Genetic Resources and Crop Evolution

, Volume 55, Issue 7, pp 1029–1046 | Cite as

Identification of artichoke SSR markers: molecular variation and patterns of diversity in genetically cohesive taxa and wild allies

  • Gabriella Sonnante
  • Anna Vittoria Carluccio
  • Angelo De Paolis
  • Domenico Pignone
Research Article


A set of 24 microsatellite markers was identified in the artichoke genome, using various approaches. A genomic library allowed the development of 14 SSR markers, whereas the other 10 were obtained from gene intron/UTR regions or from other species. Allelic variation was scored in C. cardunculus (artichoke, cultivated cardoon, and wild cardoon) samples, and in other wild Cynara allies. For the 23 polymorphic loci, a total of 165 alleles were scored, 135 of which in the artichoke primary genepool, and the remaining ones in the other Cynara species. Some allele combinations were able to identify artichoke varietal types, and some alleles were unique to specific groups. This makes these markers potentially useful in product traceability and in contributing to the saturation of genetic maps. The percentage of shared alleles between C. cardunculus taxonomic groups, and Nei’s genetic distances indicated that wild cardoons from the Eastern Mediterranean were more closely related to artichoke and less to cultivated cardoon in comparison to wild cardoons from the Western Mediterranean, and the genetic distance between the two wild cardoon genepools was rather high. The UPGMA dendrogram based on Nei’s genetic distances revealed that artichokes formed a fairly defined cluster, whereas Eastern wild cardoons occupied another branch, and Western wild cardoons were clustered together with cultivated cardoons. The transferability of microsatellite markers to other Cynara wild species was quite good. Sequencing alleles at three loci showed that, apart from microsatellite length variation, point mutations and insertion/deletions were quite abundant especially when comparing C. cardunculus to the other Cynara species. In the sequenced regions, some SNPs were identified which distinguished artichoke on one side, and cultivated and wild cardoon on the other, while other SNPs were apportioned according to the geographic distribution of Cynara wild species.


Artichoke Cardoon Cynara Genetic diversity Microsatellites Wild relatives 



The authors are grateful to the colleagues who donated seeds, and to Ms. Anita Morgese for DNA sequencing. This study was funded by: CNR, Project ‘AG.P02.004, Banca del DNA vegetale’; CRA-MiPAF, Project ‘FAO-RGV: Implementazione Nazionale del Trattato Internazionale FAO Risorse Genetiche Vegetali’; and EU Project AGRI GEN RES 063, CYNARES.


  1. Basnizki J, Zohary D (1994) Breeding of seed planted artichoke. Plant Breed Rev 12:253–269Google Scholar
  2. Bianco VV (2005) Present situation and future potential of artichoke in the Mediterranean basin. Acta Hortic 681:39–55Google Scholar
  3. Calabrese N, Bianco VV (2000) Effect of gibberellic acid on yield and quality of seed grown artichoke (Cynara cardunculus L. var. scolymus (L.) Fiori). Acta Hortic 514:25–32Google Scholar
  4. De Paolis A, Pignone D, Morgese A, Sonnante G (2008) Characterization and differential expression analysis of artichoke phenylalanine ammonia-lyase coding sequences. Physiol Plant 132:33–43PubMedGoogle Scholar
  5. Elia A, Miccolis V (1996) Relationships among 104 artichoke (Cynara scolymus L.) accessions using cluster analysis. Adv Hortic Sci 10:158–162Google Scholar
  6. Foury C (1989) Ressources génétiques et diversification de l’artichaut (Cynara scolymus L.). Acta Hortic 242:155–166Google Scholar
  7. Grattapaglia D, Sederoff VR (1994) Genetic-linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross mapping strategy and RAPD markers. Genetics 137:1121–1137PubMedGoogle Scholar
  8. Hammer K, Knüpffer H, Laghetti G, Perrino P (1999) Seeds from the past. A catalogue of germplasm in Central and North Italy. CNR, BariGoogle Scholar
  9. Jain S, Jain RK, McCouch SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109:965–977PubMedCrossRefGoogle Scholar
  10. Jump AS, Dawson DA, James CM, Woodward FI, Burke T (2002) Isolation of polymorphic microsatellites in the stemless thistle (Cirsium acaule) and their utility in other Cirsium species. Mol Ecol Notes 2:589CrossRefGoogle Scholar
  11. Kahru A, Dieterich JH, Savolainen O (2000) Rapid expansion of microsatellite sequences in pines. Mol Biol Evol 17:259–265Google Scholar
  12. Kutil BL, Williams CG (2001) Triplet-repeat microsatellites shared among hard and soft pines. Am Genet Assoc 92:327–332Google Scholar
  13. Lacape JM, Dessauw D, Rajab M, Noyer JL, Hau B (2007) Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Mol Breed 19:45–58CrossRefGoogle Scholar
  14. Lanteri S, Acquadro A, Comino C, Mauro R, Mauromicale G, Portis E (2006) A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers. Theor Appl Genet 112:347–357CrossRefGoogle Scholar
  15. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398Google Scholar
  16. López Anido FS, Firpo IT, García SM, Cointry EL (1998) Estimation of genetic parameters for yield traits in globe artichoke (Cynara scolymus L.). Euphytica 103:61–66CrossRefGoogle Scholar
  17. Macaulay M, Ramsay L, Powell W, Waugh R (2001) A representative, highly informative ‘genotyping set’ of barley SSRs. Theor Appl Genet 102:801–809CrossRefGoogle Scholar
  18. Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J (2002) Microsatellites in Zea – variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet 104:436–450PubMedCrossRefGoogle Scholar
  19. Nei M (1972) Genetic distance between populations. Am Nat 106:283–292CrossRefGoogle Scholar
  20. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  21. Pignone D, Sonnante G (2004) Wild artichokes of south Italy: did the story begin here? Genet Resour Crop Evol 51:577–580CrossRefGoogle Scholar
  22. Porceddu E, Dellacecca V, Bianco VV (1976) Classificazione numerica di cultivar di carciofo. In: Proceed. of the 2nd international congress on Artichoke, Bari 1973. Minerva Medica, Turin, Italy, pp 1105–1119Google Scholar
  23. Pujol B, David P, McKey D (2005) Microevolution in agricultural environments: how a traditional Amerindian farming practice favours heterozygosity in cassava (Manihot esculenta Crantz, Euphorbiaceae). Ecol Lett 8:138–147CrossRefGoogle Scholar
  24. Rallo P, Tenzer I, Gessler C, Baldoni L, Dorado G, Martìn A (2003) Transferability of olive microsatellite loci across the genus Olea. Theor Appl Genet 107:940–946PubMedCrossRefGoogle Scholar
  25. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023PubMedGoogle Scholar
  26. Rohrer JR, Ahmad R, Southwick SM, Potter D (2004) Microsatellite analysis of relationships among North American plums (Prunus sect. Prunocerasus, Rosaceae). Plant Syst Evol 244:69–75CrossRefGoogle Scholar
  27. Rottenberg A, Zohary D (1996) The wild ancestry of the cultivated artichoke. Genet Resour Crop Evol 43:53–58CrossRefGoogle Scholar
  28. Rottenberg A, Zohary D (2005) Wild genetic resources of cultivated artichoke. Acta Hortic 681:307–311Google Scholar
  29. Rottenberg A, Zohary D, Nevo E (1996) Isozyme relationships between cultivated artichoke and the wild relatives. Genet Resour Crop Evol 43:59–62CrossRefGoogle Scholar
  30. Sambrook J, Russell RW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring, New YorkGoogle Scholar
  31. Scott LJ, Shepherd M, Henry RJ (2003) Characterization of highly conserved microsatellite loci in Araucaria cunninghamii and related species. Plant Syst Evol 236:115–123CrossRefGoogle Scholar
  32. Sethy NK, Chouldhary S, Shokeen B, Bhatia S (2006) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor Appl Genet 112:347–357PubMedCrossRefGoogle Scholar
  33. Sonnante G, De Paolis A, Lattanzio V, Perrino P (2002) Genetic variation in wild and cultivated artichoke revealed by RAPD markers. Genet Resour Crop Evol 49:247–252CrossRefGoogle Scholar
  34. Sonnante G, De Paolis A, Pignone D (2004a) Relationships among artichoke cultivars and some related wild taxa based on AFLP markers. Plant Genet Resour 1:125–133CrossRefGoogle Scholar
  35. Sonnante G, Ippedico M, De Paolis A (2004b) Microsatellite and AFLP markers in a world artichoke collection. Acta Hortic 660:61–68Google Scholar
  36. Sonnante G, Carluccio AV, Vilatersana R, Pignone D (2007a) On the origin of artichoke and cardoon from the Cynara gene pool as revealed by rDNA sequence variation. Genet Resour Crop Evol 54:483–495CrossRefGoogle Scholar
  37. Sonnante G, Pignone D, Hammer K (2007b) The domestication of artichoke and cardoon: from Roman times to genomics age. Ann Bot 100:1095–1100PubMedCrossRefGoogle Scholar
  38. Taylor JS, Durkin JMH, Breden F (1999) The death of a microsatellite: a phylogenetic perspective on microsatellite interruptions. Mol Biol Evol 16:567–572PubMedGoogle Scholar
  39. This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini L, Crespan M, Dangl GS, Eisenheld C, Ferreira-Monteiro F, Grando S, Ibáñez J, Lacombe T, Laucou V, Magalhães R, Meredith CP, Milani M, Peterlunger E, Regner F, Zulini L, Maul E (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458PubMedCrossRefGoogle Scholar
  40. Van Treuren R, Kuittinen H, Kärkkäinen K, Baena-Gonzales E, Savolainen A (1997) Evolution of microsatellites in Arabis lyrata, outcrossing relative of Arabidopsis thaliana. Mol Biol Evol 14:220–229PubMedGoogle Scholar
  41. Viruel MA, Escribano P, Barbieri M, Ferri M, Hormaza JI (2005) Fingerprinting, embryo type and geographic differentiation in mango (Mangifera indica L., Anacardiaceae) with microsatellites. Mol Breed 15:383–393CrossRefGoogle Scholar
  42. Wiklund A (1992) The genus Cynara L. (Asteraceae-Cardueae). Bot J Linn Soc 109:75–123CrossRefGoogle Scholar
  43. Whitton J, Rieseberg LH, Ungerer MC (1997) Microsatellite loci are not conserved across Asteraceae. Mol Biol Evol 14:202–209Google Scholar
  44. Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX (1997) POPGENE, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada (program available from:
  45. Zhu Y, Queller DC, Strassmann JE (2000) A phylogenetic perspective on sequence evolution in microsatellite loci. J Mol Evol 50:324–338PubMedGoogle Scholar
  46. Zohary D, Basnizki J (1975) The cultivated artichoke Cynara scolymus. Its probable wild ancestors. Econ Bot 29:233–235Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Gabriella Sonnante
    • 1
  • Anna Vittoria Carluccio
    • 1
  • Angelo De Paolis
    • 2
  • Domenico Pignone
    • 1
  1. 1.National Research Council (CNR) – Institute of Plant GeneticsBariItaly
  2. 2.CNR – Institute of Sciences of Food ProductionLecceItaly

Personalised recommendations