Q&A: What can plant evolution teach people about breeding better crops?

This Q&A addresses

• how biological diversity and plant evolution help researchers develop healthier crops and wild plants and
• how AI, bioniformatics, genomic sequencing and other tools are enhancing this research. 

UNIVERSITY PARK, Pa. — Today (May 22) is United Nations International Day for Biological Diversity, drawing attention to a critical resource for developing crops that are resilient or resistant to extreme weather and other threats to their health, according to Jesse Lasky, associate professor of biology at Penn State.

Lasky has studied plant evolution and adaptation for more than 15 years and has published dozens of papers on the topic. Emerging research tools like artificial intelligence (AI) and genetic analysis are enabling scientists to unlock the secrets of biological diversity and protect plant populations in a rapidly changing world, Lasky said.

In this Q&A, Lasky discussed how leveraging biological diversity and understanding plant evolution could lead to healthier crops. He also explained how several emerging technologies and techniques can support these investigations.

Q: How can the history of plant evolution guide future plant breeding and crossbreeding efforts?

Lasky: Around the world, environments are changing really quickly, which has huge impacts on the health of plants that we need, like crops. We can reduce the negative impacts on our crops and also wild plants by helping those plants adapt. This can be accomplished either by breeding crops that will do better in future environments or by developing strategies that facilitate wild plants' evolutionary adaptation to new environments.

Historically speaking, breeding did not use molecular data interpreted in light of evolution. More recently, some researchers have been looking for solutions that have already occurred naturally — without conscious human intervention — where plants have adapted to their environments. From these natural examples, we seek to learn how to improve crops.

Plant breeding is a form of evolution. So, to breed plants more effectively, we might as well harvest knowledge from the rich history of evolution that has already occurred. In fact, ignoring the available information about how things have already evolved would be a waste of a resource; we would be missing out on an opportunity.

Q: What are plant genomics, and why are they essential for understanding how crops can adapt to different climates?

Lasky: People bred plants for millennia without genomics, which is the study of the function and evolution of an organism's complete DNA. Without genomics, people have been broadly able to adapt local crop varieties to a wide range of environments. Using genomic data, however, can speed up that process.

Crop diversity is harder to take advantage of with traditional plant-breeding methods. Consider gene banks, for example. People have built seed collections containing thousands and thousands of varieties of crops, and we call these gene banks because they contain as much genetic diversity as possible. For a plant breeder trying to identify useful traits, traditional breeding could require really an immense effort. You would have to grow huge numbers of plants while controlling the environmental conditions and measuring the plants’ traits.

If researchers sequence the genomes of the plants in those gene banks, and we also understand the genomic patterns of adaptation to the environment in those plants, we may be able to detect which parts of the genome are useful for adapting to the environment. Then we can isolate the varieties in the gene that carry useful traits for certain environments.

If a region experiences a shift in temperatures or rainfall or a new insect pest emerges, people will need crop varieties that are resistant to that new problem, and they will need that solution quickly. Plant genomics can provide a faster, more efficient way to exploit the diversity stored in gene banks to solve problems faced by farmers anywhere in the world.

Q: How can bioinformatics and AI modeling predict how plants respond to climate stress?

Lasky: Researchers, including my lab, are working to understand what changes in specific DNA sequences mean for an organism. There are some aspects of the genetic code that are simple and well understood, like how some amino acids are encoded in a protein. But there are many aspects of genetic variation that are less understood.

The level at which a gene is expressed — how much of it is made — is controlled by DNA, but not in a way that we understand well, and it can be noisy and complicated. AI approaches to bioinformatics — the use of computer science and mathematics to analyze DNA — could be useful for untangling the problem of understanding how genetic variation might influence the expression of a gene, which is very complicated.

The big picture is that we have massive amounts of genetic variation across the genome. We still don't really know much about how that variation affects a plant's traits or how the genes interact with their environment. So, there's a lot of opportunity for AI modeling to predict how genetic variation influences how organisms respond to environments and environmental change.

Q: What does genetic diversity tell us about the future of agriculture and food systems?

Lasky: The genetic diversity in widespread plants provides clues about how past evolution has already solved certain problems. For example, if researchers think a specific gene is important for adapting to hotter environments, but there's no naturally occurring genetic diversity in that gene, it may mean that gene is best kept unchanged. In other words, that gene may not be a great target for breeding or engineering, because over the past no variation was able to persist in this gene.

Genetic diversity also gives us a lot of information about past evolution and what kind of changes might be important in plant breeding for future environments. Genetic diversity is the raw material for natural evolution, so — as we discussed — gene bank seed collections are important because they house a lot of genetic diversity that can be used in breeding. But the genetic diversity in natural plant populations can allow species to adapt to rapid environmental changes.

Populations that lack genetic diversity will likely be less able to adapt to environmental changes — especially very quick ones — so they'll probably feel negative effects of environmental change to a much worse degree than diverse populations.

With the emergence of new approaches and tools, this is an exciting time to study genetic diversity in plants. By combining sequencing of plant genomes and building new statistical and AI models, someday, genome-based forecasting may support food-security and biodiversity conservation solutions, identifying problems before they occur. Only time will tell.