Dataset Information

Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

ABSTRACT: In recent years the scientific community has been heavily engaged in studying the grapevine response to climate change. Final goal is the identification of key genetic traits to be used in grapevine breeding and the setting of agronomic practices to improve climatic resilience. The increasing availability of transcriptomic studies, describing gene expression in many tissues and developmental, or treatment conditions, have allowed the implementation of gene expression compendia, which enclose a huge amount of information. The mining of transcriptomic data represents an effective approach to expand a known local gene network (LGN) by finding new related genes. We recently published a pipeline based on the iterative application of the PC-algorithm, named NES²RA, to expand gene networks in Escherichia coli and Arabidopsis thaliana. Here, we propose the application of this method to the grapevine transcriptomic compendium Vespucci, in order to expand four LGNs related to the grapevine response to climate change. Two networks are related to the secondary metabolic pathways for anthocyanin and stilbenoid synthesis, involved in the response to solar radiation, whereas the other two are signaling networks, related to the hormones abscisic acid and ethylene, possibly involved in the regulation of cell water balance and cuticle transpiration. The expansion networks produced by NES²RA algorithm have been evaluated by comparison with experimental data and biological knowledge on the identified genes showing fairly good consistency of the results. In addition, the algorithm was effective in retaining only the most significant interactions among the genes providing a useful framework for experimental validation. The application of the NES²RA to Vitis vinifera expression data by means of the BOINC-based implementation is available upon request (valter.cavecchia@cnr.it).

SUBMITTER: Malacarne G

PROVIDER: S-EPMC6161569 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

Malacarne Giulia G Pilati Stefania S Valentini Samuel S Asnicar Francesco F Moretto Marco M Sonego Paolo P Masera Luca L Cavecchia Valter V Blanzieri Enrico E Moser Claudio C

Frontiers in plant science 20180921

In recent years the scientific community has been heavily engaged in studying the grapevine response to climate change. Final goal is the identification of key genetic traits to be used in grapevine breeding and the setting of agronomic practices to improve climatic resilience. The increasing availability of transcriptomic studies, describing gene expression in many tissues and developmental, or treatment conditions, have allowed the implementation of gene expression compendia, which enclose a h ...[more]

PMID: 30298082

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Project description:IntroductionClimate change has been driving warming trends and changes in precipitation patterns and regimes throughout Europe. Future projections indicate a continuation of these trends in the next decades. This situation is challenging the sustainability of viniculture and, thus, significant efforts towards adaptation should be then carried out by local winegrowers.MethodEcological Niche Models were built, using the ensemble modelling approach, to estimate the bioclimatic suitability of four main wine-producing European countries, namely France, Italy, Portugal, and Spain, in the recent past (1989-2005), for the cultivation of twelve Portuguese grape varieties. The models were then used to project the bioclimatic suitability to two future periods (2021- 2050 and 2051-2080) to better understand the potential shifts related to climate change (modeled after Intergovernmental Panel on Climate Change's Representative Concentration Pathways 4.5 and 8.5 scenarios). The models were obtained with the modeling platform BIOMOD2, using four bioclimatic indices, namely the "Huglin Index", the "Cool Night index", the "Growing Season Precipitation index", and the "Temperature Range during Ripening index" as predictor variables, as well as the current locations of the chosen grape varieties in Portugal.ResultsAll models performed with high statistical accuracy (AUC > 0.9) and were able to discriminate several suitable bioclimatic areas for the different grape varieties, in and around where they are currently located but also in other parts of the study area. The distribution of the bioclimatic suitability changed, however, when looking at future projections. For both climatic scenarios, projected bioclimatic suitability suffered a considerable shift to the north of Spain and France. In some cases, bioclimatic suitability also moved towards areas of higher elevation. Portugal and Italy barely retained any of the initially projected varietal areas. These shifts were mainly due to the overall rise in thermal accumulation and lower accumulated precipitation in the southern regions projected for the future.ConclusionEnsemble models of Ecological Niche Models were shown to be valid tools for winegrowers who want to adapt to a changing climate. The long-term sustainability of viniculture in southern Europe will most likely have to go through a process of mitigation of the effects of increasing temperatures and decreasing precipitation.

Project description:In many areas of the world, maintaining grapevine production will require adaptation to climate change. While rigorous evaluations of adaptation strategies provide decision makers with valuable insights, those that are published often overlook major constraints, ignore local adaptive capacity, and suffer from a compartmentalization of disciplines and scales. The objective of our study was to identify current knowledge of evaluation methods and their limitations, reported in the literature. We reviewed 111 papers that evaluate adaptation strategies in the main vineyards worldwide. Evaluation approaches are analyzed through key features (e.g., climate data sources, methodology, evaluation criteria) to discuss their ability to address climate change issues, and to identify promising outcomes for climate change adaptations. We highlight the fact that combining adaptation levers in the short and long term (location, vine training, irrigation, soil, and canopy management, etc.) enables local compromises to be reached between future water availability and grapevine productivity. The main findings of the paper are three-fold: (1) the evaluation of a combination of adaptation strategies provides better solutions for adapting to climate change; (2) multi-scale studies allow local constraints and opportunities to be considered; and (3) only a small number of studies have developed multi-scale and multi-lever approaches to quantify feasibility and effectiveness of adaptation. In addition, we found that climate data sources were not systematically clearly presented, and that climate uncertainty was hardly accounted for. Moreover, only a small number of studies have assessed the economic impacts of adaptation, especially at farm scale. We conclude that the development of methodologies to evaluate adaptation strategies, considering both complementary adaptations and scales, is essential if relevant information is to be provided to the decision-makers of the wine industry.

Dataset Information

Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

Publications

Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

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