FRUITBREEDOMICS

 
 
 
 
 
 
The Project
 
 

The Project

  • Overview

    An international consortium has designed FruitBreedomics, an ambitious research project which aims to improve and make use of the latest methodologies, technologies and knowledge to improve the efficiency of current fruit breeding programmes. Its strategic aim is to bridge the existing gap between molecular genetic research and breeding. It will focus primarily on apple and peach, two major fruits in Europe, but many tools and much knowledge gained will also be of benefit to other species of the Rosaceae family via the strong genomic and functional ancestral relatedness among these species.

    A major breeding tool to be developed is a validated pipeline for Marker Assisted Breeding and its implementation in ongoing commercial breeding programs. FruitBreedomics will prepare for and make available to the consortium selected pre-breeding material. It will also evaluate a way to reduce the introgression time of new traits from wild species to pre-breeding material with advanced fruit quality by inducing early flowering thanks to fast-breeding technology (Flachowsky et al., 2009).

    The research efforts will be directed to improve our understanding of the genetics of some major horticultural traits and develop innovative research tools to efficiently find marker trait associations in breeding and genebank germplasm. To overcome the main issues of the past genetic studies on fruit trees (narrow genetic diversity, low mapping density, single environment), FruitBreedomics will focus on two innovative and complementary genetic mapping approaches based on a wider genetic diversity: i) pedigree-based analysis (PBA) and ii) Linkage disequilibrium (LD) mapping over the whole genome, i.e. genome-wide association (GWA) mapping.

    Additionally, the project aims at increasing the accessibility of breeders to the genetic diversity present in germplasm collections, thus contributing to widening the genetic basis of cultivated fruit trees. To implement the scientific approach, FruitBreedomics will be built on two research pillars ( “the European Breeding Platform” and the Diversity and QTL mapping pillar), one research workpackage (new traits knowledge), one support pillar (tool and data management)” .

    FruitBreedomics has been accepted by the European Commission in the frame of the seventh Framework Programme. It will start in March 2011 and end in 2015. It regroups 24 participants including four non EU countries.

  • Project structure

    The project is structured in 8 Workpackages. WP1 will develop a validated pipeline for Marker Assisted Breeding and it will implement this major breeding tool in ongoing commercial breeding programs. WP2 will prepare for and make available to the consortium selected pre-breeding material. It will also evaluate a way to reduce the introgression time of new traits from wild species to pre-breeding material with advanced fruit quality by inducing early flowering thanks to fast-breeding technology. The research efforts will be directed to improve our understanding of the genetics of some major horticultural traits and develop innovative research tools to efficiently find marker trait associations in breeding and genebank germplasm. To overcome the main issues of the past genetic studies on fruit trees (narrow genetic diversity, low mapping density, single environment), FruitBreedomics will focus on two innovative and complementary genetic mapping approaches based on a wider genetic diversity: i) pedigree-based analysis (PBA) (WP3) and ii) Linkage disequilibrium (LD) mapping over the whole genome, i.e. genome-wide association (GWA) mapping (WP4). WP5 will concentrate in gaining novel traits by understanding the genetics and developing high throughput phenotyyping. WP6 will develop marker and gene arrays for highthroughput genotyping and WP7 will develop sowtware and data management tools with interface for breeder usage. Finally, WP8 will take care of dissemination and communication tasks while WP9 will manage the project.

  • Activities
    • WP1-Increasing efficency of (marker assisted) breeding

      The general objective of this workpackage is to develop more efficient breeding programmes applying markers assisted breeding. To reach this goal, WP1 will design and develop:

      • Selection strategies and schemes to be tested in pilot studies
      • Molecular markers (SNPs) tightly linked to specific major horticultural traits will be developed
      • Cost-efficient marker-assisted breeding (MAB) pipeline(s) will be implemented and used to genotype the plant material of the pilot study
    • WP2-Establishment of pre-breeding material

      This work package is aimed at the establishment of pre-breeding material in apple and peach in a more efficient way and the improvement and application of a fast-breeding system in apple. Pre-breeding material can be defined as material carrying new traits or trait combinations which can be used as donors to improve cultivar breeding by the introduction of the traits. The development of pre-breeding material is necessary if desired traits or combinations are not present in existing advanced breeding material and if the donors are far from advanced breeding material and/or the introduction process is too time consuming or expensive. Prebreeding material with new resistance genes, new combinations of resistance and/or quality traits and material homozygous for important traits necessary and useful for breeders to improve breeding of apple and peach cultivars more suited for sustainable production and the increasing demands of the markets will be developed. The efficiency of pre-breeding will be increased by the choice of donors and the selection of progeny with less genetic drag (apple and peach) and the development of strategies to shorten the generation cycle in apple.

      The targeted traits are:

      • For apple: resistance to scab (Rvi11/Vbj, Rvi12/Vb), resistance to fire blight (Fb-ELG10, Fb-R5-LG3), pyramiding resistance to powdery mildew (Pl1, Pl2, Pld), homozygosity of scab resistance genes. The traits chosen are either still not introduced in domesticated apple or not present in more advanced breeding material which could be used for cultivar development. Until now no material is available with three pyramided powdery mildew resistance genes or clones homozygous for pyramided scab resistance genes.
      • For peach: resistance to powdery mildew (Vr1, Vr2), Monilinia, green peach aphid (Rm1, Rm2); combination of resistance genes.

      New traits can be added depending on the results of WP5.

    • WP3-Identification and characterisation of QTL for fruit quality and disease resistance by the pedigree based analysis approach

      The objectives of WP3 are:

      • Extension of PBA based software for application to high density SNP- genotyping
      • Identification of QTL for new traits by classical QTL mapping
      • Reduction of confidence intervals and characterisation of known QTL & Identification of nearby markers
      • Assessment of genetic diversity as exploited within European breeding programmes
      • Mining QTL-alleles over wider breeding germplasm
      • Validation of QTL-alleles over climatic regions and harvest dates
    • WP4-Exploring the phenotypic and genetic diversity in apple and peach germplasm and its exploitation by AG approach

      The objectives of WP4 are to:

      • Improve the knowledge of genetic variability distribution in apple and peach European collections
      • Explore the phenotypic and allelic diversity available in apple and peach European germplasm collections
      • Define apple and peach unstructured (or merely structured) subpopulations
      • Survey the level and extension of linkage disequilibrium (LD) in the defined subpopulations
      • Identify genomic regions contributing to the genetic control of major horticultural traits through genome-wide association genetics (LD mapping)
      • Confirm already-known QTL and explore QTL-allele diversity
      • Reduce confidence interval (CI) around QTL
      • Find new QTLs
      • In combination with WP3, supply WP1 with tightly linked molecular markers for implementation into the MAB pipeline.
    • WP5-Enhancing the knowledge of genetics underlying novel traits and providing phenotypic methods

      The objectives of WP5 are to:

      • Develop tools for novel trait determination
      • Investigate novel and complex traits using ‘omics’ approaches and modelling
      • Make novel trait analysis high throughput and applicable for the research community and the breeding industry
    • WP6-Development of marker/gene arrays for high trhougput genotyping

      The objectives of WP6 are to:

      • Development of a low-density genotyping array for efficient gene/QTL mapping in apple.
      • Development of species-specific SNP arrays suitable for Genome-wide association mapping in apple and peach.
      • Testing new low-expensive high-throughput technologies for marker-assisted breeding.
    • WP7-Tools and data management

      The FruitBreed DB model will provide a unique tool specifically adapted for geneticists and breeders working mainly on apple and peach, especially when the aim is to combine phenotypic and molecular marker data. It will support Pedigree Genotyping, LD association mapping, marker-assisted breeding. This database will be useful in intercontinental collaboration on marker-trait associations, validation of candidate genes and functional allelic diversity. Its structure will form a firm foundation on which other users can build their own applications. In agreement with our US partners, already set framework of the US database GDR (Genome Database for Rosaceae will be used. It will be complemented and integrated with the structure and the functions developed for AppleBreed DB. New informatics tools will be developed that will operate on the integrated database such as a Breeding Information Management System (BIMS). It will be easily extended to include various crops, thus forming a base for a RosBREED DB. The new data coming from the project will be stored in this merged DB keeping however the breeding site separate and independent from GDR.

      • To manage the available and “to be produced” phenotypic data of apple and peach from the genetic materials present across EU from different locations
      • To develop and utilise tools to study model traits based on functional and structural genomics
      • To manage the available and “to be produced” genotypic data of apple and peach for
      • the development of a comprehensive platform including gene/QTL map position, gene ontology
      • To combine phenotypic and molecular marker data for PBA/LD/MBA analysis
      • To improve collaboration on apple/peach genome studies
      • To speed breeding procedures (synthesis of data to select parents; direct identification of elite individuals by markers, etc.).
    • WP8-Outreach

      The objective of WP8 is three-fold:

      • Make the best possible use of the project results by the stakeholders of the fruit industry, notably but not exclusively breeders
      • Ensure fruitful exchange with the scientific community, including individuals and collaborative initiatives, senior and early scientists;
      • Inform European citizens and policy makers about the stakes of the project, the challenges encountered by the fruit industry, the impact on citizens’ well-being, and the contributions brought by the project to respond to stakeholders’ needs and meet consumer demands.

      WP8 will make a discerning analysis of the research and technical outputs of the project, and ensure that they are effectively disseminated among the above stakeholder groups. Dissemination will be based on participatory methods during stakeholder congresses and national or international scientific events. To ensure a broader dissemination, specific training sessions targeting scientists from countries not represented in the Fruit Breedomics consortium will contribute to disseminate Fruit Breedomics results all over Europe.

    • WP9-Management

      The coordination and overall management of the Fruit Breedomics project will utilise the project management expertise of two partner institutions (partner 1 INRA and 11 INRA Transfert) together with the expertise of WP leaders.

      The overall coordination will be the responsibility of INRA who will be the legal entity responsible for all contractual arrangements and reporting to the EC, while INRA Transfert (an INRA subsidiary specialised in management of European research and development project) will carry out the operational technical and financial management. INRA Transfert will be in charge of the operational management, the day-to-day administrative and financial administration (collecting information from the partners, consolidation of management reports, monitoring of expenses against budget allocations, consolidation of financial summary sheets, etc.); while the dministration of payments from the EC and the transfer of funds to the partners will be managed by the coordinator, INRA.

      The responsibilities of the Coordinator, the Governing Council, the Executive Committee and the Project Manager are described in Section B2.1 which also describes the project management structure and procedures. In the first 3 months a range of activities will focus on establishing the rules for efficient management of this project (collaborative workspace and project management guidelines).

      The overall management plan designed by this project is aimed at achieving four main objectives:

      • Co-ordination of scientific and financial activities according to the work plan;
      • Monitoring results to control their scientific quality regarding the fulfilment of the planned objectives, quality of the result, timing, spent resources and worldwide state of the art;
      • Efficiency of the organization setup to support the project, with special attention paid to financial, logistics, information, coordination issues, quality and conformity to EC rules and procedures;
      • Prepare the financial and technical reports for the Commission.
 
 
 
 
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