polymorphism than RAPD data. Since this and for other reasons (simplicity, possibility of automation, multiplexation, etc.), microsatellite markers are preferable. Cluster analysis using RAPD and SSR data was used to examine genetic relationships within the collection. Results closely resembled pedigree relations between cultivars, and cultivars with similar origins or belonging to the same breeding program were grouped together in the same cluster. The obtained results confirmed the utility of RAPD and SSR markers to discriminate among closely related raspberries and to determine the genetic diversity among cultivars. This information is useful for germplasm characterization and identification of cultivars, including legal issues like assessing infringements on plant breeders’ rights.Peer reviewe

Transcriptional differences among ripening berries of different density in Tempranillo and Albariño Spanish wine cultivars

Increased temperature and drought, related to climate change, are hastening grapevine reproductive development and ripening and affecting grape berry composition at harvest time, which alters its quality for winemaking. The final composition of the berry reflects not only the genotype but summarizes its interaction with all the environmental conditions experienced by the berry during its ripening process. However, transcriptional analyses reflect a transcriptome composition also dependent on the genotype, but linked to the specific conditions experienced by the berry at the time of sampling. Given the effects of climate change conditions in reproductive development and ripening, berry sampling becomes a crucial step to avoid misinterpretation oftranscriptional analyses results influenced by developmental time shifts. In this report we have used berry stratification in NaCI solutions of different densities to characterize consistent transcriptional changes taking places during berry ripening. We have also tested the possible effect of the NaCl based process on berry gene expression to identify any possible interaction of the sample selection method with the transcriptome. The results showed that berries with increased density grown under the same conditions and harvested at the same time displayed gene expression differences affecting about 800 genes which expression is being tumed off or tumed on during the ripening process independently of vineyard or year. Most of these transcriptional changes are consistent among different cultivars and indicative of increased ripening states. Minor specific transcriptional variation among different density berries could be considered cultivar specific. In addition we showed that exposure to NaCI during the sampling process did not significantly alter berry transcriptome.Trabajo presentado en el IX International Symposium on Grapevine Physiology and Biotechnology, celebrado en La Serena (Chile) del 21 al 26 de abril de 2013.Peer Reviewe

Daily oscillatory transcriptional programs in Grape vine ripening berries

Trabajo presentado en la 2nd Annual ConferenceFleshy Fruit Development & Ripening (COST Action FA1106 QualityFruit), celebrada en Chania (Grecia) del 22 al 25 de septiembre de 2013.Temperature and solar radiation are factors influencing grapevine berry ripening. High temperatures decrease anthocyanin accumulation and hasten organic acid metabolization, while light promotes proanthocynidin and terpenes accumulation. Temperature and radiation conditions cyclically fluctuate in a daily period under field environment. Indeed, the strength of this daily variation affects berry ripening and quality. The intensity of daily temperatures fluctuation modifies flavonoid partitioning, while cold and light during night time enhance anthocyanin accumulation. Transcriptome alterations in grapes under different set temperature and light conditions has been documented. Additionally, a circadian clock signaling that modulate the expression of a high proportion of the genome is present in plants. This circadian clock in connection with other factors controls multiple developmental processes like flowering or dormancy. Nevertheless, the effect of these daily cycling elements over the ripening transcriptional program has not been characterized in detail. In order to determine whether different ripening transcriptional programs are activated during a day in different grape tissues, we followed the berry skin and flesh transcriptome in six time points throughout a 24-hours cycle using the NimbleGen Vitis HX12 microarray. Tempranillo berries with the same density (~19º brix) were selected in all time points from plants grown under controlled greenhouse conditions. In that manner, four different profiles of differentially expressed genes (5% FDR in Limma and ¿2-fold change) were identified in both tissues. Two different oscillatory cycles correlated with them, one involving temperature variation along the 24-hours cycle, while the other presented two opposite peaks at the end of the light and the dark period, respectively. Functional enrichment analysis showed that a thermotolerance response including the activation of HSP chaperones took place at noon time in both tissues. More genes with expression changes following light oscillation were identified in the skin. They were enriched in regulatory genes involved in circadian clock and ethylene signaling pathways as well as in WRKY and AP2 transcription factors and protein kinases. Analogous thermotolerance and signaling responses were found in Verdejo whole pericarp from field grown conditions, while other specific changes could be related with the experimental settings. Genes involved in metabolism were not greatly altered, suggesting that daily variations of conditions could affect berry ripening by mechanisms other than transcriptional control. These results indicate daily oscillatory changes in the grapevine berry transcriptome to occur and they could help to a better understanding of the progress of berry ripening in short term time scales.Peer Reviewe

Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method

The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grape-vine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was transcriptomically assessed as a grape ripening staging strategy. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmen- tal differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when berry sugar concentration increases through dehydration

An intervarietal study on the architectonical characteristics of the grapevine bunch that affect its compactness

Trabajo presentado en el IX International Symposium on Grapevine Physiology and Biotechnology, celebrado en La Serena (Chile) del 21 al 26 de abril de 2013.Chemical composition and sanitary status are two important factors for the definition of grape quality. Consequently, they may vary the commercial value of grapes and grape-derived products. In this sense, bunch compactness is a trait with great relevance in this attribute, since it rnay cause heterogeneous ripeness of the berries and the occurrence and development of undesirable diseases. This trait is consequence of the interaction of many individual characteristics of the bunch, whose combination may generate the compaction of the berries along the rachis, reducing the number and size of empty spaces in the bunch structure. In this sense, different architectonical elements of the bunch have been pointed out by different authors as key factors on its definition (number of berries, length of the rachis and primary branches, length of the internodes). Nonetheless, such conclusions are based on the study of a reduced number of grapevine varieties. This work has aimed to identify the phenotypic characteristics of grapevine bunch architecture that play an important role on bunch compactness through the study of a large number of bunches (2185) belonging to more than a hundred cultivars during two vintages (2011 and 2012). After the detailed phenotyping of bunches, statistical analysis revealed that compactness is a multifactorial trait, with sorne variables having a higher implication. Among them, the length ofthe main axes ofthe rachis (length of the rachis and its primary branches) has shown an important role on the definition of bunch compactness, as well as the number of berries of the bunch. On the other hand, the number of seeds per berry has positively correlated with bunch compactness in both years of study, revealing sorne kind of relationship between both traits.Acknowledgments: Project AGL2010-15694. Fellowship BES-2011-047041.Peer Reviewe

Multicultivar and multivariate study of the natural variation for grapevine bunch compactness

[Background and Aims] Grapevine bunch compactness is an important trait with impact on fruit quality, mainly affecting the susceptibility to bunch rot. Many and different variables have been reported to have a significant influence on the variation of bunch compactness in particular cultivars, but little is known about the role of such variables in a wider framework. The aim of this work was to identify and weight the features responsible for the natural variation in bunch compactness in a large and diverse grapevine collection.[Methods and Results] Different statistical tests were sequentially applied to select the determining variables most influencing bunch compactness. Significant and low correlation was obtained for most of the variables studied for three consecutive seasons, confirming the multifactorial nature of this trait. Multivariate analyses indicated that there are three groups of variables with a significant influence on bunch compactness. Two groups, represented by the total number of berries per bunch and by the length of the first ramification of the bunch, are major factors responsible for the trait variation, whereas berry dimensions have a secondary role.[Conclusions] Bunch compactness is defined by the difference between its morphological (apparent) volume and its actual (solid) volume. The results showed that the actual volume is mainly determined by the total number of berries, whereas the morphological volume also depends on its spatial arrangement, determined by the architecture of the rachis.[Significance of the Study] This is the first multiyear study of bunch compactness at a multicultivar level, and it has allowed the selection and weighting of the main variables affecting the trait. These variables are suitable targets to study the underlying genetics of the trait. © 2015 Australian Society of Viticulture and Oenology Inc.This work was supported by the Spanish MINECO (AGL2010-15694). Mr Javier Tello acknowledges the MINECO for his predoctoral fellowship (BES-2011–047041).Peer Reviewe