Crop breeding

The future of plant disease management

Just like human beings, plants get sick. Microorganisms such as fungi, oomycetes, bacteria, viruses and nematodes (tiny worm like organisms) can infect their plant hosts, with deadly consequences. This might not be a big deal for the sad looking Ficus in your living room. After all, you can always replace it.

Diseases that affect our global food supply are another story. Losses due to plant disease can have tremendous consequences for food security. One of the most famous examples in history is the Irish Potato Famine. A disease called Late Blight devastated potato crops in the 19th century. This resulted in mass starvation and emigration from Ireland.

Orange powdery mildew - called rust - on barley leaves

Stripe rust is a disease that affects barley plants. Credit: Rahulkumar Patel

This famine was before scientists and farmers were aware that microorganisms could cause disease in plants. So, they didn’t know practices that could prevent disease, or solutions for managing them when they happened. Today the field of plant pathology is dedicated to the study of plant diseases and the development of management strategies. However, global crop losses due to plant disease are still estimated to range from 10 – 15% (1).

Why – more than 150 years after the devastation caused by the Late Blight pathogen – do farmers still have to worry about this and many other plant diseases?

Though we now know much more about the organisms that cause diseases, we still have very few tools to prevent crop loss. Pesticides can provide some protection, and in some cases are very effective. But, they can be expensive. If pesticides are used frequently, the population of disease-causing organisms can generate a genetic mutation. This mutation can give the population a new ability to withstand this pesticide. This is called pesticide resistance.

Plant scientists are looking for ways to help plants withstand infection. One of the best ways is to find plants that seem to have their own resistance. You might know individuals who never get a cold or flu – their immune systems seem to manage infections better than others. It’s the same in the plant world. Somewhere along the evolutionary path, these plants developed a natural resistance to one or more pathogens. These are the plants that are still in the field after others have died, or that yield well when others can’t.

Hands holding a capsule about to touch the pistil of a white potato flower.

Breeders are able to collect pollen from one plant, and fertilize another. Shown, cross breeding of potato plants. The seeds that result will be planted, and the new plants studied for disease resistance. Credit: SV Fisk

To tackle the problem of plant diseases, once plant breeders identify these individuals with natural resistance, they cross-pollinate that plant with another with high yield, or other desirable attributes. The hope is to develop a new plant variety, which is genetically unique, that has both high yield (or good flavor, etc.) and disease resistance.

However, finding individuals naturally resistant to disease is difficult and identifying them takes time. Even after years of research, there is always the possibility that naturally occurring resistance just doesn’t exist in the plant population. Further, the cross-pollination efforts take many growing seasons – testing in the lab, in greenhouses, and the field. Overall, generating a disease resistant crop variety can take a decade, or more. But, when we have a devastating disease to a major crop, we need a solution, and fast. Given that the microorganisms we are battling can generate their own genetic mutations to overcome plant disease resistance, traditional plant breeding cannot always provide a long-term solution.

Gloved hands putting tubes into a centrifuge machine

Studying the DNA of plants, as well as bacteria, has led to disease-resistant crops. Shown, a crop breeder putting tubes of extracted plant DNA into a centrifuge for concentration. Credit: SV Fisk

For these reasons, genetic engineering will be the future of generating disease-resistant crops. Remember that one in a million, naturally resistant plant that is required to generate resistant crops using plant breeding today? What if scientists could create that resistant plant?

Well, by using a technique called CRISPR scientists can. CRISPR stands for “clustered regularly interspaced short palindromic repeats.” That is a very complicated name for something that was found as a “coping mechanism” by bacteria. Yes, CRISPR is a strategy that some bacteria evolved as a defense against viruses. Bacteria can get the flu too!

The CRISPR process in bacteria works like this: Bacteria save virus DNA sequences within their genome in regions of their DNA at some point in their recovery process. The place where this information is saved contains clusters of repetitive DNA sequences, hence the name. The saved virus DNA sequences then act as “mug shots” for an enzyme in the bacteria called Cas9. If the bacteria’s Cas9 enzymes see another invading virus that has the matching DNA sequence in the bacteria’s genome, they act as molecular scissors to chop it up. It’s a lot like a bouncer at the door of a bar!

Scientists have discovered that this same process can be applied to plants. Researchers specializing in plant genetics have several methods they have developed to deliver the bacterial enzyme, Cas9, to living plant cells. They deliver Cas9 along with a “guide RNA”. The guide RNA then does as its name implies and guides the Cas9 to the target gene – the one with the matching mug shot. This gene is then disrupted by Cas9’s cutting action.

Due to the unique regenerative capabilities of many plants, an entire plant can then be grown out of the cells transformed by this CRISPR process! This results in a plant that lacks the targeted susceptibility gene and thus is resistant to disease. Breeders can then start their process – already armed with a ready-made disease resistant plant. Thus, using CRISPR greatly speeds up the process to generate disease resistant crops.

You might wonder how this technique differs from the tools used to create genetically modified organisms, or GMOs, that farmers are already growing. Older genetic engineering approaches were used to take genes from say, a bacterium, and insert them into a plant, say corn. This helped develop corn that is resistant to certain insect pests. That plant is what people call a GMO, because it has DNA from another organism in it. GMOs have not been shown by scientific research to be harmful to human health, but they do not always enjoy a positive reputation.

CRISPR is an approach that doesn’t require the addition of foreign DNA to a plant. It simply makes a small cut in the plant genome which will provide big benefits. It is also faster, less expensive and easier to use than older genetic engineering techniques.

The challenges to our food supply are great. Besides droughts, heat, cold, and all the other stresses our crops must cope with, there is also disease. New techniques, like CRISPR, can help us look forward to a future of more abundant, more sustainably grown food.

Answered by Audrey Kalil, North Dakota State University

  1. Pinstrup-Andersen, P. 2001. The Future World Food Situation and the Role of Plant Diseases. The Plant Health Instructor.  DOI: 10.1094/PHI-I-2001-0425-01.

About us: This blog is sponsored and written by members of the American Society of Agronomy and Crop Science Society of America. Our members are researchers and trained, certified, professionals in the areas of growing our world’s food supply while protecting our environment. We work at universities, government research facilities, and private businesses across the United States and the world.

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