INTERNATIONAL WHEAT GENOME SEQUENCING CONSORTIUM
(IWGSC) www.wheatgenome.org. [p. 13-15]The mission of the International Wheat Genome Sequencing Consortium is to advance 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 and to ensure that these tools and the sequence are available for all to use without restriction and without cost. Information in this report can be found at the IWGSC website: www.wheatgenome.org.
The International Wheat Genome Sequencing Consortium (IWGSC) is a collaboration focused on building the foundation for advancing agricultural research for wheat production and utilization by developing DNA-based tools and resources that result from the complete genome sequence of common (hexaploid) wheat. The IWGSC was established to facilitate and coördinate international efforts toward obtaining the complete sequence of the common wheat genome. To this end, the IWGSC will continue to refine the strategic roadmap, integrate existing international resources, and develop a sequencing strategy that will capture international participation and a broad funding base.
Membership in the IWGSC is open to any individual, laboratory, or entity with an active interest in meeting the objectives of the IWGSC; that can contribute substantially to this effort in resource development, sequence activity, annotation, scientific expertise, or funding; and that agrees to comply with the guidelines and spirit of this agreement. The IWGSC will complement the IGROW effort in which obtaining the sequence and annotation for wheat is a discrete objective in furthering our understanding of wheat at the genome, molecular, and physiological levels.
The principal goal of the IWGSC is to obtain a publicly available, complete sequence of common (hexaploid) wheat since it is grown on over 95 % of the wheat growing area and the complete sequence of this particular wheat holds the key to genetic improvements that will allow growers to meet the growing demands for high quality food produced in an environmentally sensitive, sustainable, and profitable manner. Having the complete genome sequence of bread wheat will accelerate improvement of this important crop, yielding the greatest rewards for economic development and global food security.
The IWGSC has selected the specific cultivar, Chinese Spring (common wheat) as the source for the project as it has available already ample genetic and molecular resources (Gill et al. 2004, Genetics 168: 1087-1096). The IWGSC understands that sequencing the large wheat genome (five times that of the human genome) represents a challenging endeavor. Sequencing costs have been decreasing steadily during the last two decades and technology is continuously improving.Ê Thus, the IWGSC believes that its goal of obtaining a complete sequence of common wheat for a reasonable price is achievable in the foreseeable future. Therefore, the following short- and mid-term goals will be pursued towards reaching the final objective of sequencing the complete bread wheat genome.
Short-term goals of the IWGSC. Develop a physical map for common wheat that is linked to the genetic map and assess alternative approaches for sequencing wheat.
Mid-term goals of the IWGSC. Sequence the genic regions of common wheat, link the sequence to the physical and genetic maps, annotate the genic regions, and obtain full-length cDNAs for all expressed genes.
Long-term goals of the IWGSC. Complete sequence of the common wheat genome and high quality annotation of the genome.
At this time, the precise method to sequence the ~17 Gb hexaploid wheat genome is not known. The hexaploid nature of the genome, coupled with the repetitive nature of the genome, will present technical challenges in current methodologies. Several methods or combinations of approaches have been proposed (Gill et al. 2004, Genetics 168: 1087-1096) including whole genome shotgun sequencing, enrichment methods such as methylation filtration or high Cot, and/or clone-by-clone sequencing. However, regardless of any method(s) selected, we currently have only limited data on the landscape of the wheat genome. Thus, as proposed by Gill et al. (2004), there will be three phases to sequencing the wheat genome. The first phase or pilot phase is designed to test genomic methods/approaches on the hexaploid wheat genome. The primary purpose of the pilot phase will be to obtain data for the assessment phase in which the effectiveness of these methods are determined.
The pilot phase has several clear goals:
After sufficient pilot data have been obtained, an assessment of the pilot phase will be performed. The assessment phase will involve determining which method(s) can be used in a cost effective manner to generate the sequence of the wheat genome. Although it is anticipated that funding for the full genome sequence of wheat may not be available immediately, selection of the methods to sequence the wheat genome should be compatible with future efforts in which the complete genome sequence is obtained.
After a full assessment, the project will move to the scale-up phase in which the optimal methods are deployed on the whole genome. The scale-up phase involves obtaining the genome sequence and annotation. As noted, this may be in stages with an initial goal of sequencing the genic space and a subsequent goal of completing the sequence.
A first pilot project led by the INRA in France has been initiated in 2004 to assess point 3 using the largest wheat chromosome (chr. 3B, 1 GB = 2x the rice genome) of hexaploid wheat as a model. The 68,000 BAC clones of a 3B chromosome specific BAC library (Safar et al. 2004, Plant J 39:960-968) have been fingerprinted using an improved SNAPshot protocol for BAC fingerprinting and high-throughput facilities at the French National Sequencing Center (Genoscope). A first contiguing phase (2,500 contigs) has been recently achieved and the anchoring of the physical contigs to the genetic map is currently underway. Fingerprinting and FPC analysis have been achieved within 6 months by a postdoc and a technician for a total cost of about 180,000 USD. This demonstrates the feasibility of the chromosome specific approach for the hexaploid wheat genome.
Next steps: Priority Research Projects. The international IWGSC believes that we must begin well-coordinated, clearly articulated projects that will lay the foundation for sequencing the common wheat genome. During 2005, the IWGSC strongly supports these high priority proposed projects and urges funding agencies to provide funding this year for these projects:
1. Construction and large-scale sequencing of Cot-based cloning and methylation filtration libraries from Chinese Spring;
2. Large scale sequencing (> several Mb) of physical BAC contigs from hexaploid wheat (from Minimal Tilling Path at different regions (gene rich/gene poor) on 3B and possibly from other loci on the genome for which large contigs (> 1 Mb) have been generated; and
3. Construction of physical maps (BAC fingerprinting) from already available (1BS and (1D, 6D, and 4D)) chromosome-specific libraries.
The IWGSC is led by six co-chairs, an executive director, and the coördinating committee (see chart). The six co-chairs are representative of Australasia (R. Appels and Y. Ogihara), Europe (C. Feuillet and B. Keller) , and the USA (B. Gill and J. Dvorak). Kellye Eversole serves as the executive director.
The Coordinating Committee is responsible for:
- Coordinating activities within the IWGSC and pertinent outside genome efforts,
- Allocating responsibilities/tasks to IWGSC members,
- Assessing and reporting on progress, and
- Monitoring data release activities.
Characterizing the wheat genome by random sample sequencing, National Science Foundation Funded Wheat Pilot Project 2005, PIs and Co-PIs: J. Bennetzen, K. Devos, and P. SanMiguel (USA). The nuclear DNA of bread wheat cultivar Chinese Spring will be investigated to determine the content and distribution of genes and other sequences in the large genome of this polyploid species. A total of 220 large fragments of wheat DNA, cloned into a BAC vector, will be randomly selected and subjected to DNA sequence analysis. The sequence analysis will be done at a low redundancy to maximize the data generated per unit cost. These 220 BACs also will be located to wheat chromosome maps by a novel PCR strategy so that the relationship between chromosomal location and DNA sequence content can be assessed. Two gene enrichment techniques, high Cot analysis and hypomethylated partial restriction analysis, which have been proven in maize, will be tested for their efficacy in wheat. All generated sequences will be analyzed for gene and repetitive DNA content. Abundant repeats also will be characterized for their degree and nature of sequence divergence and their possible differential distribution across the wheat chromosomes. These experiments and analyses will determine the basic molecular characteristics of the wheat genome, provide insights into the nature of sequence evolution in this polyploid cereal, and lay the foundation for future genomic characterizations of wheat. Access to project outcomes and all data and analyses will be made available through a project website (accessible via http://www.genetics.uga.edu/jlblab/index.html), public databases, and publication in peer-reviewed scientific journals.
Chromosome 3B, a model to study the structure, function and evolution of the wheat genome, Agence Nationale de la recherche (ANR) Funded Wheat Pilot Project 2005, PIs and Co-PIs: C. Feuillet, J. David, I. Bonnin and O. Panaud (France). Improvement of bread wheat quality and yield in the context of sustainable agriculture has to be achieved in the next decades to meet human needs by 2050. Significant advances in the understanding of the wheat plant biology as well as in the management and exploitation of genetic resources are necessary to address this challenge. Genomic analyses can support this effort through a better understanding of the organisation, function, and evolution of this large and complex genome. Recent advances in wheat genomics already have led to better marker-assisted selection and to the positional cloning of a number of genes of agronomic interest. However, this knowledge remains too limited and larger scale studies are needed now to develop more efficient tools and strategies to support wheat improvement. Although the size and the complexity of the wheat genome do not allow yet detailed studies at the scale of the whole genome, recently it has become possible to work on single chromosomes. This project aims to exploit the first physical map of chromosome 3B of bread wheat that is under construction currently in the coördinating laboratory as a model to study the structure, function, and evolution of the wheat genome. This unique resource will allow us to address a number of important biological questions, such as:
The organization of the gene space and the duplication of the genome. These studies focus on characterizing the gene islands (distribution along the chromosome, gene density within and outside islands), identifying ancestral genome duplications through comparative analyses with rice, and studying their impact on gene function and evolution.
The recombination and its effect on genome evolution. Analyses will be performed in different genetic contexts (homology, homoeology, ploidy) and at different scales (whole chromosome, saturated deletion bins, and targeted sequenced regions) to study the recombination frequency and distribution as well as the effect of recombination on gene and genome evolution. Moreover, linkage disequilibrium and its use in association genetics will be evaluated.
The mechanisms of rearrangements that have shaped the wheat genome during evolution. As a model, we will study the evolution of the disease resistance locus Rph7 in grasses. Rearrangement mechanisms leading to deletion and/or translocation of genes as well as gene sequence evolution at this locus will be studied through intraspecific (rice sub-species; wheat homoeologous chromosomes) and interspecific (barley, Brachypodium, rye-grass, maize, sorghum) comparative analyses.