Date: Tuesday, January 17, 2012
Time: 2:40 PM
Time: 2:40 PM
Room: Pacific Salon 4-5 (2nd Floor)
Cynara cardunculus L. (2n=2x=34, haploid genome size ~1.08Gbp) includes three botanical taxa: the globe artichoke (var. scolymus), the cultivated cardoon (var. altilis), and their progenitor, the wild cardoon (var. sylvestris). Italy is the world's leading producer of globe artichoke, while the cultivated cardoon is grown mainly in Southern Europe for comestible purposes. The species has been also proposed as a source of biomass/biodiesel and nutraceuticals. In the last years at DIVAPRA – Plant Genetics and Breeding (University of Torino) many efforts have been made in developing genetic maps for this species based on F1 progenies obtained by crossing a globe artichoke genotype both with a cultivated and wild cardoon ones. We have recently developed the most saturated map of the species using ~1,000 informative markers, including a set of 172 EST-SSRs, developed within the Compositae Genome Project. Here we report the outcome of 454-based cDNA sequencing of the three mapping parents which generated 1.7M reads (695Mbp). The reads were assembled into 38,726 reference transcripts, which were then annotated. Sequence data from Illumina cDNA paired-end sequencing (46M reads, 6.9Gbp) of further eight C. cardunculus genotypes, were aligned on reference transcripts and 195,400 SNPs were called. A sample of sites was validated by Sanger re-sequencing (90% positives). In parallel, the RAD tag sequencing approach was explored on gDNA to identify candidate SNPs, segregating in the mapping progenies. From 1Gbp of sequence (Illumina), 19,061 RAD contigs were generated and ~17k SNPs mined. A subset of them was validated via CAPs marker conversion and mapped.