Potato blight fight stands up to global crop disease

Potato late blight (Phytophthora infestans) is a severe threat to the production of potatoes and tomatoes worldwide, and the cause of the Irish Famine - one of the worst in human history. Potatoes are one of the most widely grown crops, thus finding ways to combat this disease is of paramount importance for world food production.

Scientists from the Earlham Institute (EI) and The Sainsbury Laboratory (TSL) have developed a faster and more efficient system of identifying and cloning resistance (R) genes from wild potato species to P. infestans. Using a combination of next generation sequencing (NGS) and bioinformatics techniques, this will pave the way for more effective crop improvement to withstand this global threat to agriculture.

This vital work has shown that the application of RenSeq SMRT to identifying R genes from wild relatives of potatoes can help us to rapidly identify and clone important resistance genes. These can be applied to various wild Solanum species, which contain the necessary genetic variability to help us combat the severe global threat of potato blight.

EI Project lead and Plant & Microbial Genomics Group Leader at EI, Dr Matt Clark, said: “Our cultivated potatoes and tomatoes are highly susceptible to potato blight, as thousands of years of selective breeding has brought with it a huge loss in genetic variation. However, within closely-related species, it is possible to find natural resistance to such pathogens.”

In order to fight against infection, plants have several defense mechanisms. Key parts are NLR (nucleotide-binding, leucine-rich repeat) proteins, which act as receptors for molecules unique to disease-bearing pathogens, such as blight and trigger the plants immune response.These genes are so commonly the basis of plant disease resistance that they are often called R genes.

Pathogens rapidly evolve to overcome plant resistances. Therefore, identifying and cloning new NLR genes can help breed crops to resist attack by pathogens, the wild relatives of our crops are an excellent resource of new NLR genes. To date, it has been slow and expensive to do this due to problems associated with isolating the correct R genes, mainly because of the number of these genes in the plant’s genome and their close similarity.

This project combined the use of resistance gene enrichment sequencing (RenSeq) with single molecule real time sequencing (SMRT) using the PacBio RS II platform. RenSeq SMRT allowed the identification of larger sequence fragments, which also allowed for greater ease of amplifying genes of interest, including Rpi-amr3i - a P. infestans R gene from Solanum americanum - a Mexican wild relative of potatoes.

Dr Clark, added: “Finding and using disease resistance genes from closely related plants is critical in the arms race against crop pathogens. This technique accelerates the process and we hope will help reduce crop losses to disease.”

The paper, titled: “Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing” is published in Nature Biotechnology. This is a collaborative project, led by Prof Jonathan Jones at TSL, with Dr Kamil Witek at TSL, EI and the Salk Institute for Biological Studies. EI’s Platforms & Pipelines Group performed the sequencing, led by David Baker.

The research project was funded by the BBSRC Responsive Mode grant (BB/L009757/1): “Controlling important diseases in potato by cloning functional NB-LRR-type resistance genes.”