Wheat data integration and applications: IWGSC, GrainGenes, Ensembl, and other data repositories

Authors: ALAUX, MICHAEL - Inrae; DYER, SARAH - Embl-Ebi; Sen, Taner

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 8/16/2023
Publication Date: 11/23/2023
Citation: Alaux, M., Dyer, S., Sen, T.Z. 2023. Wheat data integration and applications: IWGSC, GrainGenes, Ensembl, and other data repositories. Book Chapter. https://doi.org/10.1007/978-3-031-38294-9_2.
DOI: https://doi.org/10.1007/978-3-031-38294-9_2

Interpretive Summary: To improve wheat breeding, research data needs to be discoverable and accessible. Global wheat databases such as ARS-funded GrainGenes, URGI, and Ensembl Plants are major databases that wheat genomic data are deposited, curated, and displayed. This book chapter covers these and other major databases for wheat data, providing details about available data sets, data types, computational and visualization tools, and other services they provide and contextualize them within global initiatives and collaborations such as the Wheat Initiative, International Wheat Genome Sequencing Consortium and the Wheat Information System.

Technical Abstract: Wheat data integration and FAIRification are key to tackle the challenge of wheat improvement. The data repositories presented in this chapter play a central role to generate knowledge and to allow data exchange and reuse. These repositories rely on international initiatives such as (i) the International Wheat Genome Sequencing Consortium (IWGSC), which deliver common genomics resources such as reference sequences and (ii) the Wheat Information System (WheatIS) of the Wheat Initiative (http://www.wheatis.org), which improve the interoperability and findability of the wheat data across the repositories.