title: Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi.
abstract: BACKGROUND
  Fusarium fujikuroi is the causal agent of bakanae, the most significant seed-borne disease of rice. Molecular mechanisms regulating defence responses of rice towards this fungus are not yet fully known. To identify transcriptional mechanisms underpinning rice resistance, a RNA-seq comparative transcriptome profiling was conducted on infected seedlings of selected rice genotypes at one and three weeks post germination (wpg).
  
  
  RESULTS
  Twelve rice genotypes were screened against bakanae disease leading to the identification of Selenio and Dorella as the most resistant and susceptible cultivars, respectively. Transcriptional changes were more appreciable at 3 wpg, suggesting that this infection stage is essential to study the resistance mechanisms: 3,119 DEGs were found in Selenio and 5,095 in Dorella. PR1, germin-like proteins, glycoside hydrolases, MAP kinases, and WRKY transcriptional factors were up-regulated in the resistant genotype upon infection with F. fujikuroi. Up-regulation of chitinases and down-regulation of MAP kinases and WRKY transcriptional factors were observed in the susceptible genotype. Gene ontology (GO) enrichment analyses detected in Selenio GO terms specific to response to F. fujikuroi: 'response to chitin', 'jasmonic acid biosynthetic process', and 'plant-type hypersensitive response', while Dorella activated different mechanisms, such as 'response to salicylic acid stimulus' and 'gibberellin metabolic process', which was in agreement with the production of gibberellin A3 in Dorella plants.
  
  
  CONCLUSIONS
  RNA-seq profiling was performed for the first time to analyse response of rice to F. fujikuroi infection. Our findings allowed the identification of genes activated in one- and three- week-old rice seedlings of two genotypes infected with F. fujikuroi. Furthermore, we found the pathways involved in bakanae resistance, such as response to chitin, JA-dependent signalling and hypersensitive response. Collectively, this provides important information to elucidate the molecular and cellular processes occurring in rice during F. fujikuroi infection and to develop bakanae resistant rice germplasm.
authors: AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.|Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.
authors: Slavica
authors: S
authors: Matić
authors: Council for agricultural research and economics (CREA), Genomics Research Centre, via S. Protaso, 302 I -29017, Fiorenzuola d'Arda, PC, Italy.
authors: Paolo
authors: P
authors: Bagnaresi
authors: Council for agricultural research and economics (CREA), Genomics Research Centre, via S. Protaso, 302 I -29017, Fiorenzuola d'Arda, PC, Italy.
authors: Chiara
authors: C
authors: Biselli
authors: Council for agricultural research and economics (CREA), Genomics Research Centre, via S. Protaso, 302 I -29017, Fiorenzuola d'Arda, PC, Italy.
authors: Luigi
authors: L
authors: Orru'
authors: AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.|Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.
authors: Greice
authors: G
authors: Amaral Carneiro
authors: AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.
authors: Ilenia
authors: I
authors: Siciliano
authors: Council for agricultural research and economics (CREA), Rice Research Unit, S.S.11 to Torino, km 2,5, 13100, Vercelli, Italy.
authors: Giampiero
authors: G
authors: Valé
authors: AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.|Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy.
authors: Maria Lodovica
authors: ML
authors: Gullino
authors: AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy. davide.spadaro@unito.it.|Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2 (ex-Via L. da Vinci 44), 10095, Grugliasco, TO, Italy. davide.spadaro@unito.it.
authors: Davide
authors: http://orcid.org/0000-0001-5207-9345
authors: D
authors: Spadaro
mesh_terms: D002686:Chitin / Q000378:metabolism; D060467:Disease Resistance / Q000235:genetics*; D005670:Fusarium / Q000472:pathogenicity* / Q000502:physiology; D020869:Gene Expression Profiling; D063990:Gene Ontology; D005838:Genotype; D005875:Gibberellins / Q000378:metabolism; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000276:immunology; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D010937:Plant Growth Regulators / Q000378:metabolism; D057865:Plant Immunity / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000276:immunology*; D020156:Salicylic Acid / Q000378:metabolism; D036226:Seedlings / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D014157:Transcription Factors / Q000235:genetics / Q000276:immunology; D059467:Transcriptome
chemical_list: D005875:Gibberellins; D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors; D002686:Chitin; C007842:gibberellic acid; D020928:Mitogen-Activated Protein Kinases; D020156:Salicylic Acid
keywords: Bakanae disease; Fusarium fujikuroi; Gibberellin; Plant-fungus interaction; RNA-seq; Rice; Transcriptome