Montpellier, France


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Meier A.,Oregon State University | Cooper L.,Oregon State University | Elser J.,Oregon State University | Jaiswal P.,Oregon State University | Laporte M.-A.,Bioversity
CEUR Workshop Proceedings | Year: 2016

An expected use case of plant phenotype ontologies will be the identification of germplasm containing particular traits of interest. If phenotype data from experiments is annotated using ontologies, it makes sense to include annotations to that germplasm source. A lack of standardized data formatting reduces the utility of these data. Standardizing germplasm data, including links to germplasm databases, or distribution locations improves collaboration, and benefits both researchers and the scientific community as a whole. All plant traits contained in the Planteome reference ontologies are searchable, and interconnected through relationships in the ontology. All data annotated to these reference ontologies will be displayed, shareable, and computable through the Planteome website ( and APIs. This manuscript will discuss the advantages of standardizing germplasm trait annotation, and the semi-automated process developed to achieve such standardization. © 2016, CEUR-WS. All rights reserved.

Bobadilla Landey R.,CIRAD - Agricultural Research for Development | Cenci A.,Bioversity | Guyot R.,IRD Montpellier | Bertrand B.,CIRAD - Agricultural Research for Development | And 5 more authors.
Plant Cell, Tissue and Organ Culture | Year: 2015

Long-term cell cultures were used in coffee to study the cytological, genetic and epigenetic changes occurring during cell culture ageing. The objective was to identify the mechanisms associated with somaclonal variation (SV). Three embryogenic cell lines were established in Coffea arabica (2n = 4x = 44) and somatic seedlings were regenerated after 4, 11 and 27 months. Phenotyping and AFLP, MSAP, SSAP molecular markers were performed on 199 and 124 plants, respectively. SV were only observed from the 11 and 27-month-old cultures, affecting 30 and 94 % of regenerated plants, respectively. Chromosome counts performed on 15 plants showed that normal plants systematically displayed normal chromosome numbers and that, conversely, aneuploidy (monosomy) was systematically found in variants. The allopolyploid structure of C. arabica allowed aneuploid cells to survive and regenerate viable plants. No polymorphic fragments were observed between the AFLP and SSAP electrophoretic profiles of mother plants and those of the in vitro progeny. Methylation polymorphism was low and ranged between 0.087 and 0.149 % irrespective of the culture age. The number of methylation changes per plant—normal or variant—was limited and ranged from 0 (55–80 % of the plants) to 4. The three cell lines showed similar SV rate increases during cell culture ageing and produced plants with similar molecular patterns indicating a non random process. The results showed that cell culture ageing is highly mutagenic in coffee and chromosomal rearrangements are directly linked to SV. Conversely, the analysis of methylation and transposable elements changes did not reveal any relation between the epigenetic patterns and SV. © 2015, The Author(s).

Cote F.,Center Pour la Recherche Agronomique Pour le Developpement | Tomekpe K.,Center Africain Of Recherches Sur Bananiers Et Plantains | Staver C.,Bioversity | Depigny S.,Center Pour la Recherche Agronomique Pour le Developpement | And 3 more authors.
Acta Horticulturae | Year: 2010

Urban centers in sub-Saharan Africa are generating a growing demand for plantain (Musa spp.). Farmers have not responded by increasing supply and this crop has gone from being a staple food to a food for special occasions. Smallholder farmers face numerous difficulties in improving production and productivity of plantain. Diseases, such as black leaf streak and Banana bunchy top virus, have spread into new areas. Shortened fallow periods and declining soil fertility have exacerbated the losses due to nematodes and weevils. Fertilizers and pesticides are difficult to obtain, expensive and not properly evaluated in plantain cropping systems. High input production has not been applied in plantain production for urban markets. In addition, this production approach is increasingly questioned due to negative impacts on the environment, the health of workers and nearby rural communities, in addition to the increasing cost of energy intensive inputs. Agroecological intensification is a practical, knowledge-based approach with potential to respond both to the needs of smallholder farmers for increased production through more efficient use of local resources and to the demands placed on the high-input export sector for more environmental sustainability. This approach does not exclude the use of external inputs, but focuses on biological mechanisms to suppress pests and diseases, strategies to increase total crop photosynthesis and conversion to yield, and management of soil nutrient cycles for a healthier and more productive crop. In this approach, management of functional biodiversity and deployment of better knowledge about agro-ecological interactions serve to reduce losses, optimize crop residue breakdown and symbiotic nitrogen fixation, and promote crop health. We conclude that agro-ecological intensification is easily applicable in export bananas. Strategies for application of the concept to plantain are facilitated by targeting approaches to specific systems defined by distance to market and quality of the natural resource base.

Mobambo P.,University of Kinshasa | Staver C.,Bioversity | Hauser S.,International Institute Of Tropical Agriculture | Dheda B.,University of Kisangani | Vangu G.,INERA Mvuazi
Acta Horticulturae | Year: 2010

The agricultural sector of the Democratic Republic of Congo continues to suffer from declining productivity after a decade of civil unrest and underinvestment. Plantain and banana (Musa spp.) are considered the second most important staple crop after cassava (Manihot esculenta). The Congo basin is a secondary centre of plantain diversity in the world. The area planted with plantain/banana declined from over 400,000 ha in the early 90s to less than 150,000 ha presently. Yields are low and declining and plantain become too expensive for poor urban households. There are numerous political, economic, social and technological constraints to increase the contribution of banana and plantain to household, community and the national economy. A number of priorities for action were identified: (a) simple and low cost strategies to estimate production and planted areas and the extent of serious pest and disease threats to guide investment in areas with the greatest impact; (b) mapping of production potential based on soils, climate and water sources and ease of market access to prioritize investment in intensification; (c) piloting of clean seed systems to contain the spread and impact of Banana bunchy top virus, and Xanthomonas wilt, to multiply highly productive clones of preferred cultivars and to conserve plantain diversity; (d) technology for land productivity stabilization and improvement, depending on access to infrastructure and natural resource quality; (e) improving field access to information on new technologies to farmers and their associations, public extension and non-governmental organizations and rural school teachers; and (f) farmer and village marketing organizations to capture greater value from plantain and banana markets where clean seed and improved land productivity are piloted.

Sist P.,CIRAD - Agricultural Research for Development | Rutishauser E.,CarboForExpert | Pena-Claros M.,Wageningen University | Shenkin A.,University of Florida | And 41 more authors.
Applied Vegetation Science | Year: 2015

While attention on logging in the tropics has been increasing, studies on the long-term effects of silviculture on forest dynamics and ecology remain scare and spatially limited. Indeed, most of our knowledge on tropical forests arises from studies carried out in undisturbed tropical forests. This bias is problematic given that logged and disturbed tropical forests are now covering a larger area than the so-called primary forests. A new network of permanent sample plots in logged forests, the Tropical managed Forests Observatory (TmFO), aims to fill this gap by providing unprecedented opportunities to examine long-term data on the resilience of logged tropical forests at regional and global scales. TmFO currently includes 24 experimental sites distributed across three tropical regions, with a total of 490 permanent plots and 921 ha of forest inventories. To improve our knowledge of the resilience of tropical logged forests, 20 research institutes are now collaborating on studies on the effects of logging on forest structure, productivity, biodiversity and carbon fluxes at large spatial and temporal scales. These studies are carried out in the Tropical managed Forests Observatory (TmFO), an international network including 24 sites and 490 permanent sample plots across South America, Africa and South East Asia. © 2014 International Association for Vegetation Science.

Haggar J.,Tropical Agriculture Research and Higher Education Center | Haggar J.,University of Greenwich | Barrios M.,Tropical Agriculture Research and Higher Education Center | Bolanos M.,UNICAFE | And 8 more authors.
Agroforestry Systems | Year: 2011

Changes in coffee economics are leading producers to reduce agrochemical use and increase the use of shade. Research is needed on how to balance the competition from shade trees with the provision of ecological services to the coffee. In 2000, long-term coffee experiments were established in Costa Rica and Nicaragua to compare coffee agroecosystem performance under full sun, legume and non-legume shade types, and intensive and moderate conventional and organic inputs. Coffee yield from intensive organic production was not significantly different from intensive conventional in Nicaragua, but in Costa Rica it was lower during three of the six harvests. Full sun coffee production over 6 years was greater than shaded coffee in Costa Rica (61.8 vs. 44.7 t ha-1, P = 0.0002). In Nicaragua, full sun coffee production over 5 years (32.1 t ha-1) was equal to coffee with shade that included Tabebuia rosea (Bertol.) DC., (27-30 t ha-1) and both were more productive (P = 0.03) than coffee shaded with Inga laurina (Sw.) Willd. (21.6 t ha-1). Moderate input organic production was significantly lower than other managements under all shade types, except in the presence of Erythrina poepiggina (Walp.) O. F. Cook. Inga and Erythrina had greater basal area and nutrient recycling from prunings than other shade species. Intensive organic production increased soil pH and P, and had higher K compared to moderate conventional. Although legume shade trees potentially provide ecological services to associated coffee, this depends on management of the competition from those same trees. © 2011 Springer Science+Business Media B.V.

News Article | November 28, 2016

"I thought it was from a piece of wood," she told AFP, recalling the day when a snake sunk its fangs into her leg. "They had to carry me back home because I couldn't walk," she said, sitting in front of a thatched hut decorated with white sea shells. Gina lives on Soga, a tiny speck of land that is one of the 88 islands of the Bijagos archipelago, an Atlantic paradise home to dolphins, tortoises—and forests full of deadly snakes. Home to some 30,000 people, the islands are recognised by the UN's world heritage body (UNESCO) for their exceptionally diverse ecosystems, but there is one creature in particular that thrives among the mangroves. "The Bijagos islands are reputed for their snakes. All the deadliest species live there, including mambas and cobras," says Aissata Regolla, a researcher at Guinea-Bissau's Institute for Bioversity and Protected Marine Areas (IBAP). "On certain islands, our staff can't walk more than five minutes without seeing one." Gina should perhaps count herself lucky. Every year around 125,000 people die after being bitten by a snake, 30,000 of them in sub-Saharan Africa. Many more are left with life-changing injuries or amputations. But finding an antivenom which is affordable is becoming increasingly difficult, prompting a warning from the World Heath Organization last year. "The price of some antivenoms has dramatically increased in the last 20 years, making treatment unaffordable for the majority of those who need it," the UN health agency said. On the continent, antivenom treatments are not generally cost-effective for the drug companies that make them. In 2010, French pharmaceuticals giant Sanofi stopped producing its widely-used Fav-Afrique serum, which is effective against the venom of 10 different snake species, with the last batch expiring in June of this year. Sanofi Pasteur, its vaccines division, said it had been edged out by cheaper competitors. But several studies have shown these low-cost rivals are far less effective in treating bites, while the delicate process of cultivating an antivenom further complicates delivery. "Antivenom is a biological product. You have to buy the venom, draw out the antibodies, purify them... it's an arduous and complex process," explains Jean-Philippe Chippaux, a snake bite expert at France's Institute of Research for Development (IRD). "Governments, local authorities and companies should all make a contribution. Today no ministry is capable of saying where the problem lies, how many bites there are or where they took place." Worst hit are children and farmers working the land. Cacutu Avis earns his living cutting down trees in the forest between the coast and the village of Eticoba. "The cacubas are the most deadly, generally if they bite you, you are a goner," he says, using the local word for mambas. "They are often in the trees and palm leaves." Soga is half an hour from the larger island of Bubaque, which has a basic hospital, and more than five hours from the capital, Bissau. But with a single dose of life-saving antivenom costing up to $150 (141 euros)—often more than a month's salary—many are forced to turn to traditional healers. "People have died in front of me at the healers' places, but others have survived," said Jose Nactum, director of the hospital in Bubaque. "We don't have antivenoms adapted for different species and we have a lot of difficulty identifying the type of snake," he admits. Antivenom must also be kept chilled in the fridge, yet only 10 percent of the country has access to electricity. Even for the new players in the market, making the antidotes cost-effective is a huge challenge. "Antivenoms don't bring in enough for the big pharma houses compared with other products," says Juan Silanes, president of Mexico's Inosan Biopharma, now Africa's top provider of snakebite serum. "But if there is a product that's fairly good, and at a good price, that could change things," he adds. Explore further: Global failure to act on snake bite costs thousands of lives each year

DeClerck F.A.J.,Tropical Agriculture Research and Higher Education Center | Jessica F.,Bioversity | Cheryl P.,Catholic University of Leuven | Roseline R.,EARTH University
Food and Nutrition Bulletin | Year: 2011

Background. Malnutrition affects a large number of people throughout the developing world. Approaches to reducing malnutrition rarely focus on ecology and agriculture to simultaneously improve human nutrition and environmental sustainability. However, evidence suggests that interdisciplinary approaches that combine the knowledge bases of these disciplines can serve asa central strategy in alleviating hidden hunger for the world's poorest. Objective. To describe the role that ecological knowledge plays in alleviating hidden hunger, considering human nutrition as an overlooked ecosystem service. Methods. We review existing literature and propose a framework that expands on earlier work on econutrition. We provide novel evidence from casestudies conducted by the authors in western Kenya and propose a framework for interdisciplinary collaboration to alleviate hidden hunger, increase agricultural productivity, and improve environmental sustainability. Results. Our review supports the concept that an integrated approach will impact human nutrition. We provide evidence that increased functional agrobiodiversity can alleviate anemia, and interventions that contribute to environmental sustainability can have both direct and indirect effects on human health and nutritional well-being. Conclusions. Integrated and interdisciplinary approaches are critical to reaching development goals. Ecologists must begin to consider not only how their field can contribute to biodiversity conservation, but also, the relationship between biodiversity and provisioning of nontraditional ecosystem services such as human health. Likewise, nutritionists and agronomists must recognize that many of the solutions to increasing human wellbeing and health can best be achieved by focusing on a healthy environment and the conservation of ecosystem services. © 2011, The United Nations University.

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