NORWICH, ENGLAND — A more complete and accurate wheat genome assembly is being made available to researchers, The Genome Analysis Centre (TGAC) announced on Nov. 12. This resource builds on international efforts in this area and will help wheat breeders accelerate their crop improvement programs and researchers to discover genes for key traits such as yield, nutrient use and bread making quality.
The wheat genome is now assembled into fewer and much larger chunks of DNA and covers regions that previous assemblies did not reach, such as complicated highly repetitive regions that form about 80% of the DNA sequences, TGAC said.
"Furthermore," said Matt Clark, group leader at TGAC, who led the sequencing work, "Wheat has a very large and complex genome made by the hybridization of three closely related grasses, each of which has a large genome itself. It has been a complex problem that has confounded scientists for several years."
Reaching this milestone has been a major U.K.-based effort to identify and understand wheat genes and develop insights into the links between them to aid breeding programs.
In this latest development, billions of bases needed to be sequenced and the assembly took three weeks to complete on one of the U.K.'s largest supercomputers, which was specially configured for work on wheat.
To assemble the wheat genome, Bernardo Clavijo, algorithms research and development team leader at TGAC, made major modifications to a software, called DISCOVAR, developed by the Broad Institute, Cambridge, Massachusetts, U.S. (previously used for specialist applications in human genome assembly) in a collaboration established by Federica Di Palma, director of science of TGAC and visiting scientist at the Broad Institute. In order to ensure all the complexity of the DNA sequence was preserved during assembly, he made a series of major overhauls to the software.
"We centered our approach on achieving maximal coverage of the genome, by distinguishing repeats,” said Clavijo. “We were very careful to use newly generated high quality input data."
These advances now mean the software can assemble several wheat genomes with high speed and great precision. This sets the stage for rapidly generating useful assemblies of many varieties of wheat, which is an essential step for breeding and research.
"The capacity to sequence and assemble many wheat genomes efficiently breaks down major barriers to wheat crop improvement,” said Mike Bevan from the John Innes Centre (JIC). “We will now be able to exploit genetic variation from ancestral wheat varieties for crop improvement in new ways."
"One of the most complex and large groups of genes in wheat are those that contribute to the nutritional and bread-making quality of the grain,” said Ksenia Krasileva, group leader at TGAC and TSL, who has conducted an initial assessment of the assemblies. “These are all present in complete copies in the genome, suggesting other hard-to-assemble genes are also accurately represented."