A multi-locus strategy for durable rust resistance in wheat, in the face of a rapidly changing pathogen landscape (Yellowhammer)

What challenge did the project address?

Yellow rust is a major threat to wheat production in temperate and maritime climates, such as found in the UK and northern Europe.

The disease is caused by the airborne pathogen Puccinia striiformis f. sp. tritici (Pst).

Use of resistant varieties is a key component of the integrated pest management (IPM) of yellow rust. However, new pathogen variants are discovered almost every year in the UK. These have new virulences and new virulence combinations, which help the pathogen to break down varietal resistance.

A well-known example relates to the ‘Warrior’ yellow rust race, which was discovered in 2011. It showed how pathogen isolates could migrate into the UK over considerable distances. Now dominant in the UK, the Warrior population is diverse.

For breeders to deploy yellow rust resistance genes in wheat varieties in the most effective way, they need comprehensive knowledge of the types of disease resistance present in UK and northern European wheat genetic material. They also need information on which resistance sources are effective against current pathogen populations.

What did the project do?

This project established a panel of 427 winter wheat varieties (the Yellowhammer panel) to represent genetic diversity deployed across the UK and northern Europe over the past 60 years.

The panel was grown across field trial sites in the UK, France, Germany, Denmark and Sweden over several years (2018–2022) with yellow rust resistance assessed.

The panel was also screened (using the Breeders 35K wheat array) for single nucleotide polymorphisms (SNPs). Each SNP represents a difference in a single nucleotide (a DNA building block). This project identified 19,703 SNPs.

SNPs were used in a Genome Wide Association Study (GWAS) to assess the yellow rust resistance in each wheat variety across the multi-site-by-year field trials. These SNP markers were mapped against the wheat Chinese Spring genome reference to identify the chromosomal location of each SNP. From these multiple GWAS analyses, marker trait associations (MTAs) for yellow rust resistance were identified. An MTA for yellow rust resistance was called if it had a significance score above a threshold of 3.0 or above 1.5 (in more than one season or location).

Near-isogenic lines (NILs) of wheat were used in a microscopic sudy. NILs are almost identical, except for a few specific locations or genetic loci. This study examined the effect of the presence or absence of three target yellow rust resistance loci (HIT1, HIT2 and Yr15) on pathogen development at specific times after inoculation.

At each time point, RNA sequence (RNAseq) data was also generated to study gene expression and to identify differences in the cellular and molecular response to yellow rust infection.

What did the project deliver?

The SNP marker work will help the project’s industry partners develop DNA markers for these sources of yellow rust resistance to use within breeding programmes.

The microscopic analysis of pathogen development has shown that different sources of yellow rust resistance interact with the pathogen in various ways, indicating potentially different resistance mechanisms. By combining resistances that function through different mechanisms, it may be possible to achieve more durable disease resistance.

Specially, the project delivered:

1. An extensive knowledge of the sources of yellow rust resistance in the UK and northern European winter wheat gene pool.

The project has provided a holistic view of yellow rust resistance sources available to winter wheat breeding programmes, including those that are relatively fixed and those that are underutilised in wheat materials.

Of the 45 marker trait associations (MTAs) identified, 29 were present in over 90% of the GWAS panel lines. This suggests that these yellow rust resistance loci have become fixed in UK and northern European winter wheat germplasm.

MTAs that occurred at a low frequency (less than 20%) were 1A011 (18.5%), 2B143 (17.2%), 2B153 (17.3%) and UN004 (6.25%). 3B004 was found in 21.7% of the GWAS panel lines.

2. Information on the effectiveness of each yellow rust resistance loci in each location (country).

Yellow rust populations in the UK and France had similar virulence profiles, as suggested by the GWAS analyses. Larger shifts in the virulence profile of the population in Sweden were apparent – harsher winters may eradicate populations with new infection initiated by migration of new yellow rust isolates into the country each year.

3. Validation of many of the yellow rust resistance loci through bi-parental mapping.

MTAs were confirmed in the varieties Dickens, Gladiator, Crusoe, Mallet and Revelation using bi-parental mapping populations. The MTAs confirmed were 1A011, 1B545, 2A019, 2A087, 2B153, 2D999, 3A010, 3B004, 4B575, 5B677, 5A685 and 6A612 and UN004.

4. A novel approach, by which to identify the genes responsible for the yellow rust resistance loci, using RNAseq data and differential gene expression analysis was demonstrated.

As a proof-of-concept, NILs with and without the cloned yellow rust resistance gene Yr15 were included in this RNAseq analysis. Comparing yellow-rust inoculated samples to uninoculated flag leaves identified the Yr15 gene, which was present in the top 10 wheat genes that were differentially expressed between these treatments.

Who will benefit from this project and why?

• Farmers will benefit through the development of new wheat varieties with effective, high levels of yellow rust resistance
• Wheat breeders will benefit through a better knowledge and understanding of the sources of yellow rust resistance within their breeding materials
• Researchers will benefit through an enhanced comprehension of how yellow rust resistance genetics functions, as well as a new approach to candidate gene identification through RNAseq data and differential gene expression analysis

Watch a YouTube video about this work

A presentation at the 2024 UK Cereal Pathogen Virulence Survey (UKCPVS) event outlined the main findings from the yellowhammer project. It was delivered by Lesley Boyd (NIAB).

Breeding durable resistance to wheat yellow rust (UKCPVS 2024 video)