Targeted association analysis for tolerance to salinity in rice using SSR markers

Negrão Sonia, Courtois Brigitte, Ahmadi Nourollah, Babo P., Frouin Julien, Greco Rafaella, Bruschi Gianluca, Vancoppenolle Sylvie, Katsantonis Dimitrios, Lupotto Elisabetta, Oliveira Margarida, Piffanelli Pietro. 2010. Targeted association analysis for tolerance to salinity in rice using SSR markers. In : Final program and abstracts of the 2nd International Symposium on Genomics of Plant Genetic Resources, Bologna, Italy, 24-27 April 2010. Rome : Bioversity International, Résumé, p. 109. International Symposium on Genomics of Plant Genetic Resources. 2, Bologne, Italie, 24 April 2010/27 April 2010.

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Abstract : Rice is considered as a crop sensitive to salinity; however, it is grown mainly in deltaic areas with salt problems all over Europe. European rice breeding programs (France, Greece, Italy, Portugal and Spain) have established an European Rice Genetic Resources Collection (ERGRC) of some 450 accessions, mainly temperate japonica, extensively characterised for agronomic traits and maintained by CIRAD. The main goal of the present study is to identify within this collection, a set of best performing genes and alleles for salinity tolerance, as well as the associated donors and molecular markers for use in breeding programs. In order to obtain the general organisation structure of the ERGRC we assessed its genetic diversity through a Bayesian analysis of genotypic data over 26 SSR loci. A sub-sample of 200 accessions maximizing simultaneously allele number and allelic associations was then extracted for association analysis. The sub-sample was phenotyped for salinity tolerance at an early vegetative stage under controlled conditions, being leaf Na+/K+ ratio the most discriminating trait. Based on literature review, we assembled a list with more than 100 rice candidate genes for salt tolerance, which are involved in signaling, ion homeostasis, stress tolerance, transcription regulation, general metabolism and unknown functions. With this information, we developed a database of rice QTLs and candidate genes for salinity tolerance ( We selected 16 of these candidate genes for association analysis. SSR markers were used for the association analysis. A first set of 58 common SSR ( covering these particular genes was used. In addition, we designed 320 SSR markers covering 100 kb up and downstream each candidate gene. In the end, we selected four of the designed SSR markers, the two closest to the gene and one in each end of the linkage disequilibrium region (100 kb each gene side). Results of association analysis between 16 target areas (using 60 SSR) and a dozen salinity tolerance traits are presented. Methodological constraints stem from the use of multi-allelic markers are discussed. (Texte intégral)

Classification Agris : F30 - Plant genetics and breeding
F62 - Plant physiology - Growth and development
H50 - Miscellaneous plant disorders

Auteurs et affiliations

  • Negrão Sonia, ITQB (PRT)
  • Courtois Brigitte, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0003-2118-7102
  • Ahmadi Nourollah, CIRAD-BIOS-UPR AIVA (FRA) ORCID: 0000-0003-0072-6285
  • Babo P., ITQB (PRT)
  • Frouin Julien, CIRAD-BIOS-UPR AIVA (FRA)
  • Greco Rafaella, Parco Tecnologico Padano (ITA)
  • Bruschi Gianluca, Parco Tecnologico Padano (ITA)
  • Vancoppenolle Sylvie, CIRAD-BIOS-UPR AIVA (FRA)
  • Katsantonis Dimitrios, NAGREF (GRC)
  • Lupotto Elisabetta, Instituto Sperimentale per la Cerealicoltura (ITA)
  • Oliveira Margarida, ITQB (PRT)
  • Piffanelli Pietro, Parco Tecnologico Padano (ITA)

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