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Annotation

The IWGSC Wheat Genome Annotation project aims to identify and assign positions in the Chinese Spring reference bread wheat sequence to important features, including genes, splice variants, pseudogenes, transposable elements, small RNAs and regulatory elements.

The long-term goal of the IWGSC is to obtain a high quality reference genome sequence of the bread wheat genome cv. Chinese Spring that is anchored to the genetic maps, integrates different data resources, provides automated and manual annotation of genes and genomic features, and links genomic data directly to agronomically important traits.

The Consortium is currently using automated pipelines to generate a set of gene models and to annotate transposable elements for a primary analysis of the wheat genome based on IWGSC RefSeq v1.0 ( released in January 2017 ).

In a survey conducted amongst the IWGSC membership in June 2016, a majority of members identified “Community based manual curation and annotation” of the bread wheat genome as a priority.

The IWGSC Annotation Project will build on the automated annotation following the methodology of the Genome Annotation Platform for wheat chromosome 7A that is currently being set up in Australia to enable cloud-based community manual annotation of chromosome 7A using the Apollo software . The annotation and analysis of specific gene families is being undertaken by groups with knowledge and interest in the biology of these genes. The ultimate goal is to achieve high quality functional annotation of the reference that links directly to important traits.

Project team

Leader: Rudi Appels, Murdoch University, Australia

Team Members:

  • Fred Choulet, INRA-GDEC, France
  • Michael Alaux, INRA-URGI, France

Rudi Appels serves as the overall strategic leader of the Annotation Project, while Frédéric Choulet will update the reference sequence, including the manual and functional annotation and serve as the “gatekeeper” of the official annotation and releases. Michael Alaux will lead activities relating to hosting all data resources.

Gene Family Analysis teams

  • NBS‐LRR gene family - Burkhard Steuernagel
  • Wall‐associated kinases - Kostya Kanyuka
  • Grain quality genes - Rudi Appels
  • Amino acid transporters - Rob King
  • Manual annotation of ABA dependent and independent gene(s) and autophagy gene(s) - Hikmet Budak
  • MAPK to MAPKKK - Song Weining
  • Dehydrins and Aquaporins - Pilar Hernandez and Sergio Galvez Rojas
  • MADS-box genes - Rainer Melzer
  • TUBBY transcription factor genes annotation - Christos Noutsos

In future, the IWGSC is planning to extend the annotation of the genome and encompass a WheatENCODE Project.