The IWGSC Survey Sequencing Initiative

The large size (17Gb) and complexity of the hexaploid bread wheat genome have posed severe challenges for the development of genomic resources to facilitate molecular strategies for wheat breeding improvement. To address these issues the International Wheat Genome Sequencing Consortium (IWGSC) has developed an approach to map and generate a reference sequence of the genome based on individual chromosomes flow-sorted from aneuploid lines of the reference variety, Chinese Spring 42. In 2012, a first draft survey sequence of the genome was generated from Illumina high throughput paired end sequence data representing 30-fold or greater depth of wheat chromosome arms. 10.2Gb of sequence was assembled in contigs greater than 200bp and assigned to individual chromosomes.  A total of 133,090 high confidence gene models were defined using a combination of wheat RNASeq and full-length cDNA datasets, as well as reference gene sets from sequenced grass genomes.  Over 93% of the gene models were assigned to individual chromosomes and 57% were assigned a putative order using a synteny approach encompassed in the GenomeZipper. Analyses at chromosomal and sub genome levels have revealed new insights on intrachromosomal duplication, the evolution of the genome following polyploidisation and the transcriptional activity of the genome. Finally, all publicly available sequence-based markers including SSR, DArTs, and SNPs have been assigned to the sequence assemblies providing an integrated marker platform to breeders and scientists for mapping in wheat. The survey sequences can be accessed on the IWGSC repository at http://wheat-urgi.versailles.inra.fr/Seq-Repository, from http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB3955 or via Ensembl Plants (http://plants.ensembl.org/Triticum_aestivum/Info/Index).