An ARIMNet project
WP coordinator: INRA-IGEPP
Other partners involved: CSIC, INRAT, CRRGC, INRAM, IAV, ARC
Objectives
- To identify genes/QTL controlling resistances to biotic (ascochyta, broomrape, fusarium, rust) and abiotic (drought) stresses (below referred to as target stresses) in pea and faba bean relevant for the development of these crops in mediterranean areas.
- To assess the stability of these QTL across pathogen variation, environments, and resistance sources
- To identify genes/QTL controlling plant architectural and developmental traits likely to contribute to the control of biotic and abiotic stresses
- To suggest choice stress resistance and architectural genes/QTL combinations for breeding for mediterranean areas
- To identify and validate candidate genes for their involvement in stress resistance or tolerance
Methodology and study materials
T4.1: Development of specific standard markers for mapping in pea: SSR markers will be developped from pea EST sequences available in public databases and that will be made available in the course of the project from current international initiatives (pea cDNA and gDNA public sequencing projects currently carried on in USA, Canada, France). Both these eSSR, previous public and published SSR markers from the Agrogene consortium, and available SNP markers will be used for mapping.
T4.2: In addition, a new set of 384 SNP markers designed within resistance genes identified (following transcriptomic or protein profiling previously published studies on target stresses), or to identify in the project course studies in T4.8, and known genes controlling plant architecture and development will be established and used for mapping. This will involve a listing of candidate genes for resistance, sequencing of these genes on a set of 16 pea parental accessions and SNP choice and design.
T4.3: Development and/or complementation of molecular maps will be conducted with SSR and SNP markers on 4 existing pea RIL populations (3 provided by INRA and 1 by CSIC) segregating for quantitative resistance to M.pinodes or for resistance to Orobanche and/or rust. Mapping will be performed using mainly markers likely to be used as bridge markers between maps (SSR and SNP markers obtained in T4.1 and T4.2) to allow comparative mapping between populations. Linkage studies will also be carried on F2 and RIL faba bean populations segregating for resistance to Orobanche.
T4.4: Phenotyping RIL and F2 pea and faba bean populations (diverse genetic backgrounds) for resistance to target stresses and plant architectural traits using methodologies developped in WP2 (biotic stresses, plant architecture) and WP3 (abiotic stresses) both in the field under multienvironment field trials and under growth chamber controlled conditions. Parental lines of RIL and F2 populations will be scored for all the biotic and abiotic stresses included in the project to discern whether these RIL populations also segregates for resistance/tolerance to additional stresses.
T4.5: Analysis of QTLs stability in different environments, towards pathogen variability, as well as in diverse genetic backgrounds (comparative analysis between populations using SSR and SNP bridge markers). Analysis of colocations between QTL controlling resistance to different biotic and abiotic constraints, and genes/QTL controlling plant architecture and development.
T4.6: Assessement of genetic progress for resistance to target stresses in large sets of accessions (192 independent pea cultivars, 300 faba bean local populations) adapted to cropping in various countries covering the mediterranean basin through (i) phenotyping for resistance and plant architecture using methodologies developped in WP2 (biotic stresses, architecture) and WP3 (abiotic stresses) both in the field and under controlled conditions; (ii) classification using anonymous SSR markers; (iii) a posteriori control of presence/absence of favourable alleles at QTL controlling resistance to stresses and architectural traits.
T4.7: Marker Assisted Breeding. Once the genes and QTLs have been identified for each stress and assessed for stability, the next step will be to select a set of markers linked to these QTLs that could be used for the simultaneous selection for different stresses. First crosses will be done for pyramiding of multiple resistances into elite cultivars and selection will be aided by these set of markers.
T4.8: Further transcriptomic or proteomic studies (CDNA-AFLP, SuperSAGE, microarrays, protein profiling) will be set up in order to identify genes or proteins differentially expressed between a resistant and a susceptible accessions to target stresses. The combination of these techniques will allow the establishment of a global and detailed picture of all genes expressed or differentially regulated during this particular interactions giving relevant information about the mechanisms of resistance acting at the molecular level. In addition, it will allow the full characterisation of candidate genes selected from the global view of the interaction, and assumed to be implicated in resistance.
T4.9: Validation of candidate genes from published, existing and planned (T4.8) transcriptomic and proteomic studies for (i) potential involvement in individual and crossed stresses, through the validation of gene expression in resistant / susceptible accessions following different stress applications by qRT-PCR (ii) development and mapping of genic molecular markers (cf T4.1) and analysis of colocalisations with QTL.
Deliverables:
D4.1: List of polymorphic eSSR and SNP markers for genetic mapping and pea map comparisons
D4.2: A set of SNP markers in pea designed in genes involved in stress resistance and plant architecture and development, likely to allow the rapid mapping or diversity study of resistance genes.
D4.3: High density pea linkage maps from populations segregating for resistance biotic and abiotic factors
D4.4: Identification, and determination of the genetic effects of the QTLs controlling polygenic traits
D4.5: Information on QTL stability across diverse field locations, pathogen variability and plant genetic backgronds
D4.6: Development of standard markers for pyramiding and rapid screening
D4.7: List of candidate genes likely to be involved in resistances to stresses.
Other partners involved: CSIC, INRAT, CRRGC, INRAM, IAV, ARC
Objectives
- To identify genes/QTL controlling resistances to biotic (ascochyta, broomrape, fusarium, rust) and abiotic (drought) stresses (below referred to as target stresses) in pea and faba bean relevant for the development of these crops in mediterranean areas.
- To assess the stability of these QTL across pathogen variation, environments, and resistance sources
- To identify genes/QTL controlling plant architectural and developmental traits likely to contribute to the control of biotic and abiotic stresses
- To suggest choice stress resistance and architectural genes/QTL combinations for breeding for mediterranean areas
- To identify and validate candidate genes for their involvement in stress resistance or tolerance
Methodology and study materials
T4.1: Development of specific standard markers for mapping in pea: SSR markers will be developped from pea EST sequences available in public databases and that will be made available in the course of the project from current international initiatives (pea cDNA and gDNA public sequencing projects currently carried on in USA, Canada, France). Both these eSSR, previous public and published SSR markers from the Agrogene consortium, and available SNP markers will be used for mapping.
T4.2: In addition, a new set of 384 SNP markers designed within resistance genes identified (following transcriptomic or protein profiling previously published studies on target stresses), or to identify in the project course studies in T4.8, and known genes controlling plant architecture and development will be established and used for mapping. This will involve a listing of candidate genes for resistance, sequencing of these genes on a set of 16 pea parental accessions and SNP choice and design.
T4.3: Development and/or complementation of molecular maps will be conducted with SSR and SNP markers on 4 existing pea RIL populations (3 provided by INRA and 1 by CSIC) segregating for quantitative resistance to M.pinodes or for resistance to Orobanche and/or rust. Mapping will be performed using mainly markers likely to be used as bridge markers between maps (SSR and SNP markers obtained in T4.1 and T4.2) to allow comparative mapping between populations. Linkage studies will also be carried on F2 and RIL faba bean populations segregating for resistance to Orobanche.
T4.4: Phenotyping RIL and F2 pea and faba bean populations (diverse genetic backgrounds) for resistance to target stresses and plant architectural traits using methodologies developped in WP2 (biotic stresses, plant architecture) and WP3 (abiotic stresses) both in the field under multienvironment field trials and under growth chamber controlled conditions. Parental lines of RIL and F2 populations will be scored for all the biotic and abiotic stresses included in the project to discern whether these RIL populations also segregates for resistance/tolerance to additional stresses.
T4.5: Analysis of QTLs stability in different environments, towards pathogen variability, as well as in diverse genetic backgrounds (comparative analysis between populations using SSR and SNP bridge markers). Analysis of colocations between QTL controlling resistance to different biotic and abiotic constraints, and genes/QTL controlling plant architecture and development.
T4.6: Assessement of genetic progress for resistance to target stresses in large sets of accessions (192 independent pea cultivars, 300 faba bean local populations) adapted to cropping in various countries covering the mediterranean basin through (i) phenotyping for resistance and plant architecture using methodologies developped in WP2 (biotic stresses, architecture) and WP3 (abiotic stresses) both in the field and under controlled conditions; (ii) classification using anonymous SSR markers; (iii) a posteriori control of presence/absence of favourable alleles at QTL controlling resistance to stresses and architectural traits.
T4.7: Marker Assisted Breeding. Once the genes and QTLs have been identified for each stress and assessed for stability, the next step will be to select a set of markers linked to these QTLs that could be used for the simultaneous selection for different stresses. First crosses will be done for pyramiding of multiple resistances into elite cultivars and selection will be aided by these set of markers.
T4.8: Further transcriptomic or proteomic studies (CDNA-AFLP, SuperSAGE, microarrays, protein profiling) will be set up in order to identify genes or proteins differentially expressed between a resistant and a susceptible accessions to target stresses. The combination of these techniques will allow the establishment of a global and detailed picture of all genes expressed or differentially regulated during this particular interactions giving relevant information about the mechanisms of resistance acting at the molecular level. In addition, it will allow the full characterisation of candidate genes selected from the global view of the interaction, and assumed to be implicated in resistance.
T4.9: Validation of candidate genes from published, existing and planned (T4.8) transcriptomic and proteomic studies for (i) potential involvement in individual and crossed stresses, through the validation of gene expression in resistant / susceptible accessions following different stress applications by qRT-PCR (ii) development and mapping of genic molecular markers (cf T4.1) and analysis of colocalisations with QTL.
Deliverables:
D4.1: List of polymorphic eSSR and SNP markers for genetic mapping and pea map comparisons
D4.2: A set of SNP markers in pea designed in genes involved in stress resistance and plant architecture and development, likely to allow the rapid mapping or diversity study of resistance genes.
D4.3: High density pea linkage maps from populations segregating for resistance biotic and abiotic factors
D4.4: Identification, and determination of the genetic effects of the QTLs controlling polygenic traits
D4.5: Information on QTL stability across diverse field locations, pathogen variability and plant genetic backgronds
D4.6: Development of standard markers for pyramiding and rapid screening
D4.7: List of candidate genes likely to be involved in resistances to stresses.
WP 4 - Marker Assisted Breeding