RESEARCH LINES

Activities

The BreedWheat project comprises a set of 5 scientific and technical research lines (identified in the figure below), as well as a line dedicated to the dissemination and transfer of results and a line dedicated to the overall project management.

Decipher the genome (research line 1)

The aim is to develop high throughput and innovative molecular resources to support efficiently the genetics studies undertaken in the BreedWheat project. Large scale sequencing will be undertaken at the genome and locus levels to provide the foundation for high throughput molecular markers development and candidate genes isolation for the traits of interest (>33 million SNP assays on 20 000 lines). Moreover, this research line will be dedicated to the genotyping of the populations and panels developed in research lines 2, 3 and 4 and to the implementation of novel genotyping technologies throughout the project.

The research line 1 will allow to:

  1. Produce a reference sequence of chromosome 1B of Chinese Spring and investigate structural polymorphisms by re-sequencing 2 other varieties.

  2. Develop and map genetically and physically, a large number of SNP markers covering the whole genome, to saturate genetic and physical maps and subsequently support efficient association genetic and diversity studies, genomic selection approaches as well as map-based cloning of genes underlying major traits.

  3. Genotype the SNPs, developed and mapped, on panels used for the research lines 2, 3 and 4 analyses, in order to (i) perform effective association genetics studies and identify chromosomic regions involved in major traits control, (ii) characterise the wheat genetic resources, and identify new alleles that can be introduced in breeding programs, and (iii) develop approaches and models for genomic selection adapted to wheat.

Adapt to the environment and global change (research line 2)

The aims is to develop combined approaches to decipher the ecophysiological, genetic and molecular basis of key factors impacting important agronomic traits such as yield, tolerance to biotic and abiotic stresses and grain protein composition in the context of sustainable systems and climate change.

A huge field phenotyping effort will be deployed (70’000 plots in more than 15 locations) to measure nitrogen use efficiency (NUE), drought and heat tolerance, as well as resistance to fungal diseases (septoriose, fusariose). In the second project phase, some high-throughput phenotyping platforms developed in the Phenome project (https://www.phenome-fppn.fr/phenome_eng/) allowing notably the study of interactions between different constrains will be used.

The research line 2 will allow to:

  1. Develop a 4D wheat structure / function model to analyze interactions at different nitrogen x fungal pathogenic levels, identify ideotypes maximising yield in different crop management and climate system scenarios, and propose relevant traits for phenotyping.

  2. Analyze and model mutli-level regulatory networks controlling grain storage protein gene expression in response to nitrogen and sulphur supply.

  3. Identify factors involved in adaptative responses to environmental abiotic factors (high temperature, drought).

  4. Identify new components of the resistance to Fusarium and Septoria diseases.

  5. Identify chromosomic regions underlying agronomic (nitrogen use efficiency, water use efficiency, disease resistance) and quality traits (grain concentration and composition) by association genetic studies that will be performed with the phenotypic data produced in the research lines 2 and 3, and the genotyping data obtained with genome wide ISBP and candidate genes markers in the line 1.

Characterise and exploit the genetic variability (research line 3)

The aim is to broaden the genetic variability available for breeding by introducing new sources of genetic diversity containing favorable alleles for resistance or tolerance to biotic and abiotic stresses targeted in BreedWheat.

Several sources of diversity will be used:

  1. Accessions selected in the INRA hexaploid wheat collection of the Small grain cereals Biological Resources Centre (11,700 different genotypes, https://www6.ara.inra.fr/umr1095_eng/Teams/Research/Biological-Resources-Centre) that represent French cultivars, from the XIX’s century onwards up to recently released cultivars, as well as old cultivars and landraces from other parts of the world.

  2. Some recent or older cultivars grown in environments prone to abiotic and biotic stress (Worldwide elite used in stressful environments).

This research line 3 will thus build two panels, a panel of 4,600 accessions representing the global wheat diversity and a smaller panel of 450 winter wheats that will be simpler to phenotype. This subset will represent the global genetic diversity and will be composed of genotypes suitable for an efficient agronomic evaluation in Western Europe. This axis will also develop 2 sets of 9 AB-QTL populations (Advanced Backcross – Quantitative Trait Locus) that will allow the introduction of an original diversity in European elite material and will be shared among all the project’s breeders.

Develop new breeding methods (research line 4)

The main is to support the development of new breeding methods that can take advantage efficiently of the information (genetic, molecular, physiology) and tools (markers, association panels) produced in the other BreedWheat research lines. The goal of these new methods is to predict the breeding value of new varieties in shorter selection cycles. This line addresses both technical and socio-economic aspects of the implementation of novel breeding strategies in seed companies and their impact on registration rules and regulation by the CTPS (Comité Technique Permanent de la Sélection) in France.

The research line 4 will allow to:

  1. Develop statistical tools and automated pipelines to test various ranges of parameters before establishing real-size experimental breeding programmes.

  2. Carry out a demonstrative, real-sized programme of pre-competitive wheat breeding and compare the efficiency of different selection schemes.

  3. Evaluate new ideotypes for yield and adaptation to innovative, sustainable and profitable cropping systems.

  4. Evaluate the impact of genomic selection on the research strategy of the seed companies and the seed innovation in wheat.

Store and share project data (research line 5)

The aim is to establish and update a central repository for the data generated by BreedWheat and to set up a user interface for the exploitation of this data and to enable large scale statistical analyses using a system integrated.

The BreedWheat Information System (BWIS) will use existing resources developed at URGI (https://urgi.versailles.inra.fr/gnpis/) and Biogemma and be complemented with an original cross querying system that enables full integration of the high throughput data and facilitates global statistical analysis for association studies. Special attention will be paid to data traceability for ensuring intellectual property policy application.

The URGI also manages the wheat portal (https://wheat-urgi.versailles.inra.fr/), which is recognized as the world reference for the storage and sharing of wheat data.

Dissemination and results transfer (research line 6)

The aim is to disseminate the knowledge and results generated within the framework of BreedWheat to the different actors of the wheat sector and to develop interactions with other international initiatives around this sector. The actors targeted are: (i) scientists, (ii) breeders, (iii) agri-food farmers and industrials, (iv) consumers, and (v) political and regulatory authorities.

The research line 6 includes:

  1. The communication about the BreedWheat project (its objectives, its results) on the occasion of events affecting key actors in the wheat sector, including company leaders and experienced researchers, farmers, the media, regulatory authorities and consumers.

  2. The organization of training courses on wheat genomics and selection techniques.

  3. The transfer of BreedWheat’s scientific and technical results and know-how to the industry.

  4. The creation of a contacts network to facilitate collaborative opportunities.

  5. The creation and maintenance of sustainable links between BreedWheat and national, European and international strategic initiatives.

Project management (research line 7)

The aim is to ensure the proper management of the BreedWheat project in terms of the production of scientific results, the use of allocated resources, communication within the consortium and compliance with the rules set out in the consortium agreement.

The research line 7 includes:

  1. The monitoring of results production by controling the achievement of objectives, their scientific quality, the initial timetable and their contribution to the advancement of the state of the art at the global level.

  2. The monitoring of the use of resources for achieving these results.

  3. The establishment of an effective organization to support the project, with particular attention to logistical, financial, coordination, dissemination of information, quality and compliance with ANR rules.

  4. The preparation of annual scientific & technical and financial reports for the ANR.

Research lines

Decipher the genome
Adapt to the environment and global change
Characterise and exploit the genetic variability
Develop new breeding methods
Store and share project data