Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library

To organize data resulting from the phenotypic characterization of a library of 30 000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13 928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13 928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB

The Spring of Systems Biology-Driven Breeding

International audienceGenetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies

Insertional mutagenesis: Lessons from Arabidopsis, gaining experience in rice

Abstract Insertional mutagenesis is a means of analyzing the function of genes through their disruption by foreign DNA followed by observation of the effect on phenotype. Insertion libraries are a key tool in plant functional genomics projects aimed at deciphering major developmental and physiological processes because they permit both the discovery of new genes through forward genetics screens and gene detection systems as well as the validation of genes of known sequence through reverse genetics strategies. Benefiting from experience accumulated over the last decade in the model dicotyledonous species Arabidopsis, large insertion line libraries in turn have been generated in rice (Oryza sativa L.), the model plant for cereals and grasses, in the last five years. The use of insertion mutagens has varied and encompasses T-DNA, delivered during co-culture with Agrobacterium, the genetically engineered maize transposable Ac/Ds system and the endogenous ty1-copia retroelement Tos17, mobilized during tissue culture. Here we review the current status of rice insertional mutagenesis by concentrating on specific features and advantages and drawbacks of each mutagen, and examine the establishment of this new resource from a rice functional genomics perspective

Insertional Mutagenesis: lessons from Arabidopsis, gaining experience in rice

Insertional mutagenesis is a means of analyzing the function of genes through their disruption by foreign DNA followed by observation of the effect on phenotype. Insertion libraries are a key tool in plant functional genomics projects aimed at deciphering major developmental and physiological processes because they permit both the discovery of new genes through forward genetics screens and gene detection systems as well as the validation of genes of known sequence through reverse genetics strategies. Benefiting from experience accumulated over the last decade in the model dicotyledonous species Arabidopsis, large insertion line libraries in turn have been generated in rice (Oryza sativa L.), the model plant for cereals and grasses, in the last five years. The use of insertion mutagens has varied and encompasses T-DNA, delivered during co-culture with Agrobacterium, the genetically engineered maize transposable Ac/Ds system and the endogenous ty1-copia retroelement Tos17, mobilized during tissue culture. Here we review the current status of rice insertional mutagenesis by concentrating on specific features and advantages and drawbacks of each mutagen, and examine the establishment of this new resource from a rice functional genomics perspective.http://aob.oxfordjournals.org/cgi/content/full/98/4/90

Rice genomics: Present and future

International audienc