Twelve lines of durum wheat representative of the genetic variability deployed in the selection programs will be used to produce 12 non-normalized Illumina libraries of the RNA-seq paired-end type using a single tissue (seedling leaves). The libraries will be sequenced using an Illumina Genome Analyser II platform. The sequences will be aligned on the transcriptome reconstructed based on publicly available information (e.g. ESTs).
In parallel, four cDNA libraries extracted from seedling leaves, seedling roots and kernel at an early and late stage of grain filling will be sequenced with a Roche GS-FLX 454 platform from DISTA, University of Bologna (prof. Tuberosa's group).
The joint analysis of these two sets of sequence data will allow us to identify a set of ca. 5,000 highly informative SNPs. This set of SNPs will be used in the second and/or third years of the project (2011-2012) to develop a high-throughput SNP platform based on BeadArray Illumina technology (GoldenGate Assay).