Plant Genomics is Blooming, and It Could Change How We Grow Food

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To tackle food insecurity and climate change, scientists are tapping into ancient adaptations, engineering super crops, and designing plants from scratch.

The  world is entering an era of climate uncertainty, in which extreme weather events are no longer rare disruptions but the new normal. Prolonged droughts are followed by catastrophic floods, temperatures continue to rise, and diseases threaten ecosystems worldwide.

These changes pose a significant challenge to plant health, crop yields, and biodiversity—at a time when one out of 11 people face hunger and the global food demand is only increasing as the population grows.

"It's really important to look across the plant kingdom because plants have solved so many problems already.

Why not read their genomes like a book and try to understand it and solve the problems using ancient knowledge?"
- Todd Michael, Salk Institute for Biological Studies

Unlike animals which can migrate to find more hospitable conditions, plants are largely rooted in place. Their dispersal is slow and limited, so they must rely on adaptation to survive. With some of the most diverse genomes on Earth, the plant kingdom contains a rich genetic toolkit to respond to environmental shifts.

However, their genetic flexibility may not be enough to withstand the current pace of climate change. Scientists are studying how plants have adapted to harsh and shifting environments, hoping to apply this knowledge to engineer resilient super plants. Luckily, they can build on solutions that already exist in nature.

"It's really important to look across the plant kingdom because plants have solved so many problems already,” said Todd Michael, a plant genomicist at the Salk Institute for Biological Studies."

“Why not read their genomes like a book and try to understand it and solve the problems using ancient knowledge?”

To achieve this, researchers first need access to genomic information. Until recently, decoding these complex genetic blueprints was beyond scientists’ reach. Now, thanks to advances in sequencing technologies, the plant genomics field is flourishing.

With the ability to read plant DNA, researchers can explore genetic alterations that help plants adapt and even look into the past to track how plants have responded to climate shifts over centuries.

The ultimate goal is to harness this knowledge and engineer future crops that can withstand harsh environments, produce higher yields, and help mitigate the effects of climate change.

A Cornucopia of Plant Genomes:

In 2000, as the consortium behind the Human Genome Project announced a “working draft” of the sequence of the human genome—an achievement celebrated with a front-page story in The New York Times and a White House ceremony—scientists reached another major milestone: the first fully sequenced plant genome. The honor went to Arabidopsis thaliana, a cosmopolitan weed and a popular model organism.

It was chosen, in part, for its relatively small genome—around 135 million base pairs. Still, sequencing it was no small feat. “It took several years and many, many millions of dollars,” said Michael.

The real challenge lay ahead—deciphering more complex plant genomes.

Unlike A. thaliana, many plants, including essential crops, have staggeringly large genomes. The New Caledonian fork fern (Tmesipteris oblanceolata), for instance, is the current record holder for the world’s largest known genome.

Coming in at 160 billion base pairs, it far surpasses the three billion base pair human genome.

Plants’ large genomes are thanks in part to their tendency to accumulate transposable elements, or duplicate copies of large sections of their DNA.

“The maize genome, for instance, is over 70 percent repeats and that's because these transposons^Wiki have basically jumped around the genome and multiplied, causing genome bloating,” said Michael.

While many plants are diploids, meaning they have two complete sets of chromosomes, many plants undergo polyploidy events, duplicating entire sets of chromosomes.

While the new genetic combinations that result from these events may be evolutionarily advantageous, it has made plant genomes historically difficult to sequence and assemble.

“Plants can make all these different things, which basically give them flexibility, which makes my job immensely fun because of the diversity of the genome structures and the states that the genomes can be in,” said Michael.

These massive and dynamic genomes may be a key factor in helping plants adapt to climate change—one of the many reasons scientists are eager to obtain their complete sequences and study them in greater depth.

By sequencing a large number of plant genomes, researchers can move beyond simply identifying strings of As, Ts, Cs, and Gs to understanding the function and regulation of each gene.

Michael emphasized that a deeper knowledge of DNA is necessary for making precise genetic modifications. He noted that large language models will be crucial in identifying patterns across vast genomic datasets.

 “I think that's the future of actually understanding how to leverage plants to do what we want,” said Michael.

Herbaria: A Time Capsule of Plant Responses to Climate Change

Throughout Earth's history, climate change has shaped ecosystems, but the Anthropocene has ushered in unprecedented shifts at a breakneck pace. Understanding how plants respond to these changes is crucial for assessing their adaptive potential and identifying new targets for future plant engineering.

By studying historical plant samples from the last few centuries, scientists can uncover clues about how plants respond at the molecular level to environmental pressures, offering valuable insights for climate resilience strategies.

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Extreme weather is now the new normal, threatening crops, biodiversity, and global food security. Scientists are unlocking plant genomes to engineer resilient crops that can withstand climate change and secure our food future.

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