Antananarivo, Madagascar
Antananarivo, Madagascar
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Andria-Mananjara D.E.,FOFIFA | Rasamoelina H.,FOFIFA | Vandeputte M.,French National Institute for Agricultural Research
Aquaculture Reports | Year: 2016

Nude carps, a genotype of common carp which are devoid of scales, have been banned from farmed populations of carp in Europe due to both the lethal effect of the N (nude) gene when in homozygous state, and to the negative pleiotropic effects on growth and survival (especially in harsh conditions) of this same gene in the heterozygous state, which produces the nude phenotype. In Madagascar, where climatic variations are less extreme than in Eastern Europe, the nude phenotype is valued both by farmers and consumers, for its good growth and supposed low number of intermuscular bones. We performed an on-farm experiment using a "common garden" design to control environmental variation, in order to compare the growth and survival, as well as the number of intermuscular bones of nude carp to two other common scale cover phenotypes of the same species, the mirror and scaly carps. We found that survival of nude carps was lower or equal to that of mirror carps at all stages of the farming process, while growth performance was lower than that of mirror carps in some ponds only. Globally, the biomass production per fish stocked was always lower in nude carp compared to mirror carp. The number of intermuscular bones was the same in nude, mirror and scaly carps. We conclude that as in Europe, it would be valuable to farm mirror rather than nude carps, as the supposed benefits of the latter are not supported by our experiment in typical Malagasy farming conditions. © 2016 The Authors.

PubMed | NAIK HAKI, CNRS Center for Marine Biodiversity, Exploitation and Conservation, French Research Institute for Exploitation of the Sea, French National Institute for Agricultural Research and FOFIFA
Type: Journal Article | Journal: Proceedings. Biological sciences | Year: 2016

The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the mirror reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.

Rasamoelina-Andriamanivo H.,FOFIFA | Rasamoelina-Andriamanivo H.,University of Monastir | Porphyre V.,CIRAD | Jambou R.,Institute Pasteur Of Madagascar
Trends in Parasitology | Year: 2013

Taenia solium cysticercosis is a zoonosis of public health importance in areas where the disease is endemic, with significant economic impacts on human health and the swine industry. Several gaps remain in the epidemiology of the parasite and the strategies of control in developing countries. We detail the key factors to consider in Madagascar in terms of the porcine husbandry system, Taenia transmission cycle, and diagnosis of cysticercosis in pigs, in order to better estimate the sanitary and economic impacts of this parasitic disease as well as to define an integrated control program. © 2013 Elsevier Ltd.

Gerardeaux E.,CIRAD - Agricultural Research for Development | Giner M.,CIRAD - Agricultural Research for Development | Ramanantsoanirina A.,Fofifa | Dusserre J.,CIRAD
Agronomy for Sustainable Development | Year: 2012

Food security in many countries is threatened due to rapid population growth. Rising temperatures and carbon dioxide, rainfall irregularity, and global warming may have serious consequences on rice production and hence food security. However, there is limited knowledge on the precise effects of global warming on crops, in particular on rice which is a major staple crop and contributor to food security. Most reports have focused on irrigated rice in India or China but much less is known about rainfed rice cropping systems in Madagascar. In the Malagasy highlands, the most populated part of Madagascar, land pressure has led to saturation of irrigated lands and the adoption of rainfed cropping systems on hilltops. The present article reports the impact of various climate changes on rice productivity in four cropping systems using the CERES-Rice model. The cropping systems include two tillages components, hand-plowed and no-tillage, and two fertilization rates: low and high nitrogen. A locally adapted rice cultivar was calibrated and validated using a dataset based on experiments conducted over a 6-year period. Daily weather data were generated for a set of 90 virtual years, from 2010 to 2099. Our results show that no-tillage systems have no advantage for climate change issues. Nitrogen was a major constraint for crops in hand-plowed and no-tillage systems. We found negative effects of climate change on soil carbon and nitrogen. By contrast, we found positive effects of temperature and increased CO2 on rice growth. The overall effects on rice yields are positive under the most pessimistic climate change scenarios but we demonstrate that the sustainability of these systems is threatened.© INRA and Springer-Verlag, France 2012.

Rakotomalala M.,British Petroleum | Pinel-Galzi A.,Montpellier University | Mpunami A.,Mikocheni Agricultural Research Institute | Randrianasolo A.,CRRSO | And 3 more authors.
Virus Research | Year: 2013

Rice yellow mottle virus (RYMV), of the genus Sobemovirus, is a major threat to rice cultivation in Africa. Long range transmission of RYMV, difficult to study experimentally, is inferred from a detailed analysis of the molecular diversity of the virus in Madagascar and in the Zanzibar Archipelago (Zanzibar and Pemba Islands; Tanzania) compared with that found elsewhere in Africa. A unique successful introduction of RYMV to Madagascar, which is ca. 400. km from mainland Africa, contrasted with recurrent introductions of the virus to the Zanzibar Archipelago, ca. 40. km from the East African coast. Accordingly, RYMV dispersal over distances of hundreds of kilometers is rare whereas spread of the virus over distances of tens of kilometers is relatively frequent. The dates of introduction of RYMV to Madagascar and to Pemba Island were estimated from three sets of ORF4 sequences of virus isolates collected between 1966 and 2011. They were compared with the dates of the first field detection in Madagascar (1989) and in Pemba Island (1990). The estimates did not depend substantially on the data set used or on the evolutionary model applied and their credible intervals were narrow. The estimated dates are recent - 1978 (1969-1986) and 1985 (1977-1993) in Madagascar and in Pemba Island, respectively - compared to the early diversification of RYMV in East Africa ca. 200 years ago. They predated by 5-10 years the first field detections in these islands. The interplay between virus sources, rice cultivation and long range dispersal which led to RYMV emergence and spread is enlightened. © 2012 Elsevier B.V.

Sester M.,CIRAD - Agricultural Research for Development | Raveloson H.,FOFIFA | Tharreau D.,CIRAD - Agricultural Research for Development | Dusserre J.,CIRAD - Agricultural Research for Development
Plant Pathology | Year: 2014

In response to the extensive development of upland rice on the hillsides of the Madagascan highlands, alternative cropping systems based on conservation agriculture have been recommended to halt declining soil fertility and to limit erosion. To assess the efficiency of these cropping systems in limiting rice blast disease and to measure their yield performance, an experiment was set up in 2003 at Andranomanelatra (1640 m a.s.l.) in the Madagascan highlands. The rice crop was planted every second year following oat (Avena sativa) after common bean (Phaseolus vulgaris), with both conventional tillage and no tillage. For each cropping system, two levels of fertilization were used: (i) organic and (ii) organic + mineral fertilization. The level of blast epidemic was measured on two different cultivars over a 5-year period. Disease severity was significantly lower in the no-tillage cropping system than in the conventional tillage system. Mineral fertilization increased the level of blast. A significant interaction between cropping system and fertilization indicated that the impact of fertilization differed with the cropping system. When the level of blast was low, yield was higher in the conventional cropping system but as soon as blast level increased, yield was better in the no-tillage cropping system. Possible interactions between cropping system and blast epidemics are explained and the problem of high performance but risky cropping systems is discussed. © 2013 British Society for Plant Pathology.

PubMed | Memorial University of Newfoundland, Jean Lorougnon Guédé University, Royal Botanic Gardens, University of Stockholm and 3 more.
Type: Journal Article | Journal: Molecular genetics and genomics : MGG | Year: 2016

The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.

PubMed | CIRAD - Agricultural Research for Development, Montpellier SupAgro and FOFIFA
Type: Journal Article | Journal: Rice (New York, N.Y.) | Year: 2016

Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers.The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance.It was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties.

PubMed | NARI Group, University of Ouagadougou, CTCRI, CIRAD and 8 more.
Type: Journal Article | Journal: PloS one | Year: 2016

Taro (Colocasia esculenta (L.) Schott) is widely distributed in tropical and sub-tropical areas. However, its origin, diversification and dispersal remain unclear. While taro genetic diversity has been documented at the country and regional levels in Asia and the Pacific, few reports are available from Americas and Africa where it has been introduced through human migrations. We used eleven microsatellite markers to investigate the diversity and diversification of taro accessions from nineteen countries in Asia, the Pacific, Africa and America. The highest genetic diversity and number of private alleles were observed in Asian accessions, mainly from India. While taro has been diversified in Asia and the Pacific mostly via sexual reproduction, clonal reproduction with mutation appeared predominant in African and American countries investigated. Bayesian clustering revealed a first genetic group of diploids from the Asia-Pacific region and to a second diploid-triploid group mainly from India. Admixed cultivars between the two genetic pools were also found. In West Africa, most cultivars were found to have originated from India. Only one multi-locus lineage was assigned to the Asian pool, while cultivars in Madagascar originated from India and Indonesia. The South African cultivars shared lineages with Japan. The Caribbean Islands cultivars were found to have originated from the Pacific, while in Costa Rica they were from India or admixed between Indian and Asian groups. Taro dispersal in the different areas of Africa and America is thus discussed in the light of available records of voyages and settlements.

PubMed | IRD Montpellier, Jean Lorougnon Guédé University, Nestlé and FOFIFA
Type: Journal Article | Journal: Molecular genetics and genomics : MGG | Year: 2016

The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7%. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53% of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.

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