Abstract
BackgroundThe globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers.ResultsA unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations.ConclusionEST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
Highlights
The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin
The transcript assembly and unigene consensus sequences are supplied as electronic supplementary materials (See Additional file 1, 2, 3: EST assembly, 19,055 unigenes, ACE assembly file)
We previously developed three mapping population for the development of C. cardunculus genetic maps by crossing one globe artichoke non spiny genotype with a spiny genotype of globe artichoke or cultivated cardoon or wild cardoon
Summary
The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. The globe artichoke Cynara cardunculus is a member of the Asteraceae (Compositae) family, and originates from the Mediterranean basin [1]. The species is subdivided into three taxa - the globe artichoke BMC Genomics 2009, 10:454 http://www.biomedcentral.com/1471-2164/10/454 wild cardoon [var. The edible part of the globe artichoke plant is provided by its immature inflorescence, referred as a capitulum or head [2], and represents a significant component of the Mediterranean diet. In spite of its economic importance, little breeding effort has been applied to date in the globe artichoke
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