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Brasilia, Brazil

The Empresa Brasileira de Pesquisa Agropecuária is a state-owned company affiliated with the Brazilian Ministry of Agriculture, which is devoted to pure and applied research on agriculture. EMBRAPA conducts agricultural research on many topics including animal agriculture and crops. For example, one National Research Center, The National Goat Research Center is located in Sobral, Ceará and conducts research on small ruminants, primarily goats and hair sheep.EMBRAPA scientists have developed an acidic-soil adapted soybean plant, which may help Brazil to become the world's number one soybean exporter Wikipedia.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: KBBE.2013.1.4-09 | Award Amount: 2.64M | Year: 2013

The continuous supply of services provided by agricultural systems is increasingly threatened by climate change in association with an estimated increase in the frequency of extreme weather events such as droughts, heat waves or heavy precipitation events. MODEXTREME has the overarching goal to help the European and non-European agriculture face extreme climatic events by improving the capability of biophysical models simulating vegetation responses to integrate climatic variability and extremes. To reach this goal, the project will achieve the following objectives: Scientific objectives: - Identify and integrate into simulation models, the responses of main crop and grassland systems to environmental conditions associated with extreme climatic events; - Improve yield monitoring and forecasting systems via multiple observational constraints to be assimilated into process-based models across different climate conditions; - Estimate possible trajectories of agricultural productivity in the short (during current season) to medium time horizons and associated uncertainties. This involves taking into account the genetic progress and its effects on responses to extreme environmental conditions. Technological objectives: - Build a consistent, multi-domain data repository for use in studying climate variability and extreme events relevant for agricultural production; - Develop generically reusable software units that implement libraries of models. This will allow (i) extending the vegetation response, as implemented in existing modelling solutions, to weather extremes, (ii) extending the multi-model platform for plant growth and development simulations of the European Commission Joint Research Centre (MARS: Monitoring Agricultural ResourceS); - Prototype alternate versions of the workflows for agricultural production monitoring and scenario analysis both using new modelling solutions composed in the project, and by focusing on extreme events.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: SSH.2011.2.1-1 | Award Amount: 10.36M | Year: 2012

One of the biggest challenges facing global society today is the widespread and growing presence of hunger and food insecurity. Given that the lead time for some social and technological solutions is long, a long-term framework on global food and nutrition security (FNS) is required. FoodSecure aims at improving the resilience of the food system, by providing a means to mitigate risks and uncertainties in the world food system caused by economic and climatic shocks while providing for sustainable economic growth. The project provides an analytical toolbox to experiment, analyse, and coordinate the effects of short and medium term policies, thereby allowing for the execution of consistent, coherent, long-term strategies with desirable consequences. The FoodSecure collaboration responds to the challenge of food shortages and volatility by providing stakeholders, in the EU and beyond, with the capacity to assess and address the short term and long term challenges of food and nutrition security both effectively and sustainably. The project draws on an expert, multi-disciplinary, science team to provide a complete set of knowledge to inform and guide decision makers and other stakeholders in formulating strategies to alleviate food shortages. The food system is analysed in relationship to the ecosystem, energy, and financial markets, all of which are potential sources of shocks that can disrupt the food system. In addition, it is examined in light of fundamental societal trends and changing attitudes towards food consumption and production. The project emphasises the diversity of challenges of FNS in countries and regions. The project delivers new empirical evidence on the drivers of global FNS, and classifies regions and livelihood systems in typologies . A harmonised data system and modelling toolbox are developed for forecasts (on short term) and forward looking (towards 2050) on future hunger. A support for effective and sustainable actions will include the identification of the critical pathways for technological and institutional change and for EU policies in the areas of development aid, climate change, trade, common agricultural policy and renewable energy, including sustainability criteria.


Lopes I.O.,EMBRAPA - Empresa Brasileira de Pesquisa Agropecuaria
BMC bioinformatics | Year: 2014

Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze the discriminant power of seven feature sets, which are used in six pre-miRNA prediction tools. The analysis is based on the classification performance achieved with these feature sets for the training algorithms used in these tools. We also evaluate feature discrimination through the F-score and feature importance in the induction of random forests. Small or non-significant differences were found among the estimated classification performances of classifiers induced using sets with diversification of features, despite the wide differences in their dimension. Inspired in these results, we obtained a lower-dimensional feature set, which achieved a sensitivity of 90% and a specificity of 95%. These estimates are within 0.1% of the maximal values obtained with any feature set (SELECT, Section "Results and discussion") while it is 34 times faster to compute. Even compared to another feature set (FS2, see Section "Results and discussion"), which is the computationally least expensive feature set of those from the literature which perform within 0.1% of the maximal values, it is 34 times faster to compute. The results obtained by the tools used as references in the experiments carried out showed that five out of these six tools have lower sensitivity or specificity. In miRNA discovery the number of putative miRNA loci is in the order of millions. Analysis of putative pre-miRNAs using a computationally expensive feature set would be wasteful or even unfeasible for large genomes. In this work, we propose a relatively inexpensive feature set and explore most of the learning aspects implemented in current ab-initio pre-miRNA prediction tools, which may lead to the development of efficient ab-initio pre-miRNA discovery tools.The material to reproduce the main results from this paper can be downloaded from http://bioinformatics.rutgers.edu/Static/Software/discriminant.tar.gz. Source


Grant
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 72.63K | Year: 2015

Project team The project team combines research leaders with complementary expertise in both the wheat host and the FHB and brusone fungal pathogens in Brazil and the UK. Pedro Scheeren (Embrapa) and Eduardo Caierao (Embrapa) have unrivalled knowledge of Brazilian wheat production, providing expertise in wheat breeding alongside knowledge of germplasm resistance status that is essential for genome wide association scans to be undertaken to identify genomic regions associated with resistance to FHB and brusone. Cristobal Uauy (JIC) is internationally recognised for his expertise in wheat genetics and gene cloning in cereals. CU collaborates closely with Ksenia Krasileva (TGAC/TSL) who leads the development of functional genomics tools in wheat, including the development of exome-capture platforms that will form one of the pillars of the project. Paul Nicholson (JIC) leads a research group investigating the genetic basis of resistance to FHB in cereals and will contribute to both host and pathogen components in the project in partnership with Flávio Santana and Maria Imaculada Moreira Lima (Embrapa), who lead research on FHB resistance. James Cockram (NIAB) has extensive experience in combining molecular genetics and genomics with statistical techniques to investigate complex traits in wheat. These skills will be used in collaboration with Luciano Consoli (Embrapa) who leads the quantitative genetics programme, to undertake association mapping of target traits in Brazilian wheat germplasm. James Cockram will provide training to Embrapa personnel to enable them to undertake additional analyses on FHB and brusone data as these become available. Joao Leodato (Embrapa) is a recognised expert on brusone disease and will work alongside Gisele Torres (Embrapa) who has extensive experience of working with the Brusone pathogen and interactions with the wheat host using functional genomics analysis. Antonio Nhani Jr (Embrapa) employs genomics to investigate virulence and hostspecificity in the brusone pathogen. The skills and knowledge provided by Embrapa researchers will be complemented those of Nick Talbot (University of Exeter) who is internationally recognised for his expertise in the genetics and virulence of the brusone fungus. Diane Saunders (TGAC/JIC) leads research into pathogen populations and virulence, providing essential insight into the structure of the populations of the FHB and brusone pathogens that will be utilised within studies of the genetics of host resistance. Resources and Infrastructure In addition to the highly complementary skill sets of the Embrapa and UK participants, the organisations contribute complementary resources and infrastructure. Embrapa has excellent field trials facilities and trained personnel across Brazil in regions where the environment is most conducive to the FHB and brusone diseases enabling them to undertake high quality disease trials. The Embrapa site at Passo Fundo is exceptionally well equipped with laboratory, computing infrastructure, glasshouse and plant growth facilities in an environment that enables the rapid growth of plants to minimise generation time and ensure efficient development of plant populations to the required level of fixation for genotyping and phenotyping purposes. The UK partners within this project (JIC, TGAC, NIAB and Exeter) all have extensive laboratory, computational and plant growth facilities, required for the host and pathogen genetics and genomics components of the project. In addition, TGAC has state of the art genome sequencing and transcriptional profiling facilities and computer hardware and software to undertake the associated data processing and analysis.


Grant
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 68.19K | Year: 2015

In total, 22 researchers are involved in this project, 12 in Brazil and 10 in the UK. Ten are EMBRAPA employees located at Trigo, Passo Fundo (5), agricultural informatics, Campinas (1), soybean, Londrina (1) and Cenargen, Brasilia (3). The two additional Brazilian scientists are University based (Vicosa and Maringa). The UK scientists are located at Rothamsted Research (RRes) in the department of Plant Biology and Crop Science (9) and Applied Bioinformatics (1). The assembled team has highly complementary skills, which are required to deliver the initial project objectives and to develop the joint studies required to deliver the full project. The skills needed to deliver on the six work packages (WPs) proposed are as follows: WP1: Phytopathology and modelling, specialising in Fusarium head blight (FHB)-wheat (Fernandes, Del Ponte and Tessmann), epidemiology, diagnostics and air dispersal of various pathogens including wheat infecting Fusaria (West). WP2: Plant, animal and fungal bioinformatics and protein modelling (Martins and Togawa), plant and pathogen genomics (King and Hammond-Kosack). WP3: T-DNA design, stable plant transformation, analysis of transformants (Huttly, Lee and Jones), transient wheat transformation (Lau), transgenic plant analyses (Bonato). Designing/conducting GM wheat field trials in Brazil (Nepomuceno) and UK (Jones). WP4: Functional genomics/genetics and plant biotechnology, including Host induced gene silencing (HIGS) and si-RNA of Fusarium graminearum (Fg) in tobacco (Aragão), wheat and Arabidopsis (Kanyuka, Hammond-Kosack). Fungal molecular genetics and Fg transformation (Urban). WP5: FHB disease assessments in controlled environment and/ or the field (Lima, Urban, Brown, Machado), mycotoxin quantification (Tibola and Urban), near-infrared reflectance analysis of wheat grain quality (Tibola), digital imaging processing (Barbedo). WP6: Grant proposal and report writing - all, either as a team or as an individual. This project reuires the use of specific resources. These include the already well characterised cereal infecting fusarium isolate collections obtained from previous wheat crops grown Rio Grande and Parana States in South Brazil. The working prototype FHB-wheat prediction model developed for South Brazil. Advanced bioinformatics pipelines established at RRes for Fg genome assembly and annotation, and at Brasilia for elimination of non-target organism effects. The highly efficient wheat transformation facility only available at RRes. The protected GM field trial site at RRes and equivalent GM trial sites in South Brazil. The licensed containment growth room facilities in place at Cenargen and RRes for exploring HIGS and si-RNA mechanisms using various transgenic plant species in combination with transgenic Fusarium reporter strains. Finally, the unique near infrared resonance analysis facility for grain analysis is only available in Passo Fundo. The four EMBRAPA institutes, two Brazilian Universities and RRes each have well developed scientific infrastructures in place to expedite the experimentation proposed, the data capture, analyses and storage required and the regular communication needed by Skype, e-mail and by using secure data exchange sites. The proposed project will be closely aligned with activities under the new UK-Brazil partnership for Yield Stability and Protection in a Changing Climate (PYSP). PYSP is part-funded by a Newton-fund joint centre award and is jointly coordinated by RRes and EMBRAPA. This project will be integrated within PYSP activities, ensuring there is adequate coordination of exchange activities with minimal duplication and maximum engagement between different groups from EMBRAPA and research groups at RRes. PYSP will provide a central focus for all RRes/ EMBRAPA activities, thereby strengthening links across projects and ensuring greater impact for all joint research undertaken.

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