TALome-based engineering of durable pathogen resistance in crops

Pesticides are of limited use against bacterial diseases in crops due to a lack of effective and non-toxic molecules. Thus, genetic selection of resistant crops remains the most effective approach to control bacterial pathogens. Resistance breeding requires a conceptual jump to efficiently design significant and durable resistance to a large variety of pathogens in a large number of crops simultaneously.

Date de début de projet :

01/11/2014

Date de fin du projet :

31/03/2019

Objectifs

 The CROpTAL project aims at identifying plant susceptibility hubs in major crops (cereals, citrus, legumes and Brassicaceae) targeted by Xanthomonas virulence-promoting TAL (Transcription Activator-Like) type III effectors. These conserved susceptibility targets could then be used for marker-assisted breeding of loss-of-susceptibility by selection of inactive variants of those hubs. These results will contribute to the development of durable resistance to a broad range of bacterial pathogens in the selected crops.

 The CROpTAL project aims at improving world food production and security by reducing yield losses due to pathogen pressure on major staple food crops, with a specific focus on bacterial diseases caused by Xanthomonas. Attaining this goal needs conceptual and technical jumps that this project will attempt to achieve.

Localisation

Europe - Ocean Indien

Description

To promote infection, xanthomonads have evolved a fascinating family of effector proteins, called Transcription Activator-Like (TAL) effectors, which are able to manipulate the host cell’s transcription 3/28 machinery. TAL effectors are injected into the plant cell, travel to the nucleus, and bind to specific promoter region(s) called Effector-Binding Elements (EBEs) in order to increase the expression of plant susceptibility(S) genes, i.e. genes that significantly contribute to disease progression.

TAL effectors offer new possibilities to rationalize resistance breeding, because (i) the in silico analysis of talgene sequences can directly point to the corresponding plant EBE sequences and (ii) the natural EBEvariants in plant genomes’ diversity likely correspond to loss-of-susceptibility alleles. The CROpTAL project will take advantage of the TAL effector system to find such potentially durable resistance loci. Our global approach to achieve this will be to sequence the repertoire of Xanthomonas tal genes, called TALome,from Xanthomonas infecting several major crops, such as cereals, Brassicaceae, citrus, and legumes, then find major TAL effector-targeted susceptibility hubs (i.e. plant genes that are convergently targeted by multiple TAL effectors and participate in disease induction). After functional validation of these hubs, we will screen the germplasm for EBE variants, thus making use of the natural diversity to find alleles formarker-assisted breeding.The medium- to high-throughput sequencing of TAL effector genes is the first technical obstacle toovercome:

 (i) tal genes contain a central region dedicated to DNA binding, composed of up to 33 virtually identical 102-bp repeats, and are thus difficult to sequence and assemble properly (Boch & Bonas, 2010).

(ii)A single Xanthomonas genome can harbor up to 30 highly similar tal genes.

One novelty of the CROpTAL project will be to sequence tal genes at a medium to high-through put scale by using the novel PacBio single-molecule sequencing technology. Before sequencing, one critical point will be to enrich Xanthomonas genomic DNA (gDNA) for tal genes. For this, the CROpTAL project proposes two original and pertinent methods. The first method is based on oligonucleotide capture, the second method is based on a sophisticated choice of restriction enzymes to degrade non-tal gene gDNA.  

These two complementary approaches have their own peculiarities and will lead to major technological break throughs for tal gene and TALome sequencing. Because of the degeneracy of the TAL effector code, which introduces some uncertainty in predicting EBEs, the second challenge will be to validate candidate EBEs that correspond to important susceptibility hubs. To this end, we will use a combination of in silico prediction of EBEs and high-through put transcriptome sequencing to identify the most promising S genes and/or S pathways targeted by TAL effectors, followed by the experimental validation of selected candidate S genes. A major strength of the CROpTAL project is that we will compile and cross-reference the results obtained for a large diversity of TAL effectors targeting different crop genomes.

Partenaires

  • Cirad -PVBMT
  • INRA-RHS
  • CNRS-LIMP
  • IRD-RPB

Equipe

  • Laurent NOËL CR1 CNRS 25.2 
  • Matthieu ARLAT  CNRS/LIPM.
  • Claudine ZISCHEK IR1 INRA 
  • Emmanuelle LAUBER CR1 CNRS
  • Sébastien CARRERE IR2 INRA 
  • David RENGEL IR2 INRA 
  • Claudette ICHER AJT INRA 
  • Boris SZUREK CR1 IRD 21 
  • Ralf KOEBNIK DR1 IRD 
  • Jamel ARIBI TR IRD 
  • Sandrine DUPLAN TR CIRAD 
  • PEREZ PhD Student IRD/RPB 
  • Mathilde HUTIN PhD Student CIRAD/PVBMT
  •  Lionel GAGNEVIN CR1 CIRAD /PVBMT
  • Stéphanie JAVEGNY TR CIRAD/PVBMT
  • Claudine BOYER TR CIRAD/PVBMT
  •  Olivier PRUVOST DR1 CIRAD/PVBMT
  •  Christian VERNIERE CR1 CIRAD/PVBMT 
  • Pierre LEFEUVRE CR2 CIRAD 
  • CHEN MCF ACOP INRA/IRHS 
  • Sophie BONNEAU TR INRA INRA/IRHS 
  • Armelle DARRASSE IE1  INRA/IRHS 
  • Martial BRIAND AI INRA 
  • Marie-Agnès JACQUES DR2 INRA/IRH
  • Perrine PORTIER IR2 INRA/IRHS 

Financement

ANR

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