Key points
The pan genome
- A pan genome describes all genes and genetic variation within a species.
- The first comprehensive wheat and barley genomes were published in 2017.
- Two international projects now aim to sequence multiple wheat and barley varieties from around the world to capture the full extent of genetic variation, the 'pan genome'.
- Australian researchers will comprehensively sequence multiple wheat and barley lines as part of the project.
It can be said that agricultural scientists are, given the chance, the world's most effective peacekeepers.
That role has now come to the fore in the global quest to lift wheat production by a massive 60 per cent in just 30 years if humanity is to avert a clearly foreseeable food crisis.
Wheat is the most widely cultivated crop on Earth, contributing about 20 per cent of total calories and 20 per cent of protein consumed.
With a predicted global population of 9.6 billion by 2050, compounded by climate change, we must double the rate of yield improvement. This will mostly have to come from crop and trait improvement.
Wheat is the most widely cultivated crop on Earth, contributing about 20 per cent of total calories and 20 per cent of protein consumed.
While new breeding technologies make the ambitious targets for yield improvement feasible, our limited knowledge of the wheat and barley genome structure and the key genes controlling yield has meant many of the new technologies are not accessible to breeders.
Genomes sequenced
However, in April 2017, a near-complete sequence for the North American barley variety, Morex, was published.
This was closely followed in July when the International Wheat Genome Sequencing Consortium (IWGSC) announced a comprehensive assembly of the 'Chinese Spring' hexaploid wheat genome.
These were great examples of the power of international collaboration and coordination to tackle a problem that had previously been regarded as intractable.
The wheat and barley genomes are the largest genomes ever sequenced and Australian researchers played a substantial role in the sequencing and analysis with GRDC investment.
However, this genome assembly was only the first step towards understanding the diversity available for wheat and barley improvement.
It is likely that one of the key reasons why these crops have such a wide geographic range and have adapted to many environmental conditions is that their genomes are highly 'plastic' in nature.
Modern wheat and barley cultivars carry a wide range of gene variants and diverse genomic structures that are associated with important traits, such as increased yield and disease resistance.
This variation cannot be captured with a single genome sequence. Only by sequencing multiple and diverse genomes can we begin to understand the full extent of genetic variation, the 'pan genome'.
This will allow us to identify regions of the gene that are subject to change and also those that have become fixed in modern varieties.
The sequencing of the barley pan genome will shed light on the genetic differences for higher yield potential between Vlamingh (PBR), left, and a mutant barley line, right. Photo: Professor Chengdao Li
Wheat genome
The 10+ Wheat Genomes Project is an international collaboration to sequence and assemble the genomes of wheat varieties from around the world and will be a huge potential resource for future research.
This project will deliver the first assembly of the genomes of multiple varieties and compare their structure and gene content. This pan genome of wheat and its characterisation is vital to understand the genetic control of key production traits.
The project will also look at the genes that are expressed at key stages of plant growth including seed development and maturation. This will allow the generation of information on genes and their potential role.
As the Australian contribution to this project, GRDC has invested in the sequencing of two varieties, Mace (PBR) and Lancer (PBR), by the University of Adelaide.
The inclusion of two Australian varieties reflecting both the northern and southern growing areas ensures that we can identify potential genetic variation of importance for adaptation to our different production environments.
The pan genome project will provide the greater understanding of plant genetics needed to increase production and profitability in Australia and beyond.
Barley target
GRDC has also invested in the International Barley Pan Genome Sequencing Consortium through Murdoch and Adelaide universities.
Barley varieties, from different regions, may hold up to 10 per cent of unique genes that enable adaptation to specific environments.
For example, the gene for vernalisation is one of the most important genes for yield and adaptation in Australia, but is missing in the reference genome sequence of Morex.
The consortium has first conducted DNA fingerprinting over 20,000 barley accessions of the worldwide barley germplasm, including 920 Australian barley varieties and key breeding lines so that key germplasm diversity can be covered in the new barley genome sequence.
We plan to fully sequence the European variety, RGT Planet (PBR), to the same level of detail as Morex.
RGT Planet (PBR) is a high-yielding spring barley recently introduced to Australia that represents a step change in yield potential and has recently received malting accreditation approval by Barley Australia.
More excitingly, we will fully sequence two barley landraces, one from Poland and one from Libya, which hold potential sources of tolerance to heat, frost, salinity and drought, as well as novel disease resistance traits.
As Australian varieties are genetically highly similar to their European ancestors, we can take advantage of high-quality sequences generated by our European colleagues.
However, we will screen 20 Australian varieties to identify any potential diversity that may warrant further sequencing.
The technology for genetic sequencing is advancing at an extraordinary speed. Work that we could have only dreamed about three years ago is now not only possible, but also attainable.
Sequencing the pan genomes for wheat and barley will support breeders' efforts to increase the rate of genetic gain necessary to sustainably increase production and profitability in Australia and beyond.
GRDC Research Codes: 9175488, 9176507
More information: Associate Professor Ken Chalmers, University of Adelaide, ken.chalmers@adelaide.edu.au, Professor Chengdao Li, Murdoch University, c.li@murdoch.edu.au and Brett Ford, GRDC, 02 6166 4500, brett.ford@grdc.com.au; 10 Genome Project