Breeding for economically and environmentally sustainable wheat varieties: an integrated approach from genomics to selection.

Publication
 

This paper presents a nice overview of the BreedWheat project results:

https://doi.org/10.3390/biology11010149

Paux, E.; Lafarge, S.; Balfourier, F.; Derory, J.; Charmet, G.; Alaux, M.; Perchet, G.; Bondoux, M.; Baret, F.; Barillot, R.; Ravel, C.; Sourdille, P.; Le Gouis, J.; on behalf of the BREEDWHEAT Consortium. Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection. Biology 2022, 11, 149. https://doi.org/10.3390/biology11010149

Data

BreedWheat Information System rely on GnpIS with dedicated access rights following the consortium agreement.

• Germplasm (public access)
  • Siregal
  • FAIDARE

• SNP discovery : Major genes , Digital , BGA , BBSRC , Candidate genes , Infinium , IWGSC genes , IWGSC intergenic , ISBP .

• Axiom TaBW420K v2
  • Genotyping data
    • TaBW420K_V2_BW_WP1_CsRe
    • TaBW420K_V2_BW_WP1_Discovery_plate
    • TaBW420K_V2_BW_WP1_ITMI_p1
    • TaBW420K_V2_BW_WP2_Core_Collection
    • TaBW420K_V2_BW_WP2_Elite_panel
    • TaBW420K_V2_BW_WP2_Extended_Elite_panel
    • TaBW420K_V2_BW_WP3_Genetic_Resources
    • TaBW420K_V2_BW_WP4_Genomic_Selection
    • TaBW420K_V2_BW_WP4_MAGIC
    • List of the 57 varieties phenotyped in the Wheatamix project: TaBW420K_V2_BW_Wheatamix.
  •  Genetic map data
    • display in GnpIS
    • download
  • Association data
    • BWP2 panel
    • BWP3 panel

• TaBW280K public markers
  • display the TaBW280K in the IWGSC_Refseq_v2.1 browser.
  • display the TaBW280K in the IWGSC Refseq v1.0 browser .
  • download  tabw280k_iwgscRefSeqv2.gff3.tar.gz (8.58 MB) file with the markers position on the IWGSC RefSeqv2.1
  • download tabw280k_iwgscRefSeqv1.gff3.gz (5.68 MB) file with the markers position on the IWGSC RefSeqv1.0.

• Phenotyping:
  • INRA Small Grain Cereals Network Phenotypic Trials dataset on 11 locations and 16 years for more than 1700 bread wheat genotypes (public access). Dataset updated with new 2015 data.
  • BreedWheat:
    • BWP2:
      • 2011-2012 : 9 trials
      • 2012-2013 : 10 trials
      • 2013-2014 : 8 trials
      • 2015-2016 : 2 trials
       
    • BWP3:
      • 2016-2017 : 11 trials
       
    • AB-QTL:
       
    • 2017-2018 : 20 trials
  • Phenomic selection (Rincent et al. 2018 ): public access of the dataset on data.inrae.fr

• Ontology:
  • Wheat INRA Phenotype Ontology (WIPO) v1.5 (public access)
  • Wheat Crop Ontology now countains WIPO variables (public access)

• Genomics: BW contributed to the bread wheat genome reference sequence hosted in the IWGSC Data Repository developed by URGI.

Tools

•  Network Inference and visualization tool

Project

BREEDWHEAT project is a long-term public-private research initiative coordinated by Jacques Le Gouis (previously Catherine Feuillet) from INRA-GDEC. In total, 39 M€ is being invested over 9 years by 26 French partners, including 11 private companies, to develop and use efficient genome sequence-based tools and new methodologies for breeding wheat varieties with improved quality, sustainability, and productivity.

"Our goal is focused singularly on accelerating genetic gain to create new, high-yielding, wheat varieties that will meet current and future global challenges in wheat production" Catherine Feuillet.

Breedwheat public website .