Genetic diversity and population structure in a european collection of rice

Courtois Brigitte, Frouin Julien, Greco Rafaella, Bruschi Gianluca, Droc Gaëtan, Hamelin Chantal, Ruiz Manuel, Clément Guy, Evrard Jean-Charles, Van Coppenole Sylvie, Katsantonis Dimitrios, Oliveira Margarida, Negrão Sonia, Matos Celina, Cavigiolo Stefano, Lupotto Elisabetta, Piffanelli Pietro, Ahmadi Nourollah. 2012. Genetic diversity and population structure in a european collection of rice. Crop Science, 52 (4) : pp. 1663-1675.

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Quartile : Q2, Sujet : AGRONOMY

Abstract : In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using modelbased and distance-based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classifi ed into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best-supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Oryza glaberrima, Collection de matériel génétique, Variation génétique, Polymorphisme génétique, Marqueur génétique

Mots-clés géographiques Agrovoc : Europe du Sud

Mots-clés complémentaires : Oryza sativa indica, Oryza sativa japonica

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA)
  • Greco Rafaella, Parco Tecnologico Padano (ITA)
  • Bruschi Gianluca, Parco Tecnologico Padano (ITA)
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Hamelin Chantal, CIRAD-BIOS-UMR AGAP (FRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8153-276X
  • Clément Guy, CIRAD-BIOS-UMR AGAP (FRA)
  • Evrard Jean-Charles, CIRAD-BIOS-UMR AGAP (FRA)
  • Van Coppenole Sylvie
  • Katsantonis Dimitrios, NAGREF (GRC)
  • Oliveira Margarida, ITQB (PRT)
  • Negrão Sonia, ITQB (PRT)
  • Matos Celina
  • Cavigiolo Stefano, Istituto Sperimentale per la Cerealicoltura (ITA)
  • Lupotto Elisabetta, Istituto Sperimentale per la Cerealicoltura (ITA)
  • Piffanelli Pietro, Parco Tecnologico Padano (ITA)
  • Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285

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