Learning about plant immune systems is one of the first steps toward finding ways to improve their defenses against pathogen attack. The difficulty is that, much like the immune system found in animals, the processes involved are highly complex and also completely different from other kingdoms of life. Finding out about the human immune system in the field of immunology gives little insight into how plants protect themselves and vice versa.

The Plant Immune System

What we do know and have discussed before is the PAMP system of defenses, the pathogen-associated molecular patterns that are used to identify pathogenic species and begin the immune response itself. Much research into plant immunity focuses on the first step of this system, the PAMP-triggered immunity or PTI response that acts as an identification signal. For if we can get plants to recognize and respond to a wider range of pathogens and in a quicker manner, then their innate defense setup is often good enough to protect them. Though this isn’t always the case for the most pernicious of attackers.

To deal with more in-depth issues, the second layer known as Effector-triggered immunity (ETI) is where to look. These effectors are controlled by resistance or R genes and the genes are commonly recognized due to their repeated structure of having domains called nucleotide binding site-leucine-rich repeats (NLRs). The R genes with these domains help to manage the unruly and varied structure of the effectors themselves that have no clearly defined domains.

The Rice Blast Fungus

Scientists working for the USDA’s Agricultural Research Service have been attempting to find better ways to give plants resistance to the pathogen known for causing rice blast. The fungal species behind this, Magnaporthe oryzae, is a deadly one and annually causes rice crop losses in the tens of billions. The amount of rice destroyed would be enough to feed around 60 million people, so fixing the problem of rice blast is a fairly high priority. There is a complication, however.

M. oryzae is a finicky fungi that can alter its genetics even without sexual reproduction necessitating such a change. The significant number of actively moving transposable elements in its genome can knock out other genes, including avirulence markers used by plants to identify the pathogen for what it is. And, when this happens, their defenses fail, and you get a full blown spreading infection of rice blast.

Thus, major research has been ongoing in identifying resistance genes against fungi, with over 100 having been found thus far and the more effective ones having already been added into major rice species in the US. The well known among these are the Pi-ta and the Pi-ta2 genes, which have been used in the cultivar Katy as a breeding line for other cultivars. An interesting thing to note is that the Pi-ta resistance complex of genes is actually made up of three components, not two.

The Atypical Ptr Gene

Prior studies published by the Agriculture Research Service identified the Ptr gene as that extra piece and it has now been found to be unique in several ways. Rather than having the NLR domain structure common to most R genes, it appears that the protein of Ptr have two separate forms, both of which use a special structure known as an Armadillo (ARM) repeat. These are a set of repetitive amino acids that create a hairpin formation with two alpha helix shapes.

When testing with the impact of Ptr as a resistance gene, the researchers found that deleting two base pairs to incapacitate the gene and make a truncated protein leaves the plant fully open to rice blast attacks. Just that one gene and protein alone appears to be critical for the rice resistance to work properly. This was further confirmed by taking a highly resistant cultivar and using CRISPR-Cas9 to mutate the Ptr gene, rendering the plant susceptible to the fungus again.

Based on this, the scientists hypothesize that the gene works as a broad-spectrum resistance gene that is independent of the rest of the Pi-ta system, making it a candidate for improving overall plant resistance directly, rather than through complex regulators. It seems to be a sort of failsafe mechanism when the main defenses fail and, since the rice blast fungus already appears to have developed mechanisms around the main lines of defense, susceptibility to the disease is heavily dependent on a working Ptr gene.

A Future Full of Rice

However, as a failsafe, it does require the main Pi-ta system to be active in order to function. While its resistance capabilities function independently, without the original resistance structure, it is incapable of working properly. Thus, if gene transfer with CRISPR and other tools is to be used, both the Ptr and Pi-ta genes need to be transferred together. This gene stacking should be able to give multiple rice cultivars (and possibly other crop species dealing with related blast fungi) strong resistance to infection.

They hope that this will enable an almost wholesale prevention of rice blast crop losses in the future, improving rice production and the capability of countries around the world to feed their populations without the risk of losing an entire year’s crop from a single deadly disease.

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Photo CCs: Oryza sativa Ear rice Stugaru roman rice IMG 3971 from Wikimedia Commons