Advertisement

Insights into the Population Structure and Association Mapping in Globe Artichoke

  • Domenico Rau
  • Monica Rodriguez
  • Giovanna Attene
  • Limbo Baghino
  • Anna Barbara Pisanu
  • Davide Sanna
  • Alberto Acquadro
  • Ezio Portis
  • Cinzia CominoEmail author
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Understanding the population genetic structure of crop gene pool is a fundamental prerequisite in plant evolutionary biology and plant breeding. Based on this consideration, in this chapter we pursued two main aims. The first was to review the status of the research pointed at deciphering the population structure of the gene pools of globe artichoke. The second was to show how the use of a well-characterized germplasm collection together with deep genotyping could serve the identification of QTLs for traits of agronomic and economic relevance in globe artichoke.

Keywords

Population structure Germplasm collection Association mapping QTLs GWA 

References

  1. Acquadro A, Barchi L, Portis E, Carrasquilla-Garcia N, Tirone M, Lanteri S, Comino C (2016) RAD2seq: an efficient protocol for plant genotyping by sequencing. Acta Hortic 1147:1–8.  https://doi.org/10.17660/ActaHortic.2016.1147.1CrossRefGoogle Scholar
  2. Acquadro A, Cerruti E, Comino C, Rodriguez M, Pisanu AB, Baghino L, Sanna D, Attene G, Portis E, Rau D (2017a) Rad-tag sequencing and association mapping in a globe artichoke germplasm collection. In: Proceedings of the joint congress SIBV-SIGA, Pisa, Italy, 19/22 Sep 2017. ISBN 978-88-904570-7-4. Poster Communication Abstract—2.19 Google Scholar
  3. Acquadro A, Barchi L, Portis E, Mangino G, Valentino D, Mauromicale G, Lanteri S (2017b) Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. Sci Rep 7:5617CrossRefPubMedCentralGoogle Scholar
  4. Basnizki J, Zohary D (1987) A seed planted cultivar of globe artichoke. HortScience 22:678–679Google Scholar
  5. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2633–2635CrossRefGoogle Scholar
  6. Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824CrossRefGoogle Scholar
  7. Cadinu M, Mallica GM, Lanteri S, Repetto A, Frau A, Portis E, Baghino L, Pisanu AB (2007) Possibilità di rilancio per lo Spinoso Sardo. Speciale carciofo. L’informatore Agrario 22:44–46Google Scholar
  8. Calabrese N (2016) From Mediterranean basin to the Andean mountains, the long journey of the artichoke that unites different people and cultures. In: IX International symposium on artichoke, cardoon and their wild relatives, pp 23–34Google Scholar
  9. Ciancolini A, Rey NA, Pagnotta MA, Crinò P (2012) Characterization of Italian spring globe artichoke germplasm: morphological and molecular profiles. Euphytica 186:433–443CrossRefGoogle Scholar
  10. Comino C, Portis E, Gianoglio S, Acquadro A, Pisanu AB, Baghino L, Sanna D, Rau D, Rodriguez M, Attene G (2016) Towards a genome-wide association (GWA) mapping approach in globe artichoke. Acta Hortic 1147. ISHS 2016.  https://doi.org/10.17660/actahortic.2016.1147.7
  11. Crinò P, Pagnotta MA (2017) Phenotyping, genotyping, and selections within Italian local landraces of Romanesco globe artichoke. Diversity 9:14CrossRefGoogle Scholar
  12. Crinò P, Tavazza R, Munoz NAR, Nisini PT, Saccardo F, Ancora G, Pagnotta MA (2008) Recovery, morphological and molecular characterization of globe artichoke ‘Romanesco’ landraces. Genet Resour Crop Evol 55:823–833CrossRefGoogle Scholar
  13. De Vos NE (1992) Artichoke production in California. HortTechnology 2:438–444CrossRefGoogle Scholar
  14. Deidda M (1967) Contributo al miglioramento genetico del carciofo. In: Atti 1° Congresso Internazionale Di Studi sul Carciofo. Minerva Medica, Torino, pp 157–174Google Scholar
  15. Dellacecca VV, Magnifico V, Marzi V, Porceddu E, Scarascia Mugnozza GT (1976) Contributo alla conoscenza delle varietà di carciofo coltivate nel mondo. In: Proceeding of international congress on artichoke. Minerva Medica, Torino, pp 119–316Google Scholar
  16. Elia A, Miccolis V (1996) Relationship among 104 artichoke (Cynara scolymus L.) accessions using cluster analysis. Adv Horticult Sci 10:158–162Google Scholar
  17. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedCentralGoogle Scholar
  18. Gaudeul M, Till-Bottraud I, Barjon F, Manel S (2004) Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers. Heredity 92:508CrossRefPubMedCentralGoogle Scholar
  19. Gill DE, Chao L, Perkins SL, Wolf JB (1995) Genetic mosaicism in plants and clonal animals. Annu Rev Ecol Syst 26:423–444CrossRefGoogle Scholar
  20. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723CrossRefPubMedCentralGoogle Scholar
  21. Lanteri S, Di Leo I, Ledda L, Mameli MG, Portis E (2001) RAPD variation within and among populations of globe artichoke cultivar ‘Spinoso sardo’. Plant Breeding 120:243–246CrossRefGoogle Scholar
  22. Lanteri S, Acquadro A, Saba E, Portis E (2004) Molecular fingerprinting and evaluation of genetic distances among selected clones of globe artichoke (Cynara cardunculus L. var. scolymus L.). J Hortic Sci Biotechnol 79:863–870CrossRefGoogle Scholar
  23. Liu HJ, Yan J (2019) Crop genome-wide association study: a harvest of biological relevance. Plant J 97:8–18CrossRefPubMedCentralGoogle Scholar
  24. Lushai G, Loxdale HD (2002) The biological improbability of a clone. Genet Res 79:1–9CrossRefPubMedCentralGoogle Scholar
  25. Mariette S, Chagné D, Lézier C, Pastuszka P, Raffin A, Plomion C, Kremer A (2001) Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers. Heredity 86:469–479CrossRefPubMedCentralGoogle Scholar
  26. Mauro RP, Portis E, Acquadro A, Lombardo S, Mauromicale G, Lanteri S (2009) Genetic diversity of globe artichoke landraces from Sicilian small-holdings: implications for evolution and domestication of the species. Conserv Genet 10:431–440CrossRefGoogle Scholar
  27. Mauro RP, Portis E, Lanteri S, Mauromicale G (2012) Genotypic and bio-agronomical characterization of an early Sicilian landrace of globe artichoke. Euphytica 186:357–366CrossRefGoogle Scholar
  28. Mauro RP, Portis E, Lanteri S, Monaco AL, Mauromicale G (2015) Clonal selection in a globe artichoke landrace: characterization of superior germplasm to improve cultivation in Mediterranean environments. J Agric Sci 153:102–113CrossRefGoogle Scholar
  29. Mauromicale G, Ierna A (2000) Panorama varietale e miglioramento genetico del carciofo. L’Informatore Agrario 26:39–45Google Scholar
  30. McKey D, Elias M, Pujol B, Duputié A (2010) The evolutionary ecology of clonally propagated domesticated plants. New Phytol 186:318–332CrossRefGoogle Scholar
  31. Orive ME (2001) Somatic mutations in organisms with complex life histories. Theor Popul Biol 59:235–249CrossRefGoogle Scholar
  32. Pagnotta MA, Fernández JA, Sonnante G, Egea-Gilabert C (2017) Genetic diversity and accession structure in European Cynara cardunculus collections. PLoS One 12:e0178770CrossRefPubMedCentralGoogle Scholar
  33. Pavan S, Curci PL, Zuluaga DL, Blanco E, Sonnante G (2018) Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon. PLoS One 13:e0205988CrossRefPubMedCentralGoogle Scholar
  34. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7(5):e37135. PubMed http://dx.doi.org/10.1371/journal.pone.0037135CrossRefPubMedCentralGoogle Scholar
  35. Porceddu E, Dellacecca V, Bianco VV (1976) Classificazione numerica di cultivar di carciofo. In: Atti 2nd Congresso Internazionale Di Studi sul Carciofo. Minerva Medica, Torino, pp 1105–1119Google Scholar
  36. Portis E, Mauromicale G, Barchi L, Mauro R, Lanteri S (2005) Population structure and genetic variation in autochthonous globe artichoke germplasm from Sicily Island. Plant Sci 168:1591–1598CrossRefGoogle Scholar
  37. Pritchard JK, Stephens M, Donnelly P (2000a) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  38. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000b) Association mapping in structured populations. Am J Hum Genet 67:170–181CrossRefPubMedCentralGoogle Scholar
  39. Rau D, Comino C, Acquadro A, Pisanu AB, Baghino L, Sanna D, Rodriguez M, Attene G, Portis E (2015) First insights into the population structure, linkage disequilibrium & association mapping in a globe artichoke germplasm collection. In: Proceedings of the joint congress SIBV-SIGA, Milano, Italy, 8/11 Sep 2015. ISBN 978-88-904570-5-0. Poster Communication Abstract—D.34Google Scholar
  40. Schlötterer C (2004) The evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63CrossRefPubMedCentralGoogle Scholar
  41. Schreiber M, Stein N, Mascher M (2018) Genomic approaches for studying crop evolution. Genome Biol 19:140CrossRefPubMedCentralGoogle Scholar
  42. Vanella B, Porceddu E, De Pace C (1981) Applicazioni di metodi di analisi numerica per il miglioramento genetico del carciofo. In: Atti 3° Congresso Internazionale Di Studi sul Carciofo. Laterza, Bari, pp 797–807Google Scholar
  43. Whitham TG, Slobodchikoff CN (1981) Evolution by individuals, plant–herbivore interactions, and mosaics of genetic variability: the adaptive significance of somatic mutations in plants. Oecologia 49:287–292CrossRefPubMedCentralGoogle Scholar
  44. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160CrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Domenico Rau
    • 1
  • Monica Rodriguez
    • 1
  • Giovanna Attene
    • 1
  • Limbo Baghino
    • 2
  • Anna Barbara Pisanu
    • 2
  • Davide Sanna
    • 2
  • Alberto Acquadro
    • 3
  • Ezio Portis
    • 3
  • Cinzia Comino
    • 3
    Email author
  1. 1.Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG)Università degli Studi di SassariSassariItaly
  2. 2.Agenzia Agris Sardegna, Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture IntensiveSassariItaly
  3. 3.DISAFA Plant Genetics and BreedingUniversity of TorinoGrugliasco, TorinoItaly

Personalised recommendations