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Crop Genome Sequences: A Critical Foundation for Food Security

Doreen Ware
Photo courtesy of Len Marks Photography, Cold Spring Harbor Laboratory


Doreen Ware is a computational biologist at the Robert W. Holley Center for Agriculture & Health in Ithaca, NY. Her work focuses on plant genomics, particularly of staple agricultural crops.

Welcome Dr. Ware to Under the Microscope.

UM: Your work contributes to food security under changing climate conditions. What are the basic challenges that climate change poses to crops?

DW: I would say that almost all crops are at risk now. With climate change, we have seen changes in weather patterns, as well as erratic weather: areas are becoming hotter or colder, we see changes in rainfall.  With erratic weather, some years, it might be waterlogging when plants are seedlings and really hot later on during the time when the seeds would be formed. We see examples of large temperature changes within a day. Those are the abiotic stresses.

We also see biotic stresses changing, things like disease. With all these changes in climate, we're seeing new populations of insects, new variants of other types of diseases, fungal pathogens, things the crops haven't seen before. A plant, unlike an animal, cannot get up and move away; it cannot create a new shelter. It must adjust and adapt. If they have not seen these changes before, plants may not a have a genetic strategy to address them. 

UM:  How can crop genome sequencing help address these challenges? Are there specific solutions it might produce?

DW: We can use it to study how plants grow and adapt to the environment, and to guide the way that we breed plants. What traits might make them more resilient and high-yielding?  For example, could we develop seedlings that survive cold temperatures very early on, so we could plant earlier, so they're not out there at the hottest point later in the year? When we think about the instructions that a genome provides, they can be broken down into smaller components: How many seeds are on an ear of corn? How many ears can you have on the plant?

Each of these traits has many genes involved, and breeders will have genetic markers to track them. This is what is traditionally done with marker-assisted breeding. What's new is an approach called genomic selection, where you have a population that has been optimized for an environment. Using the sequence from the population, you can develop a model to predict which germplasm will have a better outcome in that environment.  So, we've gone from selecting for a few traits and a few genes with large effects to being able to use information across the whole genome, reducing the time it takes to create new crops.

UM: What does crop genome sequencing involve? Are plant genomes different from other kinds of genomes in any significant ways?

DW: Sequencing is the process of discovering and describing the layout of the genome – which parts are active, which genes are present, and how they are configured. What's very different about plant genomes is that they are far more fluid than animal genomes. Out in nature, plants can duplicate their genomes, becoming polyploid (having multiple genomes in each cell). The wheat used to make bread is a hexaploid, with six copies of its genome in each cell, whereas corn is an ancient tetraploid that had four copies, and now has two.  Plants make additional copies of genes, providing a rapid way to change how much, where, or when a gene may be expressed.  Plant genomes, relative to animals, have a high percentage of mobile elements – in corn, it's more than 80% – providing a large pool to draw on to introduce new diversity within a species.  Plants have a lot of variation that we haven't been able to monitor until recently.

Doreen Ware in a research field. (Photo courtesy of Constance Brukin, Cold Spring Harbor Laboratory).

UM:  How do the features of plant genomes affect how we can develop crops for sustainability?

DW: A genome sequence can provide insights into the life history of a species, and the differences between individuals provide a footprint of what has been selected in nature. Has the plant seen a disease, and has it developed an adaptive strategy? We can look at the genomes and find signatures for genes associated with disease, or plant architecture, helping a plant adapt by opting to grow the root deeper and longer, or to have a bunch of lateral roots, or to make a flower fertile, or to increase the number of seeds. We can identify which functional allele (one or more alternative forms of a gene) may provide the best fitness outcome in a specific environment.  

UM: Is crop genome sequencing safe?

DW: Sequencing a genome is very safe. Essentially, we're just producing a map of the plant's genetic instructions. What has shifted over the last 5 years is the economics of it, and the sensitivity and accuracy of it. Fifteen years ago, sequencing a maize genome cost more than $50 million. Now it could be as low as $1,000. We used to get a single reference (a generic record of the genome of a type of organism), and now we're able to get reference sequences from multiple individuals, and that helps us better dissect some of their traits. But the most important effect is that it accelerates breeding cycles and functional characterization.

UM: Are certain crops or kinds of crops better suited than others to genome sequencing?

DW: Twenty years ago, the best genome to sequence would have been a small diploid genome with few repeat sequences. Technologies now allow us to read very long pieces. That's really important because in these plant genomes that are very fluid, some of these repetitive elements are very big. It's more challenging to deal with larger genomes and polyploid organisms, but the barriers associated with obtaining complete references are going away.

Now I would say the door is opening so we should be able to sequence all genomes, but the organisms that have very big genomes and multiple copies of their genomes will cost more. The corn genome is the size of the human genome, but trees, which would be used for forestry, for instance, are much larger. So, some plants are still easier to sequence, but because our technology is better, that doesn't have to limit us in the way that it used to.

UM: Are certain crops or kinds of crops more at risk due to climate change?

DW: Some crops may have lower resiliency, the ones that need to be babied and need a lot of care, to be grown in a field, watered, and fertilized, for instance.  We're going to have to re-think sustainability in everything that's put into inputs: fertilizer, pesticide, water. We have to consider both changing climate conditions and sustainability.

Perennial crops (plants that grow over several years) are at risk, because it takes longer to establish them, and they may not be as productive early on. If you think about a tree, its environment's going to change 10 years from now. What if you don't have enough cooling days, and a plant doesn't produce fruit? Depending on how you look at it, all crops are at risk. They all face different risks.

UM:  How are we going to feed 2 billion more people by 2050? What role does crop genome sequencing play in addressing this challenge?

DW: We're going to need to increase farm productivity, to start using acreage that is less desirable, and to teach plants how to improve their performance on those marginal lands. And then we're going to have to look at alternative ways of farming – think about urban farming as an example. For each of those tactics, we're asking: how do we identify the best germplasm? We might take our existing crops and consider how they'll grow in other ways. We might even look at domesticating new crops. There are a lot of wild relatives that might have some desirable traits.

We want to optimize germplasm; we want to leverage what one species has learned to transfer it to another. For instance, if we were looking at disease resistance genes, we might want to mine existing diversity collections and identify disease resistance there, and then move that trait into other plant populations. We could also create new genetic diversity, where we use chemical modifications that change the DNA of a plant. That's been a traditional practice in making seeds for a long time. Ultimately, there's not one solution that's going to fix it all, but the ability to sequence these genomes is certainly going to contribute to the effort.