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

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.¹

"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.² 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.

Todd Michael, a plant genomicist at the Salk Institute, uses modern sequencing technology and computational tools to explore how genomics differences help plants adapt to their environment.

Kelly Colt

The real challenge lay ahead—deciphering more complex plant genomes.³ 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.⁴ 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 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.

When researchers first sequenced the A. thaliana genome, they relied on Sanger sequencing, a method that deciphers DNA one fragment at a time. If you’re working with a 160 billion base pair genome, this would take a while. Then, in 2007, next-generation sequencing emerged, which dramatically accelerated the process. Using a short-read sequencing approach, scientists could sequence many short (50 to 3,000 bases) DNA fragments in parallel. This breakthrough was soon followed by long-read sequencing, which as the name implies, allows scientists to simultaneously read longer stretches of DNA, with fragments ranging in size from 1,000 to 20,000 base pairs. In 2018, Michael and his team used this technology to sequence A. thaliana in only one week.⁵

Michael noted that long-read sequencing has been instrumental for deciphering the genomes of particularly tricky plants, such as cannabis, which has just a handful of transposable elements that are nested together.^6,7 “People had dabbled in wheat and large genomes like that—things that are polyploid and also have lots of transposable elements—but some of the more complex genomes just weren't touchable.”

Newer sequencing instruments can now process larger DNA fragments—up to millions of bases—big enough to span entire transposable elements, making it easier to piece together even the most bloated genomes.

“If you look at the number of genomes that have just come out in the last two years, it's phenomenal,” said Michael. “We're starting to see the highest quality genomes come out, and that's really changed how we do things.”

“With genome sequencing there's so much information that we can get—[herbaria specimens] are essentially witnesses of this global experiment that climate change is."
- Patricia Lang, University of California, Berkeley

In the last few years, a number of high-quality reference genomes have emerged, including species of sugarcane, oat, and maize, providing unprecedented insights into plant genetics and opening doors to new discoveries.^8-10

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.¹¹ “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.

In her lab at the University of California, Berkeley, Patricia Lang studies phenotypic and molecular changes in historical herbarium samples to understand plant responses to environmental change.

Patricia Lang

Patricia Lang, a plant biologist at the University of California, Berkeley, has been fascinated by plants since childhood. “I had a little plant press early on as a kid, but just used that for making art, and didn't really think it was something that you could do science with,” she said. While studying molecular mechanisms in present-day plants as a graduate student in Detlef Weigel's lab, Lang had a eureka moment when Hernán Burbano—who had worked on sequencing the Neanderthal genome—joined the lab and began analyzing genomes of historical plant specimens from herbaria. Lang learned that these collections—meticulously preserved plants amassed by generations of botanists—could be a powerful tool for studying plant adaptation to climate change, a topic she was eager to explore.¹²

“These herbaria are incredible treasure troves of information for understanding how plants respond to global change that are really underused,” said Lang. The more than 3,500 herbaria worldwide house nearly 400 million specimens, some dating back to the 17th century.¹³ “They cover almost exactly [the] time frame that we're interested in with anthropogenic climate change of the last 250 years or so,” said Lang.

Historically, research using herbaria has focused on morphological and phenological shifts, such as changes in plant size or flowering time.¹⁴ But little was known about the genetic changes that accompanied these responses. Now, thanks to advances in high-throughput sequencing and ancient DNA analysis, scientists can extract vast amounts of genetic information from these historical gems.¹⁵

“With genome sequencing there's so much information that we can get—[herbaria specimens] are essentially witnesses of this global experiment that climate change is,” said Lang.

Photo of two herbarium specimens with colored labels pointing to leaves. To the left of the specimens are tools for dissection and sampling, including scissors, tweezers, and dishes. — On a recent visit to the California Academy of Sciences, Lang sampled tissue and generated leaf imprints of A. thaliana specimens from Spain, which were on loan from the herbarium at the University of Málaga.
Patricia Lang

In addition to being the first plant through the sequencing gates and one of the most well-studied plants in terms of functional characterization of its genes, researchers have preserved A. thaliana samples from around the world for centuries, making it an excellent model for tracking genetic changes over time. In a recent paper, Lang focused her attention on stomata—tiny surface pores on leaves that regulate gas exchange and influence water-use efficiency.¹⁶ As atmospheric CO₂ concentrations rise, the density of stomata decreases. However, whether this response is driven by genetic adaptations is unclear.

Using previously published whole-genome sequencing data from both historical and modern samples, Lang and her team analyzed 42 key genes involved in stomatal development, comparing genetic variations between past and present A. thaliana specimens. Although this genomic data suggests that there has been a decline in stomatal density over the past two centuries, without direct access to the preserved plant samples for microscopic validation, they could not confirm this prediction. To address this, the team has now generated leaf surface imprints and whole-genome sequences of an additional set of herbarium samples, with which they aim to verify their findings.

Beyond tracing past adaptations, historical herbarium specimens also offer a roadmap for the future. They can help identify candidate genetic variants for further study in the lab. Using genetic and synthetic biology tools, scientists can manipulate these variants to determine whether specific genetic modifications could produce beneficial traits under conditions such as increased temperatures or elevated CO₂ levels.

Getting to the Root of the Problem

Intensive farming activities in the US play a major role in climate change, as large-scale monocropping, heavy fertilizer use, and deforestation release massive amounts of CO₂ while depleting the soil’s ability to store carbon. In 2021, agriculture accounted for 10.6 percent of the country’s greenhouse gas emissions. This creates a conflict between the need to produce more food to feed the world’s growing population and the goal of reducing emissions.

Despite its environmental impact, agriculture presents a rare opportunity to bring these goals into alignment—not only can scientists develop crops that are more resilient to climate change and capable of higher yields, but plants themselves could play a critical role in mitigating the crisis. With an already massive agricultural infrastructure in place, optimizing plant biology could pave the way for a carbon net-negative system, where farming not only feeds the world but also helps pull carbon from the atmosphere.

This vision is at the heart of the Salk Institute’s Harnessing Plants Initiative (HPI). Through their project CO₂ Removal on a Planetary Scale (CRoPS), researchers, including Michael, are exploring ways to enhance plants’ natural ability to sequester carbon. Plants already excel at capturing carbon, converting it into essential materials like sugars, polymers, and cellulose. However, much of this carbon eventually returns to the atmosphere. But plants have another powerful carbon storage up their sleeve (or down their roots)—the biopolymer suberin. This water- and gas-insoluble compound forms a protective barrier in roots, helping plants retain moisture, block pathogens, and, crucially, store carbon for extended periods.

At the HPI, researchers aim to engineer crops with larger, deeper-growing roots enriched with suberin, effectively pulling carbon deeper into the soil where it can be stored long-term. In one study examining natural variation in Arabidopsis root systems, HPI researchers identified a gene that regulates root architecture, causing roots to grow deeper into the soil.¹⁷ In a recent paper, they generated a comprehensive gene expression atlas of the Arabidopsis root, which allowed them to identify cells that may be important for specific types of growth, such as radial thickening, and genes that are essential for suberin synthesis.¹⁸ While the research is still in its early stages, researchers hope to uncover more genes that promote deep root growth and increased suberin production and eventually transfer these traits into staple crops such as rice, sorghum, and soybeans—potentially transforming agriculture into a powerful tool for both food security and climate change mitigation.

Building Plants from the Bottom Up

While tweaking genetic systems holds promise for improving crop yields and increasing carbon uptake, these modifications are ultimately small adjustments to an intricate and highly complex system. However, some scientists have their eyes set on an even more ambitious goal—designing plants from the ground up.

Photo of a quarter surrounded by different genera of duckweed on a black background. — Over the last few years, Michael has been developing duckweed, a tiny, minimalist aquatic plant, as a model system and chassis for synthetic biology experiments.
Kelly Colt

To this end, Michael has spent the last several years developing duckweed as a model system for plant biology with the hope that this minimalist plant can serve as the perfect chassis for synthetic biology experiments.^19,20 If you’ve ever walked past a pond, you’ve likely seen this tiny aquatic plant floating on the water’s surface. “And ducks love them—that’s why they’re called duckweed,” Michael explained. But ducks aren’t the only ones with a taste for it. “I think it tastes great, and it's high in protein, and has lots of other benefits—antioxidants and micronutrients and things like that.” He added, “A lot of people are like duckweed, whatever!” But NASA and other international space agencies are paying attention—duckweed’s high nutritional content, rapid growth, and adaptability make it an attractive food source for future space missions.

Recent genome sequencing data from Michael’s team revealed that Spirodela polyrhiza and Wolffia australiana, two duckweed species, have a remarkably streamlined genetic code—containing 25 percent fewer protein-coding genes than A thaliana.^21,22 “We think this is a great system because, basically, it doesn’t have roots, shoots, or leaves,” said Michael. Instead, the floating plant has a small leaf-like body that performs its photosynthetic functions.

A long-term goal of Michael’s research is to develop artificial chromosomes for plants, which could introduce entirely new traits into these simplified plant models. With this approach, scientists could introduce suites of genes encoding complex beneficial characteristics, such as disease resistance, higher yield, and improved carbon capture—creating entirely new plant varieties.

Ultimately, Michael’s research seeks to harness insights from these reference genomes to design synthetic plants with traits tailored to address food security and climate change. As scientists sequence more genomes and study adaptation in both historical and modern specimens, they hope to move from tinkering with genes in the lab to creating organisms with a global impact. By engineering plants from the ground up, scientists hope to unlock new possibilities in agriculture—transforming plants into climate solutions rather than climate casualties.²³