Biogemma SAS

Anzin-Saint-Aubin, France

Biogemma SAS

Anzin-Saint-Aubin, France
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Pouvreau B.,CNRS Laboratory of Plant Reproduction and Development | Baud S.,French National Institute for Agricultural Research | Vernoud V.,CNRS Laboratory of Plant Reproduction and Development | Morin V.,CNRS Laboratory of Plant Reproduction and Development | And 6 more authors.
Plant Physiology | Year: 2011

WRINKLED1 (WRI1), a key regulator of seed oil biosynthesis in Arabidopsis (Arabidopsis thaliana), was duplicated during the genome amplification of the cereal ancestor genome 90 million years ago. Both maize (Zea mays) coorthologs ZmWri1a and ZmWri1b show a strong transcriptional induction during the early filling stage of the embryo and complement the reduced fatty acid content of Arabidopsis wri1-4 seeds, suggesting conservation of molecular function. Overexpression of ZmWri1a not only increases the fatty acid content of the mature maize grain but also the content of certain amino acids, of several compounds involved in amino acid biosynthesis, and of two intermediates of the tricarboxylic acid cycle. Transcriptomic experiments identified 18 putative target genes of this transcription factor, 12 of which contain in their upstream regions an AW box, the cis-element bound by AtWRI1. In addition to functions related to late glycolysis and fatty acid biosynthesis in plastids, the target genes also have functions related to coenzyme A biosynthesis in mitochondria and the production of glycerol backbones for triacylglycerol biosynthesis in the cytoplasm. Interestingly, the higher seed oil content in ZmWri1a overexpression lines is not accompanied by a reduction in starch, thus opening possibilities for the use of the transgenic maize lines in breeding programs. © 2011 American Society of Plant Biologists.

Depge-Fargeix N.,Ecole Normale Superieure de Lyon | Depge-Fargeix N.,French National Institute for Agricultural Research | Depge-Fargeix N.,French National Center for Scientific Research | Javelle M.,Ecole Normale Superieure de Lyon | And 18 more authors.
Journal of Experimental Botany | Year: 2011

OCL1 (OUTER CELL LAYER1) encodes a maize HD-ZIP class IV transcription factor (TF) characterized by the presence of a homeo DNA-binding domain (HD), a dimerization leucine zipper domain (ZIP), and a steroidogenic acute regulatory protein (StAR)-related lipid transfer domain (START) involved in lipid transport in animals but the function of which is still unknown in plants. By combining yeast and plant trans-activation assays, the transcriptional activation domain of OCL1 was localized to 85 amino acids in the N-terminal part of the START domain. Full-length OCL1 devoid of this activation domain is unable to trans-activate a reporter gene under the control of a minimal promoter fused to six repeats of the L1 box, a cis-element present in target genes of HD-ZIP IV TFs in Arabidopsis. In addition, ectopic expression of OCL1 leads to pleiotropic phenotypic aberrations in transgenic maize plants, the most conspicuous one being a strong delay in flowering time which is correlated with the misexpression of molecular markers for floral transition such as ZMM4 (Zea Mays MADS-box4) or DLF1 (DELAYED FLOWERING1). As suggested by the interaction in planta between OCL1 and SWI3C1, a bona fide subunit of the SWI/SNF complex, OCL1 may modulate transcriptional activity of its target genes by interaction with a chromatin remodelling complex. © 2010 The Author.

Cadic E.,French National Institute for Agricultural Research | Cadic E.,French National Center for Scientific Research | Cadic E.,BIOGEMMA SAS | Coque M.,BIOGEMMA SAS | And 20 more authors.
Theoretical and Applied Genetics | Year: 2013

Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0. 08 to 0. 26 cM for a threshold of 0. 20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach. © 2013 Springer-Verlag Berlin Heidelberg.

Sosso D.,University of Lyon | Sosso D.,French National Institute for Agricultural Research | Sosso D.,French National Center for Scientific Research | Sosso D.,Carnegie Institution for Science | And 22 more authors.
Plant Cell | Year: 2012

RNA editing plays an important role in organelle gene expression in various organisms, including flowering plants, changing the nucleotide information at precise sites. Here, we present evidence that the maize (Zea mays) nuclear gene Pentatricopeptide repeat 2263 (PPR2263) encoding a DYW domain-containing PPR protein is required for RNA editing in the mitochondrial NADH dehydrogenase5 (nad5) and cytochrome b (cob) transcripts at the nad5-1550 and cob-908 sites, respectively. Its putative ortholog, MITOCHONDRIAL EDITING FACTOR29, fulfills the same role in Arabidopsis thaliana. Both the maize and the Arabidopsis proteins show preferential localization to mitochondria but are also detected in chloroplasts. In maize, the corresponding ppr2263 mutation causes growth defects in kernels and seedlings. Embryo and endosperm growth are reduced, leading to the production of small but viable kernels. Mutant plants have narrower and shorter leaves, exhibit a strong delay in flowering time, and generally do not reach sexual maturity. Whereas mutant chloroplasts do not have major defects, mutant mitochondria lack complex III and are characterized by a compromised ultrastructure, increased transcript levels, and the induction of alternative oxidase. The results suggest that mitochondrial RNA editing at the cob-908 site is necessary for mitochondrion biogenesis, cell division, and plant growth in maize. © 2012 American Society of Plant Biologists.

Sosso D.,CNRS Laboratory of Plant Reproduction and Development | Wisniewski J.-P.,CNRS Laboratory of Plant Reproduction and Development | Khaled A.-S.,CNRS Laboratory of Plant Reproduction and Development | Khaled A.-S.,Sohag University | And 4 more authors.
Plant Science | Year: 2010

Maize endosperm is both a crucial contributor to world nutrition and a model system for plant developmental biology. For both aspects promoters with expression zones restricted to particular domains of the endosperm would be a valuable tool. The β-glucuronidase (Gus) reporter gene was fused to upstream fragments of three genes whose expression is limited to specific domains of the endosperm: Vacuolar pyrophosphatase 1 (Vpp1) encoding an H+ translocating vacuolar pyrophosphatase and expressed in the aleurone layer, Embryo surrounding region 6 (Esr6) encoding a defensin-like protein and expressed specifically in the embryo surrounding region (ESR) and Outer cell layer 4 (OCL4) encoding a transcription factor of the homeo domain-leucine zipper IV (HD-ZIP IV) family and expressed in the aleurone layer. The sequence analysis of the upstream fragments revealed several putative cis elements conserved either with the rice orthologues or with other maize genes sharing the same expression domain. The phenotypic characterisation of transgenic promoter- Gus lines revealed for Vpp1 a delay in the onset of GUS activity, as compared to in situ data, and a dynamic pattern shifting from the adaxial to the abaxial side of the aleurone layer. The two closely related genes Esr6a and Esr6b discovered during the cloning process diverged strongly in their upstream sequences but showed GUS signals very similar to each other and to the in situ signal: a strong, ESR-specific GUS signal at 8 days after pollination (DAP) and 16 DAP, which disappeared at 22 DAP. While Esr6b was likely the stronger promoter, a point-like signal outside the ESR on the abgerminal side at the junction of the basal endosperm transfer layer (BETL) and the aleurone layer was only found in prEsr6a- Gus plants. The GUS signal of pr. OCL4- Gus plants only partially reflected the in situ data; whereas OCL4 in situ signal was seen in the epidermis of male and female flowers, embryos and endosperm, prOCL4- GUS signal was only observed in female flowers and endosperm where it confirmed the high specificity for the outer cell layer and exhibited a dynamic pattern similar to Vpp1. While the upstream fragment used likely contained only some but not all the cis elements governing OCL4 expression, the fortuitously obtained truncated promoter may be of greater biotechnological interest than the complete promoter because of its more restricted expression zone that still includes the highly interesting aleurone layer. © 2010 Elsevier Ireland Ltd.

Muniz L.M.,University of Alcalá | Royo J.,University of Alcalá | Gomez E.,University of Alcalá | Baudot G.,Biogemma SAS | And 2 more authors.
BMC Plant Biology | Year: 2010

Background: Two component systems (TCS) are phosphotransfer-based signal transduction pathways first discovered in bacteria, where they perform most of the sensing tasks. They present a highly modular structure, comprising a receptor with histidine kinase activity and a response regulator which regulates gene expression or interacts with other cell components. A more complex framework is usually found in plants and fungi, in which a third component transfers the phosphate group from the receptor to the response regulator. They play a central role in cytokinin mediated functions in plants, affecting processes such as meristem growth, phyllotaxy, seed development, leaf senescence or tissue differentiation. We have previously reported the expression and cellular localization of a type A response regulator, ZmTCRR-1, in the transfer cells of the maize seed, a tissue critical for seed filling and development, and described its regulation by a tissue specific transcription factor. In this work we investigate the expression and localization of other components of the TCS signalling routes in the maize seed and initiate the characterization of their interactions.Results: The discovery of a new type A response regulator, ZmTCRR-2, specifically expressed in the transfer cells and controlled by a tissue specific transcription factor suggests a previously unknown role for TCS in the biology of transfer cells. We have characterized other canonical TCS molecules, including 6 histidine kinases and 3 phosphotransfer proteins, potentially involved in the atypical transduction pathway defined by ZmTCRR-1 and 2. We have identified potential upstream interactors for both proteins and shown that they both move into the developing endosperm. Furthermore, ZmTCRR-1 expression in an heterologous system (Arabidopsis thaliana) is directed to xylem parenchyma cells, probably involved in transport processes, one of the major roles attributed to the transfer cell layer.Conclusions: Our data prove the expression of the effector elements of a TCS route operating in the transfer cells under developmental control. Its possible role in integrating external signals with seed developmental processes is discussed. © 2010 Muñiz et al; licensee BioMed Central Ltd.

Wells R.,John Innes Center | Trick M.,John Innes Center | Fraser F.,John Innes Center | Fraser F.,The Genome Analysis Center | And 7 more authors.
BMC Plant Biology | Year: 2013

Background: The detection and exploitation of genetic variation underpins crop improvement. However, the polyploid nature of the genomes of many of our most important crops represents a barrier, particularly for the analysis of variation within genes. To overcome this, we aimed to develop methodologies based on amplicon sequencing that involve the incorporation of barcoded amplification tags (BATs) into PCR products.Results: A protocol was developed to tag PCR products with 5' 6-base oligonucleotide barcode extensions before pooling for sequencing library production using standard Illumina adapters. A computational method was developed for the de-convolution of products and the robust detection and scoring of sequence variants. Using this methodology, amplicons targeted to gene sequences were screened across a B. napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome. Furthermore, using one-dimensional 8-fold pooling, 4608 lines of a B. napus mutation population were screened for induced mutations in a locus-specific amplicon (an orthologue of GL2.b) and mixed product of three co-amplified loci (orthologues of FAD2), identifying 10 and 41 mutants respectively.Conclusions: The utilisation of barcode tags to de-convolute pooled PCR products in multiplexed, variation screening via Illumina sequencing provides a cost effective method for SNP genotyping and mutation detection and, potentially, markers for causative changes, even in polyploid species. Combining this approach with existing Illumina multiplexing workflows allows the analysis of thousands of lines cheaply and efficiently in a single sequencing run with minimal library production costs. © 2013 Wells et al.; licensee BioMed Central Ltd.

Biogemma S.A.S. | Date: 2010-09-27

The invention provides a transformation method comprising inoculation and co-cultivation of a target tissue, from a target plant, with Agrobacterium, at a time when the target tissue is in its natural plant environment, followed by generation of a transgenic plant via dedifferentiation and regeneration of the target tissue.

Biogemma S.A.S. | Date: 2012-09-14

The invention relates to modified restriction enzymes capable of being used for promoting homologous recombination in organisms, in particular plants, making it possible to either target gene integration or excise unwanted DNA sequences in the genome of said organisms.

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