Securing the world's food supply in a changing climate may be one of the biggest challenges we face in this century. In six of the past eight years, the human race consumed more corn, wheat, and rice than it grew.

Every day, 18,000 children under age five die of hunger and malnutrition. Almost all of them live in developing countries, the very countries most vulnerable to climate change.

Understanding the molecular underpinnings of how plants adapt to challenging environments and defend themselves against insects and fungal infections will be crucial to ensuring the world’s food supply into the future, making basic plant research more important than ever.

Founded 25 years ago, the Salk’s Plant Biology Laboratory is home to some of the world’s leading plant biologists. Their groundbreaking research profoundly impacts many areas of science, from agriculture to stem cell research, from tumor biology to drug development.

"Our lab is interested in identifying the mechanisms that plants use to respond to changes in their environment, particularly light. Our hope is that by discovering the molecular triggers that determine whether a plant matures into a spindly or robust specimen, we can contribute to efforts to increase crop yield and alleviate hunger."

Plants by nature may be rooted to one spot, but they are remarkably adept at making the most of their digs. Activating a complex series of molecular switches that regulate their growth patterns, they literally seek their place in the sun by reacting to changes in their surroundings in ways that maximize their chances for survival.

Chory and her team have recently identified two pathways that govern different aspects of plant growth. For light-loving plants, competing with larger flora for a share of the sun can lead to so-called shade avoidance syndrome—a set of responses in which they expend their growth resources toward stem elongation rather than bulking up harvestable portions such as leaves and seeds. Using the reference plant Arabidopsis thaliana, Chory's group identified a series of genes that plays roles in the shade response and identified one that encoded a new enzyme. She and her colleagues determined that the enzyme uses the amino acid tryptophan to synthesize auxin, a hormone that regulates plant growth. This pathway is rapidly deployed to synthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance. Despite auxin's importance for plant growth and development, the details of how it is synthesized have puzzled plant biologists. Multiple biochemical pathways for the production of auxin have been proposed, but the specific function of each pathway and how they all intersect is not known. Now the role of at least one pathway has become clearer.

Starlight, not daylight, lies at the heart of another recent discovery by Chory and her colleagues. At least since Charles Darwin, scientists have known that many plants grow in regular nightly spurts, with plant stems elongating fastest in the hours just before dawn. Chory's lab has identified the genes controlling those bursts of rhythmic growth. They found that expression of a large number of genes scattered around the Arabidopsis genome dealing with hormone biosynthesis, hormone signaling, and hormone metabolism are all tightly correlated with rhythmic plant growth.

These discoveries could eventually allow scientists to design crops that can grow substantially faster and produce more food than the most productive varieties today.

"Nature vs. nurture, genes vs. environment—what is more important? My group is interested in understanding the roles of genetic and 'epigenetic' processes in cell growth and development. By understanding how the genome and epigenome talk to one another, we hope to be able to untangle the complexity of gene regulatory processes that underlie development and disease in plants and humans."

Our view of heredity has largely been written in the language of DNA, but recent discoveries in a field known as epigenetics—the study of heritable changes in gene function that occur without changing the letters of the DNA alphabet—show that how a cell "reads" those letters is critical. Adding molecules such as methyl groups to the backbone of DNA can change how genes interact with the cell's transcribing machinery and hand cells an additional tool to fine-tune gene expression. The genomes of higher eukaryotes are peppered with modifications, but until scientists were able to take a detailed look at the whole genome, there was no way of knowing whether a particular chemical tag was critical or not.

Ecker and his team pioneered new technologies that allowed them to capture the genomewide DNA methylation pattern of the plant Arabidopsis thaliana and chart its effect on the activity of any of Arabidopsis's roughly 30,000 genes. Cells employ a whole army of enzymes that add methyl groups at specific sites, maintain established patterns, or remove undesirable methyl groups. When Ecker and his colleagues compared normal cells with cells lacking different combinations of these enzymes, they discovered that cells put a lot of effort into keeping certain areas of the genome methylation-free. On the flipside, they found that when they inactivated a whole class of methylases, a different type of methylase would step into the breach for the missing ones. This finding is relevant for a new class of cancer drugs that work by changing the methylation pattern in tumor cells.

Being able to study the epigenome in great detail and in its entirety will provide researchers with a better understanding of plant productivity and stress resistance, the dynamics of the human genome, stem cells' capacity to self-renew, and how epigenetic factors contribute to the development of tumors and disease. Ecker and his team are already looking into how methylation affects the development of human stem cells as they differentiate into other types of cells.

"A plant's shoot system is responsible for all of the above-ground portions of the plant, such as leaves, branches, and flowers, and is the site of photosynthesis. The root system lies below the ground and provides water and nutrients to the plant. My lab's research is focused on how a plant embryo sets up this apical/basal polarity."

Controlled by a tightly regulated choreography that determines what should go up and what should go down, plants develop along a polar axis with a root on one end and a shoot on the other. But scientists and home gardeners alike have been messing with plants' basic architecture for years. Permanently switch on a gene called BODENLOS (or "bottomless"), and they forgo root development altogether. Dip plant cuttings into hormone rooting powder, and roots start to sprout where none have been. The active ingredient, a synthetic version of the plant hormone auxin, which regulates root growth, overrides the molecular switch that keeps auxin-responsive genes turned off in parts of the plant that are above ground.

Long discovered that the switch is none other than a protein called TOPLESS. It had become clear that TOPLESS functions as a so-called co-repressor, which regulates gene expression by inhibiting the activity of transcription factors. Transcription factors control gene activity by binding to DNA sequences adjacent to a gene. But exactly how TOPLESS silences genes necessary for root development has remained unclear.

Hoping to gain insight into how TOPLESS functions by looking at the company it keeps, Long and his team searched for interacting partners in the plant Arabidopsis thaliana. This wee weed was the first flowering plant to have its genome unlocked and is loved by plant biologists for its short generation time. They discovered that BODENLOS, a transcriptional repressor that silences auxin-responsive genes, recruits the co-repressor TOPLESS to help with the job. While auxins are found throughout the whole plant, BODENLOS is only active in the shoot, ensuring that no accidental roots sprout above ground unless a gardener, "Dip'N Grow®" in hand, tips the balance.

Understanding how seedlings ensure that they are neither all shoot nor all root is fundamental to engineering plants that develop in ways that better suit agricultural needs.