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. 2018 Aug 17;19(1):111.
doi: 10.1186/s13059-018-1491-4.

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Michael Alaux  1 , Jane Rogers  2 , Thomas Letellier  3 , Raphaël Flores  3 , Françoise Alfama  3 , Cyril Pommier  3 , Nacer Mohellibi  3 , Sophie Durand  3 , Erik Kimmel  3 , Célia Michotey  3 , Claire Guerche  3 , Mikaël Loaec  3 , Mathilde Lainé  3 , Delphine Steinbach  3   4 , Frédéric Choulet  5 , Hélène Rimbert  5 , Philippe Leroy  5 , Nicolas Guilhot  5 , Jérôme Salse  5 , Catherine Feuillet  5   6 ; International Wheat Genome Sequencing Consortium; Etienne Paux  5 , Kellye Eversole  7 , Anne-Françoise Adam-Blondon  3 , Hadi Quesneville  3
Affiliations

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Michael Alaux et al. Genome Biol. .

Abstract

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

Keywords: Big data; Data integration; Information system; Wheat genomics, genetics and phenomics.

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Conflict of interest statement

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Conceptual view of wheat data links in GnpIS. Arrows illustrate existing links between data types allowing data integration. Red arrows highlight links between genomics and genetics
Fig. 2
Fig. 2
Screenshots of the web interfaces for a practical use case to explore all the genomic data in the vicinity of a dedicated gene and find out if there are genetic studies pointing to this genomic region. Search the gene name (e.g. TraesCS5A01G033100) in the data discovery tool (1A, [5]) or BLAST the sequence of the gene against IWGSC RefSeq v1.0 (1B, [30]). The results are displayed in Tables (2A, 2B) with links to JBrowse directly zooming in on the gene [48]. Explore the region around the gene to find a marker (3, e.g. wPt-4131_PURr). By clicking on the marker, display additional information stored in GnpIS-coreDB (4, [49]) showing that the marker is used in GWAS experiments (5A, [50]) and is linked to a QTL (5B, e.g. GY_ml.8.Np_5A, [51]). From the trait description of this QTL (6, [52]), display all the phenotyping experiments performed on this trait (7, e.g. grain yield, [53])
Fig. 3
Fig. 3
The Wheat@URGI portal node in the WheatIS ecosystem. Boxes represent the different information systems queried by the WheatIS data discovery tool
See this image and copyright information in PMC

References

    1. IWGSC website. http://www.wheatgenome.org/. Accessed 10 April 2018.
    1. International Wheat Genome Sequencing Consortium (IWGSC). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, in press. DOI: 10.1126/science.aar7191. - PubMed
    1. Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018. doi: 10.1038/sdata.2016.18. - DOI - PMC - PubMed
    1. Steinbach D, Alaux M, Amselem J, Choisne N, Durand S, Flores R, et al. GnpIS: an information system to integrate genetic and genomic data from plants and fungi. Database J Biol Databases Curation. 2013;2013:bat058. - PMC - PubMed
    1. Wheat@URGI portal. https://wheat-urgi.versailles.inra.fr. Accessed 10 April 2018.

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