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How does the publication of the draft sequence impact the IWGSC roadmap?

Kellye Eversole – IWGSC director
Kellye Eversole

There are three key milestones in the IWGSC roadmap: (1) achieving survey sequences of the 21 bread wheat chromosomes; (2) developing physical maps that can serve as a substrate for sequencing; and (3) completing the reference sequence for each of these chromosomes. This publication describes the achievement of the first milestone.

Which methodology was used to produce the draft sequence?

Jane Rogers – IWGSC co-director
Jane Rogers

The draft sequence was generated from DNA of the bread wheat cultivar Chinese Spring that was isolated from individual wheat chromosome arms, or the whole chromosome in the case of chromosome 3B. The chromosomes were separated using flow-sorting by Jaroslav Dolozel’s laboratory at the Institute of Experimental Botany, Olomouc, in the Czech Republic.

The shotgun sequencing method was used to fragment the chromosomal DNA into pieces with an average size of 500 base pairs and to create libraries for sequencing using the paired end sequencing technology of Illumina, Inc. Sequence reads with a length of 100 or 150 bases were produced that covered the chromosomes to a depth of more than 30-fold.

The sequence reads were trimmed as necessary to remove poor quality bases. Then, bioinformaticians at The Genome Analysis Centre in Norwich, United Kingdom, assembled them using the assembly algorithm ABySS that was developed at the Michael Smith Genome Sciences Centre, in Vancouver, Canada.

The sequences were assembled into lengths (contigs) with an average size of 2,400 bases that, in total, covered 10.2 Gb, or approximately 60% of the wheat genome. The assemblies contained very little information to position them along the chromosomes, so Klaus Mayer and colleagues at the Helmholtz Institute, Munich, in Germany, used an approach called the GenomeZipper to produce a pseudo-order by aligning the contigs against wheat genetic maps and other sequenced grass genomes.

The sequences represented in the assemblies contain a large proportion of the wheat genes, whilst the most repeated sequences that make up large tracts of DNA between the genes, are not captured in the draft sequence.

In what way have the data from the drat sequence helped you in your work?

Julien Bonneau – Postdoctoral Researcher, University of Melbourne, Australia

I have been a user of the IWGSC databases and would recommend its use to any scientist working on wheat, specifically when one wants to increase marker density and gain access to gene-based markers in positional cloning and gene discovery projects.

These databases, along with those related to the 3B physical map and reference sequence, have allowed us to get into candidate gene discovery to improve wheat grain yield where plants are grown in challenging environmental conditions such as drought and/or heat. Without this information we would be far behind and struggling to make progress.‬

In addition, our group has been able to identify a large gene family (up to 20 genes) potentially involved in Iron and zinc uptake. This information is extremely precious not only in the context of increasing production but even more with regards to grain quality and to combat malnutrition.‬

In fact without these resources we wouldn’t have been able to discover these genes as fast as we did! It’s really important to make fast progress in understanding mechanisms in micronutrient uptake to product crops that would benefit human health in the future.‬

Jorge Dubcovsky – Professor, University of California Davis, and HHMI-GBMF researcher, United States
Jorge Dubcovsky

The IWGSC chromosome shotgun sequences and associated data have been a fantastic resource for our laboratory. Development of genome specific primers, which used to take several weeks of work and painful sequence of the three genomes can now be done in hours. Mapping of any sequence to the specific chromosome arm can now be done in silico in minutes. In addition to the acceleration if day to day work in wheat genetics, this resource has made possible analyses at the genome level that were not possible before. It provides a reference for RNASeq studies, gene capture, promoter identification, evolution of homoeologs, etc.

Cristobal Uauy – Project Leader, John Innes Centre, Norwich, United Kingdom
Christobal Uauy

The IWGSC CSS data is making a massive difference in how we do wheat genetics today. It has opened up new areas of science in wheat, for example, by providing access to promoter sequences across multiple genomes. It has enabled us to establish high-throughput methods for marker development allowing us to quickly generate genome-specific assays for fine mapping and breeding purposes. The CSS data is also proving fundamental in our efforts to generate an in silico TILLING mutant collection in bread and pasta which will further accelerate functional genomics in wheat.

Jan Gielen – Senior Scientist Applied Genomics, Syngenta, France
Jan Gielen

Marker assisted breeding for wheat has shifted gears since the resources developed through the IWGSC initiative became available. The chromosome survey sequences revealed instrumental for increasing the throughput of various marker technologies and marker applications at ever lower cost in a hexaploid crop like wheat.