Wheat Genome Sequenced on Roche’s 454 GS FLX

Hits:2208   Date: 9/9/2010

August 31, 2010 -- A team of researchers in the UK last week released the first sequence coverage of the wheat genome. The researchers sequenced the genome to five-fold coverage on Roche’s 454 GS FLX and covered around 95 percent of known wheat genes.

The project, which took around a year, was funded by the UK ’s Biotechnology and Biological Sciences Research Council under a two-year £1.7 million ($2.6 million) grant.

Over the next year, the researchers plan to analyze the results of their sequencing, validate their SNP calls, and sequence four additional wheat varieties on Life Technologies’ SOLiD platform.

The goal is not to generate a complete draft assembly of the wheat genome but instead to identify "useful polymorphisms between different wheat varieties — SNPs we can link to genes and specific genome copies," Neil Hall, professor of functional and comparative genomics at the University of Liverpool and lead researcher of the project, told In Sequence .

Hall said that the sequencing was done on the 454 using Titanium chemistry and that they had average read lengths of around 400 base pairs. The team also did some runs with longer read lengths of 650 base pairs. Additionally, Hall said they have done some transcriptome sequencing in order to help determine which SNPs fall in the gene coding regions, and also to determine expression.

He said they chose to use 454 for the sequencing because the wheat genome is large — 16 gigabases — and an incredibly complex hexaploid genome with lots of repetitive regions.

He said while the sequencing on 454 was more expensive and time consuming than a shorter read platform, the longer reads would help determine whether a particular SNP was specific for a certain variety of wheat, and whether it was heterozygous or homozygous.

"The sequence coverage will provide an important foundation for international efforts aimed at generating a complete genome sequence of wheat in the next few years," Mike Bevan at the John Innes Centre, who was part of the project, said in a statement.

The researchers said that the sequence of the reference variety of wheat, Chinese Spring wheat, will allow them to better understand the genetic differences between wheat strains that lead to phenotypic traits of agricultural interest, such as drought or salinity tolerance and higher yields.

Jane Rogers, a member of the coordinating committee of the International Wheat Genome Sequencing Consortium and director of BBSRC’s Genome Analysis Centre, said in a statement that the release of the wheat genome data "will be a useful resource for scientists and the plant breeding community and will provide a foundation to identify genetic differences between wheat varieties."

The researchers said that sequencing the wheat genome was particularly challenging because it is one of the largest genomes to be sequenced — around five times as large as the human genome.

While the researchers are not planning to generate a draft assembly of the wheat genome, Hall said that the results of this sequencing study could help in efforts by other groups to create a draft assembly. "I expect a combination of next-gen approaches along with more traditional BAC-based approaches will be the way to get a full map," he said. "We hope our data will be useful for generating a full map."

The sequence data has been uploaded to the short read archive at the European Bioinformatics Institute and the US ’s National Center for Biotechnology Information.

A draft assembly would require "further read-throughs, significant work on annotation, and the assembly of the data into chromosomes," the team noted in a statement.

About Roche

Headquartered in Basel, Switzerland, Roche is a leader in research-focused healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is the world's largest biotech company with truly differentiated medicines in oncology, virology, inflammation, metabolism and CNS. Roche is also the world leader in in-vitro diagnostics, tissue-based cancer diagnostics, and a pioneer in diabetes management. Roche's personalised healthcare strategy aims at providing medicines and diagnostic tools that enable tangible improvements in the health, quality of life and survival of patients. In 2009, Roche had over 80,000 employees worldwide and invested almost 10 billion Swiss francs in R&D. The Group posted sales of 49.1 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan. For more information: www.roche.com.

source: Roche