Tools

In the last 50 years, extensive genetic and cytogenetic (aneuploide and deletion lines) studies have led to the identification and characterisation of the 21 chromosomes of bread wheat and to get insights into the evolutionary relationships which exists between the A, B and D homoeologous genomes. In the last ten years, a number of international initiatives (such as the International Triticeae Mapping Initiative ( ITMI ) and the International Triticeae EST Consortium ( ITEC ) ) have led to the development of large collections of molecular markers (RFLP, SSR, EST) which have been used to develop dense genetic maps (as the ITMImap for example) in a number of mapping populations. Very recently, a number of large insert genomic libraries (BAC libraries) have been constructed from different wheat genomes. This has allowed the isolation of genes of agronomic interest by map-based cloning and to start the analysis of this complex genome at the molecular level through the sequencing and annotation of BAC clones.

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A long term project in wheat is to decipher the chromosomal location and biological function of all genes. This knowledge should greatly enhance our understanding of the biology of the wheat plant and create a new paradigm for the improvement of this major crop. Moreover, because of the genetic and metabolic conservation among species in the grass family, efforts to decipher gene function in wheat and its close relatives will work synergistically with similar efforts in maize, rice, sorghum, and other grasses for a global understanding of the function, structure, and evolution of the grass genomes ( US Wheat Genome Project ).In November 2003, the IGROW (International Genome Research on Wheat) was established to set up the basis of an international collaboration on wheat genome sequencing (Gill et al. (2004) Genetics168: 1087-1096). In January 2005, an International Wheat Genome Sequencing Consortium was launched with the mission of advancing agricultural research for wheat production and utilization by developing DNA-based tools and resources that result from the complete sequence of the common (hexaploid) wheat genome ( IWGSC ). The first objectives of the consortium are :

A number of projects are currently developed worldwide to address these questions.

At the UMR 1095 INRA-UBP Génétique, Diversité & Ecophysiologie des Céréales in Clermont-Ferrand (France), we are leading a collaborative pilot project to explore the feasibility of approaching the genome, chromosome by chromosome. Our project focuses on the structural, functional and evolutionary analysis of chromosome 3B using a chromosome-specific BAC library produced after flow sorting of the 3B chromosome (2-fold the rice genome) from hexaploid wheat cv. Chinese Spring (Vrana et al. (2000) Genetics 156:2033-2041; Safar et al. (2004) Plant J. 39:960-968; Paux et al. (2006) Plant J. 48:463-474). We are currently (i) developing a physical map of the 3B chromosome by fingerprinting and contiging the BAC library, (ii) anchoring the physical map to the genetic map and (iii) identifying and characterizing gene rich islands on this chromosome.

In this context, a large amount of wheat genomic sequences will be produced in the coming years and deposit within a repository in GrainGenes under the umbrella of the IWGSC . It is therefore essential to develop and offer to the scientific wheat community new resources for efficient BAC sequence analysis, as well as a platform for the re- annotation of BAC sequences as knowledge of the wheat genome sequence is increasing and new genes and elements are identified.

The aim of TriAnnot pipeline is to provide a wheat & barley automated annotation (Genes, Transposable Elements and tRNAs) for annotating new BAC sequences, make online manual expertise and regularly updating previous BAC annotations.

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Availability

There is no distribution package for the TriAnnot pipeline.

References

There is no publication of the TriAnnot pipeline yet.
However, you may refer to :
Sabot F, Guyot R, Wicker T, Chantret N, aubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M (2005)
Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.
Mol Gene Genomics 274:119-130 The TriAnnot pipeline has been presented at several international congress. See What is New paragraph.

Intellectual Property

A firts version of TriAnnot has been deposited on January 31th, 2006 to the French APP ("Agence pour la Protection des Programmes")repository for intellectual property (APP # IDDN.FR.001.05008.000.R.C.2006.000.31235).
The TriAnnot V2.0 will be deposit by 2009 to the French APP as well.

Contact us

We welcome comments and suggestions on the system and if you want to participate for improving the TriAnnot pipeline, please contact us at leroy[at]clermont.inra.fr