Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Volante Andrea, Tondelli Alessandro, Desiderio Francesca, Abbruscato Pamela, Menin Barbara, Biselli Chiara, Casella Laura, Singh Namrata, McCouch Susan, Tharreau Didier, Zampieri Elisa, Cattivelli Luigi, Valè Giampiero. 2020. Genome wide association studies for japonica rice resistance to blast in field and controlled conditions. Rice, 13:71, 17 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
Published version - Anglais
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Abstract : Background: Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. Results: The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11–2 and BRGC11–3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. Conclusions: We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.

Mots-clés Agrovoc : Oryza sativa, Pyricularia oryzae, Maladie des plantes, Résistance aux maladies, Expérimentation au champ, Résistance génétique, pyriculariose du riz

Mots-clés libres : Rice, Rice blast, Resistance, GWAS, Japonica

Classification Agris : H20 - Plant diseases
H01 - Protection of plants - General aspects

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Auteurs et affiliations

  • Volante Andrea, CREA (ITA) - auteur correspondant
  • Tondelli Alessandro, CREA (ITA)
  • Desiderio Francesca, CREA (ITA)
  • Abbruscato Pamela, Parco Tecnologico Padano (ITA)
  • Menin Barbara, Parco Tecnologico Padano (ITA)
  • Biselli Chiara, CREA (ITA)
  • Casella Laura, SA.PI.SE. Coop. Agricola (ITA)
  • Singh Namrata, Cornell University (USA)
  • McCouch Susan, Cornell University (USA)
  • Tharreau Didier, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0003-3961-6120
  • Zampieri Elisa, CREA (ITA)
  • Cattivelli Luigi, CREA (ITA)
  • Valè Giampiero, CREA (ITA) - auteur correspondant

Source : Cirad-Agritrop (

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