Feeding the world: the importance of crop genomics

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Dr Ksenia Krasileva, Triticeae Genomics Group Leader at TGAC, and her team are working on large-scale projects that promise to make significant advances in global food security.

 

20 October 2015

Dr Ksenia Krasileva,TriticeaeGenomics Group Leader at TGAC, and her team are working on large-scale projects that promise to make significant advances in global food security.

Wheat is of utmost importance in global food security – there is intense pressure to increase global yields to feed our growing population. Dr Ksenia Krasilevaheads TGAC’s research group that studies wheat, with a strong focus on its resistance to one of the most devastating wheat fungal disease, Yellow Rust.

Dr Krasileva is analysing an extremely large collection of wheat lines to identify novel resistance genes to various diseases and understand the mechanism of action of these genes.

Now that it is possible to compare DNA sequences of any wheat line with the wheat reference genome published last year, we have an efficient way to identify those genes that differ in our lines and are involved in a given line’s relative disease resistance. Thus we are able to enrich the cultivated wheat gene pool with novel, economically important genes.

The reference wheat genome also allows us to use an efficient way of re-sequencing of any wheat line by a cost-effective method called ‘exome capture’. By this powerful method, we are sequencing only a protein-coding fraction comprising just 2 per cent of the very large wheat genome.

Predicting gene function and how any genetic change will affect the plant is extremely difficult. In cultivated wheat, this prediction is complicated by the nature of the genome – a hybrid of older wild wheat species, containing multiple copies of most genes. In our method, we first use a safe, proven and publicly accepted method of chemical treatment that allows us to induce changes in the genes. In field trials we identify treated wheat lines that show valuable traits, such as disease resistance, and then we compare these plants genomes against the published reference genome.

Why not just use historical wheat lines to find new diversity?

The historical collections and the wild ancestors of wheat constitute a great resource for wheat improvement and study of wheat evolution. However, in practical terms, deployment of genes from wild wheat is usually a tedious and time-consuming process. Wild relatives contain undesirable traits that were painstakingly bred out from elite cultivars; we don’t want these inherited with the desirable traits. By comparison, a mutant of an elite line already has the benefits of that breeding work. In addition, looking at minor genetic variants of the same wheat is a more efficient way to isolate the genes involved in plant-pathogen interactions. For us even the Rust SUSCEPTIBLE mutants are valuable (they can show us HOW resistance works).

You are using sequencing to expedite your discoveries. What is the most challenging aspect of it?

Wheat has a huge genome of 17GB, which is five times larger than the human genome. In order to analyse the data, we need intensive computational power. What’s more, we usually work with more than one sample at once…

When is the study going to be published/how is the analysis going?

We have identified our first elite wheat lines that showed gain-of-resistance to yellow rust in 2013 and tested them now across two continents (USA and UK), both in the field and in controlled laboratory conditions. Now, we are deploying sequencing to isolate the causative changes that give wheat immunity to yellow rust. The first sets of analyses are running, and we aim to identify the genes within next two-three years.

Another of Ksenia’s projects looks closely at important molecules in plant immunity; they are antennas that recognise pathogen at the front line of attack.

Which molecules involved in plant immunity are you currently working on?

Most of the time, one molecule is not enough to recognise the pathogen, and the plant employs several of them, including ‘decoys’ to trick pathogens to reveal themselves. Examples of such ‘decoy’ and antenna molecules have been studied in Arabidopsis and rice and we find that their equivalents are actually fused together in other plant species, including wheat – a striking indication of their mutual importance.

When will we hear more about this?

We just submitted another manuscript. The aim is to understand the evolution of plant immune receptors across flowering plants (plants have innate immune system – very similar to ours!). We are characterising all publicly available data for plants.

We have secured funding for a Doctoral training position to study how immune system evolves across plants. Please, spread the word:http://www.biodtp.norwichresearchpark.ac.uk/projects/project-detail/project/191.

The calibre of our staff expertise and resources are crucial in facilitating such work; most of our wheat sequencing pipelines were planned and implemented by Leah Clissold, Platforms & Pipeline Group Leader’s team and Head of Research Faculty Christine Fosker. In the analyses of the data, we use the considerable computing power funded by our National Capability in Genomics.

Source: http://www.tgac.ac.uk/news/237/68/Feeding-the-world-the-importance-of-crop-genomics/

Photo credit: tgac.ac.uk

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