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Work Package 4: Genomic analysis systems applied to biodiversity

WP Leader: P.Piffanelli (P2). Participants: P1-P4.
The objective of WP4 is the development of a genomic toolbox to support the characterisation of the existing biodiversity of rice in Italy, to carry out association analysis for specific target traits phenotyped in WP1 (blast resistance), and in WP2 (abiotic stress tolerance), to create the suitable bioinformatics infrastructure for the analysis of the metagenomic data generated in WP3 and a structured database integrsating the data generated in the course of the project. WP4 is structured in the following 5 activities.


WP4.1 Whole Genome Scan (WGS) genotyping analysis of the ITALORYZA collection
A collection of 192 accessions representing the genetic pool (biodiversity) of the Italian rice germplasm was created and characterised with a set of neutral markers (RICEIMMUNITY project - Fondazione Cariplo). For the in-depth genomic characterisation, the collection will be regenerated and plants manually selfed before carrying out DNA isolation and preparation of a DNA biorepository. A panel of 44K SNPs will be validated and employed to carry out the whole genome genotyping scan of the ITALORYZA collection and of a collection of 96 accessions representing the overall biodiversity of cultivated rice worldwide. The objective of WP4.1 is to create a haplotype map (1 SNP marker every 10 kb) to perform association studies with the data generated by the in-depth phenotyping of the ITALORYZA collection (see WP1 and WP2). The SNP genotyping data generated with the 44K SNP panel will also allow to precisely define the genomic regions introgressed in the Italian rice accessions from Asian or North-American rice germplasm, potentially carrying the genetic determinants of relevant agronomic traits for rice culture in Italy.


WP4.2 Exploitation of the Volano TILLING population
The TILLING population (1500 lines) created during the VALORYZA (MIPAAF funded) project will be integrated with the genotypic and phenotypic characterization of 500 additional mutagenised lines obtained in the course of 2009 (P2+P1). The complete (2000 lines) TILLING resource will be exploited as a platform for the functional validation of a set of candidate genes identified in the experimental activities of WP1, 2 and 3. Targeted screening for mutations in 20 candidate genes - chosen among the most representative as implicated in the control of the target traits - will be carried out using the FLUOTILL technology developed by P2 or using the 454 technology (in collaboration with P10). (c) The genotypic and phenotypic data relating to the TILLING lines will be organised in a dedicated database module accessible via a web interface to the project partners (see WP4.4).


WP4.3 Genotypic characterisation of the biodiversity of the pathogen M. oryzae in Italy
The entire collection of 150 isolates of M. oryzae derived from recent field isolations by P1 and P4 (year 2008, 2009, in the course of the project-see WP1) and from the P4 collection (strains collected in the period 1998-2000), will be systematically genotyped with a set of 13 SSR markers adopted at the international level for the molecular characterisation of biodiversity of this fungus. This activity will be carried out by P2 in strict collaboration with CIRAD-Montpellier (France). The phylogenetic analysis of the obtained data will allow to define the evolutionary patterns of M. oryzae over time, compare isolates causing leaf vs neck blast disease, select recently isolated strains representative of the existing biodiversity for the evaluation of rice genetic material for blast resistance. This new set of representative fungal isolates will also be important for the accomplishment of the phenotyping for blast resistance planned in WP1, and of the MAS approach for durable blast resistance.


WP4.4 Creation of a Bioinformatics Platform
The objective of this activity is the development of suitable bioinformatic tools to:

  1. create an ad hoc database organised in specific modules, suitable web interface to gather and integrate all genomic, phenotypic and agronomic data generated in the course of the project (see WP1-WP4);
  2. perform statistical analyses of the whole genome genotyping data and develop suitable software modules to carry out genotype-phenotype association analyses for target agronomic traits
  3. create a dedicated database module and web interface for the Volano TILLING population integrating the recorded phenotypic data, the identified mutants in candidate genes for each line under examination.