BACKGROUND: The 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. RESULTS: A 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. CONCLUSION: EST-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.
BACKGROUND: The 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. RESULTS: A 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. CONCLUSION: EST-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.
Authors: Dorotea López-Molina; María Dolores Navarro-Martínez; Francisco Rojas Melgarejo; Alexander N P Hiner; Soledad Chazarra; José Neptuno Rodríguez-López Journal: Phytochemistry Date: 2005-06 Impact factor: 4.072
Authors: B McDougall; P J King; B W Wu; Z Hostomsky; M G Reinecke; W E Robinson Journal: Antimicrob Agents Chemother Date: 1998-01 Impact factor: 5.191
Authors: Adam Heesacker; Venkata K Kishore; Wenxiang Gao; Shunxue Tang; Judith M Kolkman; Alan Gingle; Marta Matvienko; Alexander Kozik; Richard M Michelmore; Zhao Lai; Loren H Rieseberg; Steven J Knapp Journal: Theor Appl Genet Date: 2008-07-17 Impact factor: 5.699
Authors: Maria Miguel Castro; Daniela Rosa; Ana M Ferro; Ana Faustino; Ana Paulino; Teresa Brás; Eliana Machado; Carla Pinto Cruz; Anabela D F Belo; Paula Nozes; João Portugal; Sofia Ramôa; Diogo Mendonça; Fernanda Simões; Maria F Duarte; Liliana Marum Journal: PLoS One Date: 2021-06-09 Impact factor: 3.240