New Genomics-Driven Surveillance To Track Crop Diseases

UK scientists from The Genome Analysis Centre (TGAC), John Innes Centre (JIC), The Sainsbury Laboratory (TSL) and the National Institute of Agricultural Botany (NIAB) have developed a new robust and rapid genomics strategy to track the devastating wheat yellow rust pathogen.

Despite modern agricultural practices, diseases of the major food crops cause up to 15% pre-harvest yield loss worldwide. Among these crops, wheat is a critical staple providing 20% of the calories and over 25% of the protein consumed by humans. One of the major fungal diseases of wheat that has re-emerged globally in recent years is yellow (stripe) rust caused by the fungus Puccinia striiformis Westend f. sp. tritici Eriks. (PST). 

This disease is widespread across the major wheat-producing areas of the world and can cause significant reductions in both grain quality and yield in susceptible cultivars. In the last decade, new PST variants have emerged that are adapted to warmer temperatures, have expanded their ability to infect different wheat varieties and are more aggressive than those previously characterised causing a serious threat to UK and global wheat production.

Improved surveillance and diagnostic systems are essential in responding to the threat of such crop diseases. A team of scientists at TGAC, JIC, TSL and NIAB with funding from BBSRC have joined forces to develop a new pathogen surveillance technique called “field pathogenomics” that can be readily applied to these difficult pathogens. Based on new gene sequencing technologies this method enables scientists to assess the population structure of these pathogens directly from infected field samples, accelerating the response time of scientists and farmers to this disease.

Working closely with the UK Cereal Pathogen Virulence Survey (UKCPVS), funded by the Home Grown Cereals Authority (HGCA) and The Food and Environment Research Agency (fera), the team used this strategy to sequence PST-infected wheat leaves from 17 different counties across the UK in 2013. Their analysis uncovered a marked increase in the diversity of PST and a complete change in the population composition when compared to older archived UK samples collected prior to 2011. 

The authors conclude that this is likely due to a recent introduction of a disparate set of exotic PST variants that displaced the previous PST populations. This detailed knowledge directly influences the management of the disease and is helping breeders develop more resistant varieties to these new PST variants. This new methodology can be used to accelerate the genetic analysis of such plant pathogen populations and could potentially be widely applied to a variety of emerging plant and animal diseases.

“Our new field pathogenomics method uses the latest sequencing technologies to rapidly generate high resolution data for describing the diversity in a pathogen population directly from infected field samples. This has been vital for characterising the recent dramatic changes in the wheat yellow rust populations in the UK, ensuring breeders, farmers and agronomists have access to the best possible information about the pathogen population to help them effectively manage disease and in breeding for enhanced resistance,” said Diane Saunders, lead author of the study and Computational Biology Fellow at TGAC and JIC.

Rapid and systematic application of “field pathogenomics” has the potential to transform current disease surveillance systems by generating high-resolution genotypic information that can inform disease incidence models and agronomic practices. The next big challenge is to develop this new method further to reduce its cost so it can be routinely integrated into national surveillance programmes such as the UKCPVS. In the long-term, this will provide earlier indications of new pathogen variants and help deploy new wheat varieties with enhanced resistance.

Dr Chris Burt, a cereal molecular geneticist at RAGT Seeds said: “There has been an explosion in the genetic diversity of yellow rust in the UK. This research provides us with a vastly improved understanding of this diversity, and a new method to monitor any future changes that occur. This is essential information to help us to develop varieties that are resistant to the wider range of yellow rust isolates that we now find in the field.”