The Gene Tamer

Late blight resistance genes isolated from wild potato relative

Published online: Jan 03, 2017
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This article appears in the January 2017 issue of Potato Grower

A team of scientists from The Sainsbury Laboratory (TSL) and the Earlham Institute (formerly The Genome Analysis Centre) in the UK have developed a new method to accelerate isolation of plant disease resistance genes. The team has also identified a new source of blight resistance genes in Solanum americanum, a wild relative of the potato.

Plant pathogens such as late blight can evolve rapidly to overcome resistance genes, so scientists are constantly on the hunt for new resistance genes. Jonathan Jones and colleagues at his lab at TSL pioneered the new technique, called “SMRT RenSeq,” and believe it will significantly reduce the time it takes to define new resistance genes.

The team plans to stack several resistance genes together in one plant, making it much more difficult for pathogens to evolve to overcome the plant’s defenses. It is hoped the deployment of this new technique will improve commercial crops and lead to higher yields, significantly reduced environmental impact and lower costs for the producer and, ultimately, the consumer.

Potato late blight remains a major threat to potato and tomato production, with worldwide crop losses estimated to be in excess of $4.2 billion. Prevention measures and crop losses constitute a significant portion of growers’ expenses each year; on-farm blight management can account for as much as half of the total cost of potato production. Managing the disease requires frequent application of fungicides, which incurs not only a significant economic cost but also environmental costs. Genetic resistance can be introduced into crop species, which reduces the need for chemical spraying. However, using conventional breeding techniques, deploying genetic resistance is long and laborious.

Sources of new plant resistance genes are difficult to find. Jones’s team investigated the wild potato relative Solanum americanum, which carries several resistance genes, and by using the new technique, rapidly isolated a new resistance gene, Rpi-amr3.

SMRT RenSeq makes the process of finding, defining and introducing genetic resistance faster and easier by combining two sequencing techniques: “RenSeq” (Resistance gene ENrichment SEQuencing)  and “SMRT” (Single-Molecule Real-Time sequencing). The technique consists of two primary steps:

  1. A subset of DNA sequences are captured using a method that selects for long DNA molecules that carry a sequence commonly associated with resistance genes.
  2. These DNA molecules are sequenced multiple times to make sure the code is determined as accurately as possible using the novel long-read SMRT technology.

The technique results in a very reliable DNA sequence for each candidate resistance gene. Genetic analysis of the results enabled the team to define which of these candidate genes were linked to blight resistance. Following this, the SMRT RenSeq method also enabled the team to identify and define the parts of the genome that regulate the resistance genes. Several candidates were introduced into a model species, of which one—Rpi-amr3—successfully provided broad-spectrum blight resistance. Led by David Baker, the TGAC Platforms & Pipelines Group performed the sequencing.

“Engineering disease resistance genes into crops is a continuous battle to stay one step ahead of new strains of disease,” says Jones. “Scientists are constantly investigating how to speed up this process. This new technique significantly reduces the time and cost of isolating candidate resistance genes, and has great potential for application to other desirable traits in potato and in other crops.”

“Our cultivated potatoes and tomatoes are highly susceptible to blight, as thousands of years of selective breeding have brought with it a huge loss in genetic variation,” says TGAC project lead Matt Clark. “However, within closely related wild species, it is possible to find natural resistance to such pathogens. 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 it will help reduce crop losses to disease.”

This work was funded by the Biotechnology and Biological Sciences Research Council and the Gatsby Charitable Foundation.