An Everyday DNA blog article
Written by: Sarah Sharman, PhD
Illustrated by: Cathleen Shaw
Strolling through your local farmers’ market, it’s easy to take today’s fruits and vegetables for granted. But behind every crunchy apple or juicy tomato is a story thousands of years in the making, and that story is written in DNA.
Just like streaming playlists have replaced mixtapes, the way we improve crops is evolving. We’re moving beyond simply selecting the best-looking plants into an era where scientists can read a plant’s entire genetic blueprint and even make precise edits to it.
In this post, we’ll explore how DNA is becoming one of agriculture’s most powerful tools, helping us grow better-tasting, longer-lasting, and more resilient crops for a changing world.
The Roots of Crop Improvement
The fruits and vegetables we enjoy today didn’t always look or taste this good. For thousands of years, humans have been shaping plants to better suit our needs by choosing seeds from the best-performing varieties: the tastiest tomatoes, the highest-yielding grains, the longest-lasting squashes.
Early farmers didn’t know what DNA was, but they were unknowingly guiding the evolution of plants by selecting for favorable traits. Over generations, this hands-on selection shaped wild plants into the grains, fruits, and vegetables we now depend on.
These early improvements were based on traits people could observe, like size, shape, or flavor. What they couldn’t see were the genetic changes that made these traits possible. That changed with the discovery of DNA. Scientists could now trace desirable characteristics back to specific genes, helping breeders make more informed, faster decisions.
Today, we’ve entered a new era where we can go directly to a plant’s DNA to find genes that affect traits that might take years to identify otherwise. This accessibility to a plant’s DNA, or genome, allows us to move from observation to precision, dramatically accelerating the pace of crop improvement.
What Can Genomics Tell Us About Crop Improvement?
If early crop improvement was guided by what farmers could see, modern improvement strategies are increasingly guided by what we can’t see: DNA.
Genomics is the study of a plant’s entire DNA sequence—its genome. Think of the genome as a detailed instruction manual. It determines how tall a plant grows, how well it survives drought, or how resistant it is to disease. Using advanced sequencing tools, scientists can now read and compare these DNA instructions with incredible accuracy to spot the genetic differences that drive valuable traits.
That means we don’t always have to wait for a plant to grow to know how it might perform. Scientists can identify the regions of the genome linked to desirable traits and trace them throughout entire populations of plants.
Genomics also lets us widen our toolbox by looking at the DNA of wild plant relatives. Many of these older plant lines contain valuable traits that were lost during domestication. These wild plant traits might help today’s crops perform better in the face of climate change or soil degradation.
Genomic Tools for Smarter Crop Improvement
Thanks to genomics, scientists and breeders now have powerful tools to navigate the plant’s genome, making crop improvement less about guesswork and more about precision. Two of the most transformative tools are marker-assisted selection and gene editing.
Marker-Assisted Selection: Faster, Earlier Decisions
Traditionally, breeders had to wait for plants to grow before knowing which ones were worth keeping. Now, they can check a plant’s DNA early (sometimes as early as the seedling stage) to make smarter decisions faster.
Scientists have identified specific DNA sequences, or DNA “markers,” that sit close to genes that confer beneficial traits. If a seedling carries the right markers, it likely inherited the desirable traits, too.
Marker-assisted methods are widely used today to improve crops like wheat, rice, peanuts, and tomatoes. They reduce the time and cost required to develop high-performing varieties. They also reduce the time and space needed to test plants in the field and help breeders zero in on the best plants faster.
Gene Editing: Precision Changes From the Inside
While marker-assisted selection uses genomic information to select the best plants, gene editing allows scientists to modify a plant’s genome directly to introduce or remove specific traits.
A widely used gene editing tool is CRISPR-Cas9, which is often compared to molecular scissors that can snip out a specific piece of DNA. With CRISPR, researchers can target an exact spot in a plant’s DNA to make a precise change, like silencing a gene that makes a plant vulnerable to disease or tweaking one to improve nutrient content.
Because these edits are precise and based on the plant’s own DNA, the changes mimic what might occur naturally, but they happen in months instead of decades.
Gene editing has already been used to make tomatoes that resist spoilage, wheat that’s less prone to fungal disease, and rice that produces higher yields with less fertilizer. It is also a really useful tool for scientists to confirm that certain gene variants are associated with traits of interest.
Science in Action
Together, these tools are helping create crops that can adapt to changing weather, use fewer natural resources, and meet the needs of a growing global population. At HudsonAlpha, we don’t just study DNA; we use it to create real-world solutions. Our scientists are applying these cutting-edge genomic tools to develop new and improved crops, helping to build a more sustainable future for agriculture. Here are two examples of our work in action:
Finding the Needle in the Genomic Haystack
Imagine trying to find one word in an entire library. That’s what researchers like HudsonAlpha faculty investigator Dr. Josh Clevenger do, except the library is made of DNA.
He and his team developed a powerful computational tool called KHUFU to sift through massive amounts of genetic data and pinpoint meaningful variants. What used to take years of lab work can now happen in months or even weeks.
Once those valuable genes are found, breeders can turn to marker-assisted selection to speed things up even more. For example, Dr. Clevenger’s team is working with Mars Wrigley to breed peanuts that are resistant to aflatoxin, a harmful mold that can ruin entire harvests. By using DNA markers, breeders can screen thousands of seedlings quickly and only grow the most promising ones, saving time, space, and resources.
Building a Sustainable Future with Precision Editing
Dr. Kankshita Swaminathan’s team at HudsonAlpha is using CRISPR to unlock the potential of bioenergy crops like switchgrass, sorghum, and Miscanthus that can be grown for fuel and fiber.
These plants are essential for sustainable fuel and fiber, but their complex genomes have made them difficult to engineer. Dr. Swaminathan’s team was the first to successfully edit genes in Miscanthus, a significant breakthrough that opens the door to improvements in a plant species once considered too genetically challenging to work with. Her work is helping to pave the way for a more sustainable energy future.
Genomic tools are helping breeders and farmers breed better crops, more efficiently and sustainably. By combining the insight of traditional agriculture with the precision of modern science, we can rise to the challenges of a changing climate, food security, and environmental impact.
At HudsonAlpha, we’re proud to be part of that future. Because in every seed lies a story written in DNA, and we’re learning to read (and write) it better than ever before.
