Data and resources
After eight years, the French Investment for the future BreedWheat (BW) project is well on track. The 28-partners collaborative project has notably produced more than two billion genotyping data points, phenotyped around 70 000 experimental plots for agronomic traits and established unique resources such as a panel of 4 600 accessions representing the world-wide genetic diversity. You can have an overview below of the main results by research lines.
BW genotyping array, SNP and sequence data
Among the main scientific results, BW has designed two Affymetrix Axiom genotyping arrays containing respectively 423 000 and 35 000 SNP markers (single nucleotide polymorphisms). They allowed to genotype about 7 800 wheat accessions at INRAE-GDEC Gentyane platform (http://gentyane.clermont.inra.fr/) (Rimbert et al., 2018). For the whole community to benefit from BreedWheat results, a large part of this array representing 280 000 SNPs is made available to third parties for both research and breeding purposes. In addition, the 35K array is available in the Affymetrix catalog, providing an easy access for the international scientific community. A genetic map comprising more than 307 000 SNPs has been constructed, one of the highest density genetic map for wheat so far. A chromosome 1B sequence has been produced and used to improve the whole-genome reference sequence developed by the International Wheat Genome Sequencing Consortium (IWGSC ; IWGSC et al., 2018).
Modelling, transcriptomic analysis and phenotyping
A Carbon-Nitrogen Wheat ecophysiological model able to simulate the post-flowering period was completed and evaluated against experimental data (Barillot et al., 2016a ; Barillot et al., 2016b). The software is available on the platform SourceSup upon request to the authors. A platform for regulatory gene network inference, RulNet (http://rulnet.isima.fr/), has been developed (Vincent et al., 2015). Several proteins involved in regulating the synthesis of grain reserve proteins have been identified (Bancel et al., 2015 ; Bonnot et al., 2015 ; Bonnot et al., 2017 ; Boudet et al., 2018). The combined analysis of a coexpression network and phenotypic data revealed metabolic pathways associated with the effect of warming on wheat grain development (Girousse et al., 2018). Data from 27 experiments conducted on more than 200 varieties related to tolerance to nitrogen deficiency, drought and diseases, mainly in field conditions, have been analyzed and adjusted for Genome Wide Association Studies (GWAS).The classification of environments using covariates derived from a crop model made it possible to identify the QTL associated with grain yield under different water stress scenarios (Touzy et al., 2019). Finally, BreedWheat shared with the Phenome-Emphasis project (www.phenome-emphasis.fr) the development of several high-throughput phenotyping methods (counting the number of plants, the number of ears, estimating the green fraction of the canopy, the height of plants) opening the way to fine characterizations of large collections of genotypes (Liu et al., 2017a ; 2017b ; 2017c ; Madec et al., 2017 ; 2019).
Exploitation of natural genetic variability
A “diversity panel” of 4 600 accessions representing the worldwide diversity has been selected among the 11 000 wheat accessions available at the INRAE-GDEC small grain cereals Biological Resources Centre (http://www.clermont.inra.fr/umr1095/). This panel has been genotyped, phenotyped and caracterised (Balfourier et al., 2019) showing that the genetic structure of landraces can be explained by ancient human migration routes, with the appearance of new alleles enriched with structural variations that could be the signature of introgressions of wild relatives after 1960. The list of these 4 600 accessions and the phenotyping data generated are today available to the scientific community. A new “association panel” of 450 lines has been selected from the “diversity panel” and phenotyped. The list of these 450 accessions is available to the international community upon request to the BreedWheat consortium. Two waves of nine recombinant populations are being generated with the aim of introducing genetic diversity into French elite materiel. These populations will be shared among BreedWheat partners who have contributed to their development.
An R-based pipeline, called BWGS (BW Genomic Selection), has been designed, offering various combinations of methods for dimension reduction, missing data imputation and genomic prediction (Ly et al., 2018). Its ability to accurately predict breeding values has been validated on a set of historical breeding data. In addition, this R script makes it possible to analyse the efficiency of genomic selection schemes compared to conventional selection, taking into account the actual costs. Ideotypes have been defined by assembling adaptive traits for various French conditions and experiments have been defined to evaluate 25 varieties close to the desired ideotypes.
A unique web portal to access the data
The BW Information System (BWIS) has been developed to store and share the huge amount of data generated within the BW project. Based on existing resources developed by INRAE-URGI and Biogemma, the BWIS has been improved to meet user needs (such as breeders), especially in the genotyping and phenotyping database architecture. So far, both BW genotyping and phenotyping data were integrated. The BWIS is also included in the URGI wheat portal (https://wheat-urgi.versailles.inra.fr/) which is the worldwide reference for wheat data storage and sharing, with notably the access to whole-genome reference sequence (Alaux et al., 2018).
A capacity to bring together different countries working on the same target
The first BW international conference, the International Wheat Innovation Workshop (IWIW), was held in Clermont-Ferrand (France) on 16th and 17th of November 2015. More than 170 researchers from the public and private sectors attended this event aiming at informing the scientific and seed communities on the main progress in genetics, genomics, ecophysiology and on wheat adaptation to major environmental constraints, and to foster discussions between teams working on wheat in major national projects. The second BW international conference, the 2nd International Wheat Innovation Workshop (IWIW2), was held in Clermont-Ferrand (France) the 22th March 2018, following the Eucarpia cereals section. During this conference, about 130 scientists from public and private communities exchanged on research strategies to put in place around five topics of interest for the community working on wheat, namely genetic resources, phenotyping, genome editing, genomic selection and bioinformatics. The summary of these discussions is available on the BW website. The UK Design Future Wheat project, the German ProWeizen alliance, the CGIAR Research Program on Wheat as well as the IWGSC and the Wheat Initiative participated to the organization.