5 results on '"Tavaud-Pirra, Muriel"'
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2. Genetic architecture of semolina yield and of its components in durum wheat (Triticum turgidum spp. durum)
- Author
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TAVAUD-PIRRA, Muriel, Ardisson, Morgane, Compan, Frederic, David, Jacques, Rocher, Aline, Sanchez, Dimitri, Roumet, Pierre, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
- Subjects
Vegetal Biology ,sélection génétique ,architecture génétique ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,triticum turgidum durum ,Biologie végétale ,ComputingMilieux_MISCELLANEOUS ,amélioration des plantes - Abstract
International audience
- Published
- 2018
3. Insights into the evolutionary history of sweet cherry (prunus avium L.)
- Author
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MARIETTE, Stéphanie, ARUNYAWAT, Uraiwan, TAVAUD-PIRRA, Muriel, ProdInra, Migration, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV] Life Sciences [q-bio] ,[SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering ,[SDV]Life Sciences [q-bio] ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,[SDV.BV] Life Sciences [q-bio]/Vegetal Biology ,[SDV.IDA] Life Sciences [q-bio]/Food engineering ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2014
4. Genotyping by sequencing polyploidy wheat using RNAseq: Pitfalls and perspectives
- Author
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TAVAUD-PIRRA, Muriel, Ranwez, Vincent, Ardisson, Morgane, Sarah, Gautier, Santoni, Sylvain, David, Jacques, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ProdInra, Archive Ouverte
- Subjects
[SDV] Life Sciences [q-bio] ,transcriptomics ,polyploids ,NGS ,[SDV]Life Sciences [q-bio] ,food and beverages ,durum wheat ,GBS - Abstract
A composite durum wheat population (Triticum turgidum, 2n=4X=28, A and B genomes) was created by crossing elite durum lines with wild (T. dicoccoides) and primitive emmer (T. dicoccum) accessions. A recessive male sterility gene was used in order to monitor the outcrossing rate in the population. Since 1997, this population is experiencing each year natural and anthropic selection with an outcrossing rate of 10 %. The EPO project aims at identifying SNPs from 100 fixed lines extracted from this important resource of diversity and to evaluate the potential of RNA seq for Genotyping by sequencing purposes. [br/] We obtained transcriptomics data for 50 individuals and built contigs using those data and standard NGS pipelines. As expected for a allotetraploid species, this first rough analysis demonstrated that for a large number of detected SNPs an excess of heterozygosity was observed. This seems to indicate that the simultaneous expression of the two A and B homeologous copies of many genes resulted in an erroneously merge of paralogous/homeologous sequences. This clearly pinpoints that such standard assembly protocols are not adapted do deal with polyploid species. [br/] We thus developed a dedicated assembly strategy that exploits strict and accession specific assemblies and Triticum monococcum and Aegilops speltoides diploids genomes to identify paralogs and homeologs in the durum wheat A and B genomes. This approach significantly increases the number of unambiguous within genome polymorphisms and offer promising perspective for genotyping by sequencing durum wheat and other polyploids of agronomic importance.
- Published
- 2013
5. Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat.
- Author
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Ranwez, Vincent, Holtz, Yan, Sarah, Gautier, Ardisson, Morgane, Santoni, Sylvain, Glémin, Sylvain, Tavaud-Pirra, Muriel, and David, Jacques
- Abstract
Background: Using Next Generation Sequencing, SNP discovery is relatively easy on diploid species and still hampered in polyploid species by the confusion due to homeology. We develop HomeoSplitter; a fast and effective solution to split original contigs obtained by RNAseq into two homeologous sequences. It uses the differential expression of the two homeologous genes in the RNA. We verify that the new sequences are closer to the diploid progenitors of the allopolyploid species than the original contig. By remapping original reads on these new sequences, we also verify that the number of valuable detected SNPs has significantly increased. Thirty accessions of the tetraploid durum wheat (Triticum turgidum, A and B genomes) were sequenced in pooled cDNA libraries. Reads were assembled in a de novo durum assembly. Transcriptomes of the diploid species, Aegilops speltoides (close B genome) and Triticum urartu (A genome) were used as reference to benchmark the method. Results: HomeoSplitter is a fast and effective solution to disentangle homeologous sequences based on a maximum likelihood optimization. On a benchmark set of 2,505 clusters containing homologous sequences of urartu, speltoides and durum, HomeoSplitter was efficient to build sequences closer to the diploid references and increased the number of valuable SNPs from 188 out of 1,360 SNPs detected when mapping the reads on the de novo durum assembly to 762 out of 1,620 SNPs when mapping on HomeoSplitter contigs. Conclusions: The HomeoSplitter program is freely available at http://bioweb.supagro.inra.fr/homeoSplitter/. This work provides a practical solution to the complex problem of disentangling homeologous transcripts in allo-tetraploids, which further allows an improved SNP detection. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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