Atlas puts wheat resistance genes on the map

An ambitious proposal to create a resistance gene “atlas” as a resource for the international wheat community has been outlined in a new review.

The R gene atlas would be a free, online directory from which combinations of resistance (R) genes could be identified by breeders and researchers and bred into wheat varieties.

The aim is to provide durable molecular protection against wheat’s major pathogens including wheat rusts, blotch diseases, powdery mildew, and wheat blast.

We sat down with Amber Hafeez and Dr Brande Wulff to find out more.

Why is a resistance gene ‘atlas’ needed?

First author of the review Amber Hafeez explains: “We lose one fifth of wheat yield annually to pests and pathogens, adding up to 209 million tonnes worth $31 billion.

To minimise that loss and reduce reliance on chemical protection we need broad spectrum and durable genetic resistance. Our atlas would bring together cloned resistance genes and pathogen virulence information so that users can pool the best combinations of resistance genes to fit local conditions.

Genetic resistance is precious; it is a finite resource and pathogens can evolve to quickly overcome individual resistance genes. We need to use resistance in a way that doesn’t squander individual genes by releasing them in a stacked or combined way so that they will be effective for a long time.”

Why now?

The idea builds upon a recent surge in genomic resources available to researchers in wheat, facilitated by advancements in sequencing technologies and bioinformatics.

In the past few years, researchers at the John Innes Centre and The Sainsbury Laboratory have rapidly identified and cloned resistance genes in wheat and its wild relatives using technologies such as AgRenSeq, MutRenSeq and MutChromSeq.

“This makes it possible to clone disease resistance genes in wheat or one of its wild relatives much faster and much more cheaply. Suddenly what was before just a pipe dream is now a potential reality: we could clone most if not “all” of the resistance genes in wheat,” says Dr Brande Wulff, another author of the review and group leader at the John Innes Centre.

How would the R gene atlas work?

Wheat R genes work by recognising corresponding molecules in the pathogen called effectors. By identifying the effectors present in pathogen and pest populations, combinations or “stacks” of R genes could be designed.

The gene atlas would be a free online portal containing this genetic information and enabling breeders to design gene stacks using computer modelling before starting their breeding in the field.

It would also enable users to design molecular markers that they could run on wheat populations to find out what resistance genes they already have in their breeding programme.

“One of the big problems currently is that breeders don’t always know whether their resistance is coming from a single gene or due to two or three different genes. If they bring in something exotic from a wild relative, for example, they need to know that it is going to complement what they already have in their breeding programme,” explains Dr Wulff.

“Our R gene atlas is like putting a little flag everywhere where there is a resistance gene, a little address tag and that would allow breeders to put their molecular net across the genome and see where all the R genes are. That would allow them to combine existing and new R genes in ways that would give strength in unity.”

The proposal details how the molecular components – R genes and effectors – involved in disease resistance could be captured from both the host and pathogen. Whole genome sequencing would be carried out on diversity panels of wheat, its progenitors and domesticated and wild relatives.

Then, association genetics – a method of seeking useful genetic variation – could be used to look for correlations between the host genotype and disease resistance or susceptibility – and the genes responsible for these traits could be identified.

Is it cost effective?

To combat eight of wheat’s major diseases, the researchers calculate it would cost around $58.6 million for the sequencing of diversity panels of the pathogens and 10 hosts, as well as funding 75 scientists to carry out the work.

This, they suggest, could be funded by contributions of $2.9 million per G20 country over five years – which is likely to be a worthwhile return when disease losses can be valued at around $31.2 billion dollars each year.

“Compared to the scale of the problem in yield losses to pests and pathogens, this represents excellent value for money,” says Amber Hafeez. “Our costs include sequencing, bulking up the seed and performing all the pathology experiments you would need for all these eight major diseases that we list as priorities, as well as including the costs of bioinformaticians and management.”

The idea of bringing together an international consortium also allows the project to draw upon existing expertise and resources.

“A lot of the pieces of the puzzle already exist, the idea is to bring them together to make sure we don’t duplicate efforts,” says Dr Wulff.

“We see it as a centrally coordinated model distributed around different countries, using existing capacity. For example, there is an institute in Denmark called the Global Rust Reference Centre which can receive and work with exotic isolates of rust in a contained environment. This would be an ideal partner for the proposed endeavour.”

How would you ensure proper use of this free resource?

“We spoke to lots of breeders in different parts of the world and asked them this question: What could we do to incentivise us to use the atlas, this finite resource, judiciously to make it last as long as possible,” says Dr Wulff.

One way involves patenting novel genes from wild relative backgrounds as a means of controlling the way they are used.

Another method of exerting control would be through the recommended lists which growers choose varieties from. The committees releasing cultivars onto the lists would award extra points to varieties which are likely to offer more durable resistance.

“The gene atlas is a route to bringing disease resistance from the lab to the field at speed and in sufficient quantity. For researchers and breeders of wheat – the most widely grown crop in the world – that can only be a good thing,” says Amber Hafeez.

Amber Hafeez’s PhD is funded by the Norwich Research Park Biosciences Doctoral Training Partnership.

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