Plant diseases present a major challenge to the livelihood of the world’s more than 500 million subsistence farmers, among them the vast majority of rice farmers in Asia and Africa. With more than 700 million tons annually, rice is the most important source of nutrition for more than half of the world’s population. It is the staple food for the majority of people in Asia, gaining importance in Africa. Bacterial blight is one of the scourges of rice production, caused by Xanthomonas oryzae pv. oryzae (Xoo).

The battle against bacterial blight is challenging, because hundreds of different Xoo strains exist worldwide. Faced with this enormous variation on the pathogen side, there is an urgent need for durable genetic resistance in rice coupled with ongoing surveillance of the pathogen population. 

Through serendipity, we discovered a key mechanism of bacterial blight disease. During rice infection, the Xoo bacteria inject so-called TAL (transcription activator-like) effectors into the host that activate rice SWEET sucrose efflux transporter genes by binding to specific sites in the regulatory elements. SWEETs function in cellular export of sucrose to the extracellular space where the bacteria reside. This way the pathogen accesses the nutrient resources of the host, which enables Xoo to reproduce massively. We found that all known Xoo strains rely on activation of SWEET transporter genes to cause disease. Natural variants in the SWEET regulatory elements that can not be recognized by the TAL effectors provide resistance to some, but not all, Xoo strains, preventing their access to the host sugar storage. 

The idea behind our humanitarian research project – called Healthy Crops (www.healthycrops.org) - was to develop promoter variants in multiple binding sites for TAL effectors in a single rice variety to deny the bacterial access to host sugars without altering the normal sugar transport in the rice cells. In our two back-to-back Nature Biotechnology publications we systematically analyzed the genomes of a worldwide collection of 95 Xoo isolates. We found that in total, individual Xoo strains have one or two of eight different TAL effectors that can target eight distinct binding sites in the regulatory elements of three different SWEET genes.

We generated rice lines with variants in the SWEET regulatory elements that cannot be recognized by the Xoo bacteria. We are excited to report that we obtained rice lines with broad-spectrum resistance against all 95 Xoo strains obtained from different geographic origins. We generated resistant variants in three rice varieties, including Kitaake, and two mega varieties, IR64 and the flooding-tolerant Ciherang-Sub1, both of importance for Asia and Africa. To be able to rapidly identify which SWEET regulatory elements are targeted by emergent Xoo strains, and to be able to develop intelligent deployment strategies for the resistant variants, we developed also a diagnostic kit that together with the resistant varieties will help to achieve broad-spectrum and durable disease resistance worldwide.

The majority of farmers suffering from bacterial blight disease are subsistence family farmers in Asia and Africa. Our Healthy Crops team is non-for-profit and is dedicated to help such farmers with our resistant rice lines and the diagnostic kit to defeat bacterial blight disease. We are excited that we have, perhaps for the first time, developed tools and rice lines that could prevent bacterial blight disease of rice.

Sarah Schmidt & Wolf B Frommer

Heinrich Heine University, Düsseldorf, Germany

Broad-spectrum resistance to bacterial blight in rice using genome editing: https://www.nature.com/articles/s41587-019-0267-z

Diagnostic kit for rice blight resistance: https://www.nature.com/articles/s41587-019-0268-y