Etude de la variation somaclonale chez le palmier à huile : mesure de la teneur en 2,4-D et en cytokinines dans les tissus végétaux pendant l'embryogenèse somatique

L'embryogenèse somatique est utilisée chez le palmier à huile pour multiplier à l'échelle industrielle les meilleurs individus issus de sélection classique. Cependant, après régénération des premiers vitroplants, il a été observé l'apparition d'une anomalie florale qui pourrait être induite par un stress lors de la culture in vitro. Des travaux effectués sur d'autres espèces ont mis en évidence que l'acide 2,4-dichlorophénoxyacétique (2,4-D) apporté dans les milieux de culture à certaines étapes du processus d'embryogenèse somatique pourrait être à l'origine de l'apparition de variants somaclonaux. Par ailleurs, d'autres études laissent à supposer que le 2,4-D aurait une action sur le degré de méthylation de façon indirecte via la teneur en cytokinines endogènes. Un protocole expérimental a alors été mis au point au laboratoire GeneTrop afin d'essayer de mettre en évidence un effet du 2,4-D sur les cytokinines endogènes. Au cours de ce travail, nous avons étudié l'effet de différentes concentrations de 2,4-D apportées au stade suspensions cellulaires, sur les teneurs en cytokinines endogènes à 2 stades de culture. Afin de mener à bien cet objectif, une technique de quantification hormonale a été adaptée pour permettre le dosage des différentes formes hormonales (2,4-D et cytokinines de formes zéatine et isopentényladénine) au sein d'un même extrait végétal. Elle est basée sur une séparation des différentes formes hormonales par HPLC, et sur leur dosage par méthode ELISA. Les mises au point techniques ont constitué la première partie de ce travail. Cette technique a ensuite été appliquée sur des échantillons de palmier à huile pour doser leurs teneurs en 2,4-D et en cytokinines... (D'après résumé d'auteur

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

<p>Abstract</p> <p>Background</p> <p>Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.</p> <p>Results</p> <p>The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10^-10) to the UniProt database.</p> <p>Conclusion</p> <p>Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.</p

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Background: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results: We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310&thinsp;kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion:The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.Additional co-authors: Thomas D Kocher, Catherine Ozouf-Costaz, Jean Francois Baroiller and Francis Galiber

Producing and selling food in the urban space: what are the risks? A case-study in Hanoi, Vietnam

International audienceIn Hanoi, many street food vendors are facing eviction by public authorities, notably with the argument that food sold in the street would be risky in terms of health. Based on qualitative interviews, on policy review and on genotoxicity analyses on vegetables and fishes, this communication addresses the ways different actors deal with these risks and argue about it. While public authorities fear bacterial and chemical contaminations and toxicity analyses suspect heavy metal contamination, consumers rather trust the food sold that is produced locally

Fish farming as a way for diversifying sources of income in the cocoa sector in Ivory Coast

International audienceIvory Coast is the largest producer of cocoa in the world, with production reaching 2 million tonnes in 2016-2017. The South-and Central-West regions are the main cocoa production areas in the country. However, cocoa production faces a significant crisis due to the instability of prices on world markets, land saturation, aging plantations, and climate change. Cocoa farmers have adopted fish farming as an additional production to generate new incomes. The objective of our study was to provide the first description of cocoa production diversification practices in the Ivory Coast through targeted questionnaires. Surveys were conducted from May to September 2021 with cocoa farmers practicing fish farming in two localities of Central-West: Bédiala (n = 21) and Sinfra (n = 12) and one in SouthWest: Méagui (n = 12). We first used an empirical approach to highlight the farming practices, and then a hierarchical clustering analysis will be applied to identify clusters of sites. Our first results showed that all the cocoa farmers interviewed in Bédiala and 70% of the cocoa farmers in Sinfra practice fish-rice farming in which rice and tilapia (Oreochromis niloticus) are cultivated in the same ponds. In addition, the cocoa plantations in Bédiala (85%) and Sinfra (82%) are characterized by the association of cocoa and cashew for shading cocoa plants. Among the cocoa farmers interviewed in the SouthWest region, 75% of them practice fish-rice farming, with the monoculture of cocoa. With incomes ranging between 400,000 and 3,000,000 FCFA per year, fish farming has become the primary source of revenues for 30%, 40%, and 5% of cocoa farmers in Bédiala, Sinfra, and Méagui, respectively. In such agriculture-aquaculture integrated systems, 51% of the farmers use the periphery of the ponds in the dry season as cacao nurseries, which allows the young crops to benefit from fertilized pond water collected by their roots. Such practices are likely to enhance crop growth while reducing the watering effort. In addition, fish ponds act as a natural barrier against bush fires. These results highlight the positive interactions that exist between cocoa and fish farming. Nevertheless, the consequences of using phytosanitary products in cacao production near fish ponds remain to be assessed for human consumers and surrounding environments. Based on a Strengths, Weaknesses, Opportunities, Threats (SWOT) analysis, we explore the possibilities that may be more promising for cocoa production diversification in Ivory Coast

Individual growth monitoring of European sea bass larvae by image analysis and microsatellite genotyping

The aims of the present study were to develop non-lethal methods to identify individual fish larvae and post-larvae before tagging and accurately follow their growth characteristics. European sea bass (Dicentrarchus labrax) was used as a model species at four different ages ranging from 71 to 100 days post fertilization (dpf). Two different methods were tested for non-lethal tissue sampling from each larva for DNA analysis: 1) using a sterile absorbent paper to sample mucus and/or epithelial cells by rubbing the fish skin and 2) fin-clip of the bottom part of the caudal fin. Whatever the age of the larvae, the genotyping rate (at 12 microsatellite markers) was low with the use of sterile absorbent paper but relatively high with fin-clip sampling at 80 and 87 dpf (on average 17 and 63% of the loci genotyped for sterile paper and fin clips, respectively). Several measurements were performed on digital pictures of sea bass larvae to model body weight. Using area, perimeter, length, height and volume, it was possible to estimate body weight with a coefficient of determination r2 = 0.98 on very small larvae (body weight ranging from 20.0 to 419.3 mg). The present results suggested that individual monitoring of the growth of European sea bass larvae can be achieved by combining image analysis and microsatellite genotyping as early as 87 dpf or 236 mg mean body weight

Temperature induced-masculinisation in the Nile tilapia causes rapid up-regulation of both dmrt1 and amh expressions

International audienc

Variation génétique des populations sauvages et des stocks issus d’élevage de tilapia du Nil (Oreochromis niloticus) à Madagascar

International audienceFour farmed stocks and four wild populations of Nile tilapia (Oreochromis niloticus), which was first introduced to Madagascar sixty years ago, were assayed for genetic variation at nine microsatellite loci to determine levels of genetic diversity within populations and genetic relationships between them. Allelic diversity overlapped with that found in previously sampled populations elsewhere in Africa. There was no evidence of deviations from allele frequencies expected under conditions of Hardy-Weinberg equilibrium or of inbreeding in studied populations. Three distinct clusters of genotypes provided evidence of three separate introductions (from Egypt and Mauritius in 1956, and from Japan in 2011), and the occurrence of genotypes from more than one cluster within a single population provided evidence of their mixing. There were significant differences between populations which were not from the same environment (wild or farmed) or were not geographically related. Wild populations may be a valuable resource to support further development of farmed stocks from the perspective of genetic diversity.Quatre stocks issus de piscicultures et quatre populations sauvages de tilapias du Nil (Oreochromis niloticus), espèce qui a été introduite initialement à Madagascar il y a soixante ans, ont été évalués pour leurs variations génétiques à partir de l’analyse de neuf locus microsatellites pour déterminer les niveaux de variabilité génétique au sein des populations et les relations génétiques entre ces populations. La diversité allélique recoupait celle qui a été rapportée dans d’autres populations africaines. Il n’y avait ni évidence d’écart dans les fréquences alléliques attendues dans les conditions d’équilibre de Hardy-Weinberg ni de consanguinité dans les populations étudiées. Trois groupes génotypiques distincts ont montré trois introductions séparées (à partir d’Egypte et de l’île Maurice en 1956, et du Japon en 2011) et la présence de génotypes issus de plus d’un groupe dans une même population a fourni la preuve de mélanges. Il y avait des différences significatives entre les populations qui ne provenaient pas du même milieu (sauvage ou d’élevage) ou qui n’étaient pas géographiquement reliées. De par leur diversité génétique, les populations sauvages pourraient être des ressources intéressantes dans la perspective d’un développement de la pisciculture du tilapia du Nil à Madagascar