Molecular characterization of the European rice collection in view of association mapping

Brigitte Courtois*, Raffaella Greco, Gianluca Bruschi, Julien Frouin, Nourollah Ahmadi, Gaëtan Droc, Chantal Hamelin, Manuel Ruiz, Jean Charles Evrard, Dimitrios Katsantonis, Margarida Oliveira, Sonia Cabrita Negrao, Stefano Cavigiolo, Elisabetta Lupotto, Pietro Piffanelli

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

In South Europe, rice is grown as an irrigated crop in river deltas where it plays an important role in soil desalinization. Specific varieties are needed for these tough conditions. We analyzed the genetic structure of a set of 305 varieties coming from the European Rice Germplasm Collection (ERGC) with 90 single nucleotide polymorphisms and compared it with a reference set representative of the diversity of Oryza sativa (mini-Germplasm Bank (GB)). These accessions had been characterized for their grain type and growth cycle duration. The polymorphism information contents of the ERGC were lower than those of the mini-GB, indicating a narrower genetic basis. Indeed, almost all ERGC accessions belong to the japonica group. Within the japonica group, both a dendrogram and a Bayesian clustering identified two major clusters. The first cluster encompassed tropical japonicas and American varieties from USA and Argentina characterized by long and narrow grains and medium to long duration. On a finer level, tropical japonicas appear separated from the other accessions. The second cluster is composed of European varieties mostly early or medium in duration and Asian temperate accessions, with a subgrouping based on grain format. A set of 200 accessions was composed for association mapping studies on traits such as salt tolerance.

Original languageEnglish (US)
Pages (from-to)233-235
Number of pages3
JournalPlant Genetic Resources: Characterisation and Utilisation
Volume9
Issue number2
DOIs
StatePublished - Jul 1 2011

Keywords

  • O. sativa
  • association mapping
  • genetic diversity
  • single nucleotide polymorphisms
  • temperate japonica

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

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