Odile Faivre-Rampant

Characterization of WRKY co-regulatory networks in rice and Arabidopsis

BackgroundThe WRKY transcription factor gene family has a very ancient origin and has undergone extensive duplications in the plant kingdom. Several studies have pointed out their involvement in a range of biological processes, revealing that a large number of WRKY genes are transcriptionally regulated under conditions of biotic and/or abiotic stress. To investigate the existence of WRKY co-regulatory networks in plants, a whole gene family WRKYs expression study was carried out in rice (Oryza sativa). This analysis was extended to Arabidopsis thaliana taking advantage of an extensive repository of gene expression data.ResultsThe presented results suggested that 24 members of the rice WRKY gene family (22% of the total) were differentially-regulated in response to at least one of the stress conditions tested. We defined the existence of nine OsWRKY gene clusters comprising both phylogenetically related and unrelated genes that were significantly co-expressed, suggesting that specific sets of WRKY genes might act in co-regulatory networks. This hypothesis was tested by Pearson Correlation Coefficient analysis of the Arabidopsis WRKY gene family in a large set of Affymetrix microarray experiments. AtWRKYs were found to belong to two main co-regulatory networks (COR-A, COR-B) and two smaller ones (COR-C and COR-D), all including genes belonging to distinct phylogenetic groups. The COR-A network contained several AtWRKY genes known to be involved mostly in response to pathogens, whose physical and/or genetic interaction was experimentally proven. We also showed that specific co-regulatory networks were conserved between the two model species by identifying Arabidopsis orthologs of the co-expressed OsWRKY genes.ConclusionIn this work we identified sets of co-expressed WRKY genes in both rice and Arabidopsis that are functionally likely to cooperate in the same signal transduction pathways. We propose that, making use of data from co-regulatory networks, it is possible to highlight novel clusters of plant genes contributing to the same biological processes or signal transduction pathways. Our approach will contribute to unveil gene cooperation pathways not yet identified by classical genetic analyses. This information will open new routes contributing to the dissection of WRKY signal transduction pathways in plants.

Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence.

In Arabidopsis, gene expression studies and analysis of knock-out (KO) mutants have been instrumental in building an integrated view of disease resistance pathways. Such an integrated view is missing in rice where shared tools, including genes and mutants, must be assembled. This work provides a tool kit consisting of informative genes for the molecular characterization of the interaction of rice with the major fungal pathogen Magnaporthe oryzae. It also provides for a set of eight KO mutants, all in the same genotypic background, in genes involved in key steps of the rice disease resistance pathway. This study demonstrates the involvement of three genes, OsWRKY28, rTGA2.1 and NH1, in the establishment of full basal resistance to rice blast. The transcription factor OsWRKY28 acts as a negative regulator of basal resistance, like the orthologous barley gene. Finally, the up-regulation of the negative regulator OsWRKY28 and the down-regulation of PR gene expression early during M. oryzae infection suggest that the fungus possesses infection mechanisms that enable it to block host defences.

Assessment of genetic diversity in Italian rice germplasm related to agronomic traits and blast resistance (Magnaportheoryzae)

Italy is the only country in Europe with a significant land area used for rice production. In this paper, the genetic diversity of 172 national varieties and 47 foreign accessions (ITALORYZA collection) was investigated using a set of neutral markers evenly distributed throughout the 12 chromosomes. Out of the 218 alleles detected in our analysis, 17 and 29% were specific to the Italian and foreign accessions, respectively. From the neighbour-joining tree generated, six sub-groups of temperate japonica germplasm were identified. Plant height and grain type measured in the source collection were fitted to the phylogenetic tree, along with the period of variety registration. This integrated genotype–phenotype analysis revealed that specific sub-groups are characterized by uniform classes of grain type, or by similar plant size, or by period of release in the market. The whole collection was also evaluated for leaf blast resistance by inoculating the plants with three strains of Magnaporthe oryzae, representing the pathogen genetic diversity existing in Italy. Only 15 out of 172 Italian accessions (8.7%) were resistant to all three fungal strains. The correlation between genotype and leaf blast phenotype revealed that the most highly resistant Italian varieties are included in a single germplasm sub-group derived from US varieties. This study represents the starting point for carrying out detailed phenotype–genotype whole-genome association studies and identification of the genetic basis of important agronomic traits for rice cultivation in temperate climates.