Bread wheat enters the DNA era

Professor Rudi Appels (left) of Murdoch University serves as Australian co-chair of the International Wheat Genome Sequencing Consortium (IWGSC). He is pictured with John Fosu-Nyarko and Hollie Webster.

Professor Rudi Appels (left) of Murdoch University serves as Australian co-chair of the International Wheat Genome Sequencing Consortium (IWGSC). He is pictured with John Fosu-Nyarko and Hollie Webster. PHOTO: MURDOCH UNIVERSITY

By Dr Gio Braidotti

Despite its unwieldy size and genetic complexity, the bread wheat genome is the latest – and the last of the major crops – to have its entire DNA targeted for sequencing.

The project seeks to make DNA technology more readily available to wheat breeders to accelerate rates of genetic gain – a key plank in the GRDC’s ongoing variety improvement strategy.

There are two stages involved in finalising the bread wheat genome project: sequencing (the complex scientific disassembling of the DNA into more manageable pieces) and then the actual mapping (the reassembling).

The results of both stages will feed into a communal dataset administered by the International Wheat Genome Sequencing Consortium (IWGSC). The consortium makes this data available through the internet to ensure access by wheat breeders anywhere in the world.

IWGSC executive director Dr Kellye Eversole says the genome sequence is essential for future crop improvement efforts, but is still some years away from implementation by breeding programs.

This is because of the time it takes to associate the sequenced DNA with the specific traits of interest to plant breeders.

But the eventual benefits, once this has been achieved, should include a much faster discovery rate of important genes and molecular markers.

It is critical work in terms of the long-term crop developments required by grain growers, but is still only part of the challenge. Other factors besides the DNA sequence also influence the expression of plant traits.

These include the gene-by-environment effects in which gene behaviour can be influenced by factors such as climate variability. Many traits are also known to be polygenic – they arise as a result of interactions among many genes. Then there is epigenetics, whereby identical genes in different plants can give rise to different traits as a consequence of gene-silencing mechanisms, which can be inherited, environmental or manipulated through gene modification.

Despite these complications (and paths still to be fully explored) IWGSC’s Australian co-chair, Professor Rudi Appels of Murdoch University, Perth, is optimistic about the project and excited about the future potential for agriculture.

“Going into the genome is like going into outer space,” he says. “There are challenges but they are also great opportunities.

“The science of genomics allows us to find out the extent of the epigenetic influence. Also we know that traits of interest are unlikely to link back to just one gene. So we need to change our thinking and work with the idea of gene networks. It makes the analysis more complex, but the bioinformatics technology is now capable of dealing with the challenge of computing vast numbers of interactions.”

To sequence the bread wheat genome, however, the single strand of DNA at the heart of each chromosome has to be first broken up into smaller pieces.

These can then be sequenced directly to produce random sequences from which individual genes can be identified. This approach to date has identified 95 per cent of bread wheat genes. But these fragments also need to be physically mapped so that the fragmented sequence can be reassembled in a way that corresponds to the true structure of the genome.

Physical mapping is essential for the sequence to find applications in breeding and it also allows the identification of genetically important DNA.

“A chromosome typically contains millions of bases but these are ultimately sequenced in runs of 100 to 1000 bases at a time,” Professor Appels says.

“So the sequence initially resembles jigsaw puzzle pieces. To assemble the sequence accurately requires knowing where in a chromosome each DNA fragment came from. That is what a physical map tells us. And that is what we are doing now with every wheat chromosome.”

The major complication is that bread wheat contains three genomes (called A, B and D) derived from three ancestral grasses. If these are sequenced conventionally, the result is one pool of jigsaw pieces from which to assemble three highly similar puzzles … a problem long considered impossible, but which the IWGSC solved.

“Within the IWGSC we based our strategy on some classic cytogenetics performed in the 1950s and 1960s in the US by ER Sears and more recently in the Czech Republic,” Professor Appels says.
“It allows us to physically distinguish and map individual chromosomes. These are then sequenced separately in Europe, the US and Japan, with the GRDC-supported Australian team assigned chromosome 7A.”

The GRDC-funded project is also using genetic maps of this chromosome (that show the approximate location of genetically inherited characters) to prioritise sequencing of regions linked to quality, disease resistance, and yield genes thought to be particularly important under drought stress.

This project is also receiving support from Bioplatforms Australia, an organisation established under the Commonwealth Government National Collaborative Research Infrastructure Strategy.

In addition to sequencing chromosome 7A, Bioplatforms Australia is compiling two datasets. The first is a wheat genomics data resource from 16 wheat varieties to explore the genomic basis of trait variation in peak Australian breeding lines.

The second dataset deals with wheat pathogens and combines existing data with new genomic, proteomic and metabolic data to help researchers better understand wheat disease resistance.

“As the IWGSC-coordinated groups assemble the physical map of each chromosome then a lot of the random sequence generated by various groups will fall into place,” Professor Appels says. “We then have a valuable resources that breeders can use to fast track genetic gain in their wheat programs.”

GRDC Research Code UMU00037
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GRDC Project Code UMU00037

Region National