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International Research Team Maps Largest Wheat Chromosome En Route to Sequencing

NEW YORK (GenomeWeb News) – Researchers participating in the International Wheat Genome Sequencing Consortium today reported that they have completed a physical map of the largest wheat chromosome, bringing them a step closer to sequencing the complex wheat genome. 
The team, led by French National Institute for Agricultural Research researcher Catherine Feuillet, isolated the largest wheat chromosome — chromosome 3B — and created a bacterial artificial chromosome library which they then used to assemble a physical map representing more than 80 percent of the chromosome. The paper, scheduled to appear online today in Science, provides a strategy for teasing apart the complex polyploid wheat genome — laying the groundwork for future sequencing projects.
“I’ve always heard that to work on wheat is impossible,” Feuillet told GenomeWeb Daily News, “so we are quite happy to see that this works.”
Both the size and complexity of the wheat genome have been stumbling blocks to traditional sequencing approaches. The hexaploid wheat genome is a whopping 17 billion base pairs, some five times larger than the human genome. In addition, more than 80 percent of the genome is composed of repetitive sequences, including long terminal repeat transposons and tandemly repeated sequences.
A whole-genome shotgun approach would not work for wheat, Feuillet explained, because it would be impossible to re-assemble the genome properly. To address such issues, she and her colleagues decided to tackle the genome of the Chinese Spring wheat genome — the cultivar selected by the International Wheat Genome Sequencing Consortium — one chromosome at a time.
Although it’s not the most economically relevant cultivar, Feuillet explained, the Chinese Spring wheat is well studied and its genome will serve as a reference that will aid future bread wheat cultivar sequencing projects.
For this paper, the researchers focused on the 995-megabase chromosome 3B, which is roughly twice the size of the entire rice genome. Using flow cytometry, Feuillet explained, the researchers isolated chromosome 3B, separating it from the other chromosomes based on its size.
They then generated BAC clones and used fingerprinting, contig assembly, and a combination of mapping techniques to create a physical map representing 82 percent of chromosome 3B, anchored with more than 1,400 molecular markers.
The next step, she noted, will be to sequence the mapped chromosome. This sequencing effort will take place at the French national sequencing center, while subsequent analysis will take place at INRA. Feuillet said that they will likely use a combination of the new Titanium 454 technology from Roche and Illumina’s platform to tackle this sequencing.
The researchers hope to produce sequence data within the next year, Feuillet said, and this data will be made available to the research community as quickly as possible.
Overall, researchers say, the paper demonstrates the feasibility of chromosome sorting as a method for mapping wheat chromosomes and, ultimately, getting at the wheat genome. “This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach,” Feuillet and her colleagues wrote.
The team has already outlined strategies for applying this mapping technique to each of the other chromosomes in the wheat genome. “The whole strategy is in place and there are already labs working on this,” Feuillet said.
That, in turn, will help crop breeders working with bread wheat. “At the moment, the breeding is made more or less blindly,” Feuillet said. Because the polyploidy in the wheat genome evolved relatively recently, she added, researchers may get new insights into crop genetics by comparing the wheat genome with those of other plants.
“Genome sequencing is the foundation for understanding the molecular basis of phenotypic variation,” the authors noted, “accelerating breeding, and improving the exploitation of genetic diversity to develop new crop varieties with increased yield and improved resistance to biotic and abiotic stresses.”
More broadly, Feuillet said the work demonstrates that the wheat genome is not insurmountably complicated. Consequently, she urges funding agencies to consider sequencing projects with economic and social relevance — regardless of how daunting the genome structure and content.
“Until now, the selection of genomes for sequencing has been determined on the basis of genome simplicity and not agronomic relevance, with serious consequences for crop improvement and food security,” the authors concluded. “Our work may pave the way for a major change in how the next genomes for de novo sequencing are selected, thereby accelerating improvements in economically important crop species.”

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