Some key dates of the project
The BreedWheat project is a 9-year project, thus allowing the characterization of populations developed in the project. Different events, results and resources mark the project progress, here is an overview:
The BreedWheat project is launched!
The BreedWheat Investments for the future project officially starts on Thursday 29th and Friday 30th September 2011 in Clermont-Ferrand, in the presence of its 28 partners, funders and the press
Selection of a panel of 4,600 wheat accessions representing global diversity
This sampling was achieved among the 11,960 bread wheat accessions coming from 108 countries and available at the INRAE Auvergne Rhône-Alpes Small grain cereals Biological Resources Centre (www6.clermont.inra.fr/umr1095/crb). The information regarding these accessions are included in the INRAE Siregal database (https://urgi.versailles.inra.fr/siregal/). The list of these accessions is available upon request to firstname.lastname@example.org
Design of a genotyping chip containing more than 420,000 SNP markers
BreedWheat designs one of the largest genotyping chips ever developed in wheat using Affymetrix's Axiom technology. Part of this chip, 280,000 SNP markers, is made available to the international scientific community.
Development of a platform for regulatory gene network inference
The RulNet platform allowing the inference of gene regulation networks (http://rulnet.isima.fr/) is developed (Vincent et al., 2015).
A new coordinator for the project
Catherine Feuillet who built this project and ensured its starting is leaving for new horizons. Jacques Le Gouis from INRAE GDEC succeeds her as coordinator.
Production of genotyping data on more than 7,000 wheat lines
The BreedWheat genotyping chip, including 420,000 markers, allows characterising more than 7,000 wheat lines comprising as much elite strains as genetic resources. This genotyping is carried out on the high-throughput genotyping platform, Gentyane, of the INRAE Auvergne Rhône-Alpes center (http://gentyane.clermont.inra.fr/).
Production of the first wave of 9 recombinant populations
A first wave of nine recombinant populations is produced in order to introgress adaptation characteristics to hydric and heat stresses in the French selection material.
Development of a tool for genomic selection
A pipeline, called BWGS (BreedWheat Genomic Selection), based on R open libraries, is developed. It allows to test different methods to construct and validate genomic selection models. An instruction manual is written following the CRAN rules, in order to make it available in a software warehouse.
An international conference brings together scientists from the wheat science community in Clermont-Ferrand
At the initiative of the BreedWheat project, an international conference called IWIW (International Wheat Innovation Workshop) is organized in Clermont-Ferrand on 16 and 17 November 2015. Details of the program, pictures and presentations are available on the website dedicated to this event: https://colloque.inra.fr/iwiw
The project is evaluated at mid-term
The members of the BreedWheat's international scientific committee evaluate the project progress at its 4th annual meeting. They are generally impressed by the advances made by the project.
Production of the annotated sequence of chromosome 1B
By sharing the sequence of chromosome 1B with the International Wheat Genome Sequencing Consortium (IWGSC), the BreedWheat project contributed to the production of the reference sequence of the whole wheat genome.
Construction of a genetic map comprising 307,270 loci
Genotyping data were used to construct a consensus genetic map comprising 307,270 loci, one of the highest density genetic maps ever produced in wheat.
Collection and formatting of phenotyping data from trials conducted in 2012, 2013 and 2014
Twenty-seven trials were conducted, between 2012 and 2014, on 220 wheat varieties (called elite panel BWP2) in order to assess their resistance related to nitrogen deficiency, drought and diseases (septoriose and fusariose). These data associated with the genotyping data allow to carry out association analyses (GWAS).
Development of a carbon-nitrogen model
A carbon-nitrogen ecophysiological model able to simulate the post-flowering period of wheat is completed and evaluated against experimental data (Barillot et al., 2016A, Barillot et al., 2016b). The software is available on the SourceSup platform upon request to the authors.
Selection of a diversity panel of 450 wheat accessions
A panel of 450 winter accessions (called diversity panel or BWP3) is selected from the 4,600 lines representing global diversity. The list of these accessions is available upon request to email@example.com.
Association studies (GWAS) coupling genotyping and phenotyping data are produced
Association studies, linked to phenotyping data obtained on the elite panel BWP2 during the 2012, 2013 and 2014 trials regarding nitrogen deficiency, drought and diseases resistance (septoriose and fusariose) are conducted.
Design of a genotyping chip containing 35,000 SNP markers
BreedWheat project develops a low-density genotyping chip (based on the 420,000 markers chip) in order to allow a higher debit and a cheaper genotyping. This chip, developed thanks to the Axiom technology, appears in the Affymetrix society catalogue and is available to the international scientific community (https://www.thermofisher.com/fr/fr/home/life-science/microarray-analysis/affymetrix.html).
Ranking of the elite panel varieties according to their resistance to nitrogen deficiency
A ranking of the 220 elite panel varieties BWP2 according to their resistance to a nitrogen deficiency is realised from the 2012, 2013 and 2014 trials. Resistance index numbers are calculated for yield and protein concentration.
A new international conference gathers wheat scientific community researchers in Clermont-Ferrand (France)
On the initiative of BreedWheat project, an international conference, called IWIW2 (2nd International Wheat Innovation Workshop), is organised in Clermont-Ferrand (France) on 22nd March 2018. Program details, presentations, and the overview of research priorities are available on https://breedwheat.fr/actualites/2eme-conference-internationale-de-bw/
Production of genotyping data on the 9 recombinant populations
The genotyping BreedWheat chip, containing 35,000 markers, enables a precise genotyping and a low price of the 9 recombinant populations. This genotyping is realised on the high throughput genotyping platform, Gentyane, of the INRAE Auvergne Rhône-Alpes centre (http://gentyane.clermont.inra.fr/). These data enable to select parents of a new wave production of recombinant populations.
The wheat genome reference sequence is published in Science journal
The BreedWheat project contributes significantly to the wheat genome reference sequence, published in Science in August 2018, providing to the IWGSC the chromosome 1B sequence and a genetic map containing 307,270 loci (https://breedwheat.fr/resultats/publications/)
Gene candidates lists linked to the use of nitrogen, heat stress and the response to septoriose and fusariose are produced
Gene candidates lists, linked to nitrogen use, heat stress and the response to septoriose and fusariose are produced and used to capture sequences in more than 700 accessions.
an improved version of the Septo 3D model is produced
The wheat Septoria model has been assessed for different climatic scenarios and shows a very good capacity to simulate the disease development. A sensitive analysis then allows to identify varietal characteristics modifying its development.
A genomic regions list linked to traits of interest is produced
A genomic regions list linked to traits of interest is produced coupling 11 trials under biotic and abiotic constrains realised on BWP3 diversity panel (450 accessions) in 2016/2017 and genotyping data obtained on this same panel.
The BreedWheat project is extended for one year!
Project partners agreed to ask for one-year extension of the scientific program (until 31st December 2020) in order to provide high-quality deliverables and to highlight the resources obtained in the frame of the project. The French National Research Agency (ANR) accepted this request of extension and amendments to the grant agreement are signed.