title: High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches.
abstract: • The use of quantitative disease resistance (QDR) is a promising strategy for promoting durable resistance to plant pathogens, but genes involved in QDR are largely unknown. To identify genetic components and accelerate improvement of QDR in legumes to the root pathogen Aphanomyces euteiches, we took advantage of both the recently generated massive genomic data for Medicago truncatula and natural variation of this model legume. • A high-density (≈5.1 million single nucleotide polymorphisms (SNPs)) genome-wide association study (GWAS) was performed with both in vitro and glasshouse phenotyping data collected for 179 lines. • GWAS identified several candidate genes and pinpointed two independent major loci on the top of chromosome 3 that were detected in both phenotyping methods. Candidate SNPs in the most significant locus (σ(A)²= 23%) were in the promoter and coding regions of an F-box protein coding gene. Subsequent qRT-PCR and bioinformatic analyses performed on 20 lines demonstrated that resistance is associated with mutations directly affecting the interaction domain of the F-box protein rather than gene expression. • These results refine the position of previously identified QTL to specific candidate genes, suggest potential molecular mechanisms, and identify new loci explaining QDR against A. euteiches.
authors.affiliation: UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Maxime
authors.initials: M
authors.lastname: Bonhomme
authors.affiliation: UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: André
authors.affiliation: UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Yacine
authors.initials: Y
authors.lastname: Badis
authors.affiliation: INRA, UMR AGAP, Montpellier, 34060, France.
authors.forename: Joëlle
authors.initials: J
authors.lastname: Ronfort
authors.affiliation: INRA, UMR AGAP, Montpellier, 34060, France.
authors.forename: Concetta
authors.initials: C
authors.lastname: Burgarella
authors.affiliation: INRA, UMR AGAP, Montpellier, 34060, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Chantret
authors.affiliation: INRA, UMR AGAP, Montpellier, 34060, France.
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Prosperi
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Saint-Paul, MN, 55455, USA.
authors.forename: Roman
authors.initials: R
authors.lastname: Briskine
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.affiliation: INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Debéllé
authors.affiliation: INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Navier
authors.affiliation: INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France.
authors.forename: Henri
authors.initials: H
authors.lastname: Miteul
authors.affiliation: INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Hajri
authors.affiliation: INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Baranger
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Tiffin
authors.affiliation: UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Dumas
authors.affiliation: INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France.
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Pilet-Nayel
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA.|Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA.
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
authors.affiliation: UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Jacquet
mesh_terms: D044744:Aphanomyces / Q000502:physiology*; D002874:Chromosome Mapping; D015169:Colony Count, Microbial; D003583:Cytokinins / Q000378:metabolism; D060467:Disease Resistance / Q000235:genetics*; D044783:F-Box Proteins / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D055106:Genome-Wide Association Study; D046913:Medicago truncatula / Q000235:genetics* / Q000254:growth & development / Q000276:immunology / Q000382:microbiology*; D009154:Mutation / Q000235:genetics; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D043367:Ralstonia / Q000502:physiology; D053204:Root Nodules, Plant / Q000378:metabolism / Q000382:microbiology; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D015854:Up-Regulation
chemical_list: D003583:Cytokinins; D044783:F-Box Proteins; D010940:Plant Proteins; D012333:RNA, Messenger; D014157:Transcription Factors
keywords: Aphanomyces euteiches; F-box protein; Genome-wide association study; Medicago truncatula; oomycete; partial resistance; root