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New wheat varieties: why is mapping essential?

Mapping wheat genes has been an epic struggle in the past. We chatted with Dr Dina Raats, Post-doc researcher in EI’s Triticeae Genomics group, about genetic and physical maps of wheat, and their importance in breeding new wheat varieties.

February 19, 2016

We desperately need to safeguard the food supply for our growing population. Wheat provides about 20 per cent of human dietary calories, but breeding new, decent strains of wheat is difficult, particularly against the trend for intensive farming in developed countries, because the genetic constitution of wheat is extremely complex.

Mapping wheat genes has been an epic struggle in the past. We chatted with Dr Dina Raats, Post-doc researcher in EI’s Triticeae Genomics group, about genetic and physical maps of wheat, and their importance in breeding new wheat varieties.

Are maps essential?

They’re the main tools for gene isolation in wheat. They’re essential for allocating any sequence to its chromosomal position, and therefore also for breeding programmes.

You can breed some traits in some crops by observing linked traits as markers and beginning genetic (linkage) maps, but to really get somewhere, you need to combine those with physical maps based on actual DNA sequence, to obtain a rich enough marker set for the less convenient trait-associated genes.

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Almost any wheat sequence has multiple similar copies elsewhere…

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A bread wheat genome is about 120 times bigger than an Arabidopsis genome and highly repetitive – the complexity is such that it has routinely taken 10-15 years to isolate and characterise a gene associated with a trait in wheat.

This is why only about 20 out of 100,000 have been isolated so far. It’s harder than finding ‘a needle in a haystack’ because this needle really looks like some of the hay.

New wheat strains can also increase yield, giving both health and economic benefits. Photo: Shutterstock / Nikifor Todorov

Phew, I knew that wheat is tough to work with, but that’s really sobering.

Yes, it’s not just the size – but also that it’s highly repetitive. Almost any wheat sequence has multiple similar copies elsewhere in there. Bread wheat is comprised of three very similar genomes derived from wild wheat ancestors, so for many genes, there are at least three similar copies. This tends to make everything difficult, and then there are the surrounding repeats, often affecting the gene expression, making up the vast majority of wheat chromosomes.

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It’s an exciting time to be in wheat research …

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Till recently, we relied on conserved gene content and order among grass species to transpose information from Brachypodium, rice and sorghum genomes and infer hypothetical positions of similar genes on a wheat genome – and then experimentally prove these positions. But look, a Brachypodium genome fits on just the small arm of wheat chromosome 1B! So that was FAR from ideal.

Today, the situation is changing. It’s an exciting time to be in wheat research, as we’re reaching a point where the resources are becoming effective and affordable. Physical maps for almost all wheat chromosomes were drafted in the last couple of years, and a new strategy for whole wheat genome assembly was recently developed by TGAC – a high-quality whole genome assembly is finally here to really help speed up research.

Improved strains can help combat the effects of drought. Photo: Shutterstock / zhuda

Will we still need genetic and physical maps with all that sequence data?

Yes – a combination of map types will still be needed. Our group is developing a rapid method of mapping-by-sequencing, made possible by recent technological advances, and we will soon be able to isolate any wheat gene in 2-3 years. Construction of linkage (genetic) maps still underlies the method and availability of high-quality physical maps will be essential in the later stages.

Thanks, Dina. Since wheat genetics is so difficult, it’s all the more encouraging to hear about recent progress.

Yes, working in wheat genomics is challenging and I am happy that we are reaching the point where gene isolation will no longer be an obstacle for functional studies … I’m sure that more young scientists will be encouraged to work on wheat now that it’s more feasible to get a concrete result from a PhD project.


EI is working closely with partners to establish a pan-genomics approach for wheat crop improvement. It has only recently become feasible to sequence multiple wheat lines in a robust, comparative manner – and this is required to address the scale of variation between some closely related breeding stock lines.

By Nigel Fosker

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