Scientific Initiatives / Plant Biology

Plant Biology Plant science is needed more today than ever before to help meet the demands of a rapidly growing human population and the disruptions of climate change. The global population recently topped seven billion and is expected to reach ten billion by 2050. More people means greater demand for food, feed, fiber and fuel, placing tremendous strains on ecosystems around the world. This growing demand, combined with extreme drought and temperature fluctuations, has resulted in widespread environmental damage, economic hardship and malnutrition. It is estimated, for instance, that one in seven people currently do not have enough to eat, and complications from malnutrition are the greatest killer of children under five.

United Nations experts predict that agricultural yield must be doubled in the next two decades to meet the demands for natural resources. At the same time, we must safeguard the environment by using less water, fertilizers and pesticides. In short, farmers must do more with less. Meeting this challenge will require developing new crop varieties and bringing precision agricultural practices to the developing world. First, however, plant researchers must unravel the molecular mechanisms of plant growth, reproduction and development. This crucial science will be the mission of a cutting-edge plant research initiative that will usher in a new era of plant biology, one focused on making agriculture more efficient, productive and sustainable: the Salk Institute Plant Science Initiative.

Using powerful new research technologies and scientific approaches, Salk’s world-renowned plant scientists have already led the way in establishing the mustard weed, Arabidopsis thaliana, as the primary model organism for understanding the basic principles of how plants grow and adapt to changing environments. Now, with so much at stake, Salk’s scientists hope to use data from Arabidopsis studies to develop predictive models of how genes and other genetic control mechanisms will influence yield and growth during climate change. They have a bold plan to expand on their seminal work on Arabidopsis to decipher these same biological systems in crop plants. Through the Plant Science Initiative, they will develop two agricultural plant models, a historic scientific advance that will allow plant biology research to have a far more direct and effective impact on agriculture, environmental sustainability and human health. Developing these crop models will allow Salk’s plant biologists to extend their knowledge about Arabidopsis to crop plants, leveraging decades of plant science discoveries to better understand agriculturally important species. The initiative will also identify holes in our understanding of crop biology, pointing the way to completely new and agriculturally important areas of plant science.

To make this vision a reality, it is clear that Salk scientists need additional resources. Launching the initiative will require hiring the best faculty and postdoctoral researchers, supporting innovative projects and building new research greenhouses and climate-controlled grow rooms. With plant biology historically underfunded compared to other areas of biology, and given reductions in government science funding, private philanthropy will be crucial to launching this vital research initiative. The outcome will be well worth the investment. The Plant Science Initiative will ultimately make agriculture more economically efficient and environmentally friendly. It will allow us to develop plants better at producing nutritious food, biofuels, renewable commodities and pharmaceuticals. And it will allow us to preserve fragile ecosystems and their incredible biodiversity. The result will be a sustainable future for farms, natural ecosystems and humanity.

Plant Science Initiative

The doubling of world food production over the past half century has now slowed and has come at a cost. Much of the best agricultural land is already in use, and a significant fraction is being lost due to overtillage, overuse of fertilizers, salinization, erosion, urbanization and industrial contamination. The genetic diversity of plants in production has narrowed, and biodiversity in natural systems is under threat. At the same time, the demand for plant-derived products is soaring. In coming decades, food and feed production will need to double again while we restore and maintain the quality of the planet's natural resources for future generations. Meeting these goals will require accelerating over the next decade discoveries in plant science that foster groundbreaking agricultural innovations.

In addition to addressing pressing agricultural and environmental issues, plants offer powerful methods for understanding and even manipulating human physiology through diet, a key step in developing new therapies for a range of medical conditions or preventing the onset of others. With the population rapidly aging, the incidence of chronic diseases, such as cancer, heart disease, stroke, Alzheimer's and Parkinson's diseases, is on the rise. At the same time, the incidence of obesity and diabetes are reaching epidemic proportions. The challenge that lies ahead is to understand, treat and ultimately prevent these conditions—an endeavor to which plant science is critical. Plants can be studied in ways that are impossible in other organisms and they provide nutrients that are now recognized as disease-preventing agents.

While the potential for discovery by Salk plant biologists is enormous, reduced public funding for research has become a serious threat to its fulfillment. Historically, the federal government has funded basic biological research, but in recent years government investment in research has declined significantly, and this trend is expected to continue for the foreseeable future, with profound effects on the pace of scientific innovation. Plant biology research, in particular, needs additional support from private philanthropy. While plant research is well funded in China, India, Germany and other countries, this is not the case in the United States. In this country, fundamental and applied research on plants receives less than two percent of the total $40 billion-plus annual federal life sciences funding—the bulk of which funds biomedical studies on human diseases.

The plant biology program at the Salk Institute is world-renowned; yet Salk scientists are hindered by an outdated plant growth facility. A major overhaul of the plant growth facilities will allow scientists to simulate real world climates (precision-controlled temperature, humidity and light), to better understand plant interactions in a changing and variable environment and to improve crop productivity and environmental sustainability. In addition, to take full advantage of cutting-edge technologies and research methods and to further integrate plant biology at the Institute, Salk's plant science program needs to recruit new faculty and postdoctoral researchers with experience in epigenetics, genomics, metabolism, integrative biology and bioinformatics.

Transforming the future of plant research at the Salk Institute relies on a few key elements:

CLIMATE SIMULATION ROOMS AND RESEARCH GREENHOUSES
The addition of precision climate simulation rooms and research greenhouses to Salk's plant science facilities will allow plant biologists to simulate real world climates by providing them with the ability to precisely control temperature, humidity and light experienced by plants during experiments. New research greenhouses are necessary to grow larger crop species for study, as Salk's current greenhouses are outdated and inadequate for this research. This will allow Salk scientists to better understand how plants respond to changing and variable environments, and how cellular pathways, genes and epigenetic variation allow plants to adapt to different climates. The level of precision allowed by the grow rooms will reveal biological mechanisms important to crop productivity and environmental sustainability.

INTEGRATIVE PLANT SCIENCE FACULTY POSITION
The plant biology program at the Salk Institute offers an unprecedented opportunity to combine research at various levels of inquiry, from the level of individual enzymes to the level of ecosystem-scale studies. To further integrate Salk’s plant science laboratories, the Institute will recruit a top researcher in the field of integrative biology. This person will bring expertise in using computational and statistical methods to combine data from different laboratories into powerful and comprehensive mathematical models of biological systems.

PLANT METABOLOMICS BIOLOGY FACULTY POSITION
In order to inventory the molecules that make up plant cells, the initiative will need additional faculty expertise in plant metabolite science. The initiative will recruit a leading researcher in metabolomics, who will focus on discovering new enzymes and metabolites, deciphering their structural properties and explaining their functions in the complex web of genetic and epigenetic mechanisms of plant cells. This scientist’s work will complement the initiative’s new integrative plant biology faculty position by providing detailed data on the molecules and biochemical interactions of plants’ metabolic systems.

INTEGRATIVE PLANT SCIENCE POSTDOCTORAL FELLOWSHIP
Unlike traditional postdoctoral training programs, which limit trainees to one laboratory, the plant biology program's unique integrative postdoctoral program will place talented young researchers in training positions spanning several laboratories. By integrating laboratories studying different aspects of plant biology—from the structure of enzymes to the structure of whole genomes— the initiative will generate new insights and a sophisticated understanding of the interlocking systems that allow plants to adapt to stressful environments. This program will train the next generation of plant scientists to conduct the interdisciplinary research needed for the complex science emerging at the cutting edge of plant science. Establishing an endowed fellowship program will enable the program to develop a highly selective first set of trainees and will ensure the success of the program far into the future.

At the core of the Salk Institute’s strategy for answering critical life science questions through plant research is integrative biology—the examination of the complex biological systems using mathematical modeling, powerful computational tools and interdisciplinary approaches to plant science. Taking this approach, for example, researchers studying plant metabolism, epigenetics and growth pathways might combine their experiments using rapid DNA sequencing, cutting-edge microscopy technologies and high-speed computers to integrate and sift through data, uncovering key molecular, genetic and epigenetic mechanisms. The Plant Science Initiative will allow our scientists to combine the powerful concept of integrative biology with Salk’s traditional strengths—recruiting the best scientists, fostering a collaborative culture, and maintaining an institutional structure free of conventional academic hierarchies.

The initiative will open the doors to discovery by focusing on four promising areas of research:

DEVLELOPING AGRICULTURAL CROP MODELS
Salk plant biologists played a prominent role in establishing a mustard weed known as Arabidopsis thaliana as the primary model organism for plant biology research—including spearheading the mapping of its genome. Arabidopsis will remain the foundational reference plant species for practical reasons of efficiency in the introduction and validation of new approaches; because of the availability of focused technologies and tools; and for conceptual reasons arising from the depth and concentration of biological understanding.

However, Salk plant scientists will move beyond this pioneering model species in order to translate current understanding to economically important plant species by developing two agricultural plant models. Most food crops, including wheat, corn and rice, are grasses, a group that evolved to survive in circumstances quite different from Arabidopsis, and which have more complex genomes and biological pathways. Many other crops come from the Solanaceae family, also known as “nightshades,” which includes tomatoes, potatoes and peppers. Developing a grass and a nightshade as model organisms will allow scientists around the world to study traits that are particular to major crop plants and otherwise inaccessible through Arabidopsis research. It will also allow for comparative studies between the new model and Arabidopsis, a technique that can provide important information about how species differ genetically. To develop this new model, Salk researchers would sequence the plants’ entire genomes and develop a suite of research tools and techniques for laboratory and field studies. Their plan to develop crop models relies on powerful new technologies, specialized plant growth facilities and scientific approaches that will allow scientists to explore deeper than ever into the molecular world of plants’ cells.

PLANT GROWTH AND STRESS RESPONSE
As primary producers, plants are the ultimate source of food, fiber and fuel for all forms of terrestrial life, including humans. In the face of rapidly changing climates and the growing human population, societies need plants to produce more, often in environments that are not conducive to the growth of current crop varieties. To develop new agricultural crops and help ecosystems adapt, scientists need to understand how a plant’s genome—the totality of its genetic material—changes over time and how this plasticity produces the diversity that allows plants to grow and thrive in stressful environments around the world. The Plant Science Initiative will decipher the mechanisms that plants use to integrate the internal, developmental and environmental signals that control their responses in the ecosystem. For instance, they will build on their foundational work identifying the mechanisms by which plants respond to changes in their light environment, which is crucial for understanding how they compete for light in agricultural fields and natural ecosystems. They will also focus on decoding the role of the plant epigenome— an extra layer of biochemical instructions in DNA—in how plants adapt and pass on acquired traits. Salk plant scientists are world leaders in epigenetics research, and their findings also help explain the role of the human epigenome in disease.

PLANT METABOLISM AND DRUG DISCOVERY
Deciphering the biochemical mechanisms of plant metabolism— the chemical reactions that drive growth, reproduction, digestion and so on—is fundamental to the development of better crops and therapies for disease. This includes the breeding of plants better adapted to challenging environments and the discovery of new medicines. Salk scientists will investigate the evolutionary mechanisms exploited by plants to generate a chemical toolbox that allows them to respond to changes in their local environment. These chemicals protect plants against microbial diseases and herbivores; facilitate beneficial interspecies interactions above and below the ground that are key to nutrient assimilation, pollination and sustainable agricultural practices; and serve as information processing molecules to switch on and off germination, growth and development as environments change.

Salk scientists will inventory the molecules that make up plant cells, from enzymes to metabolites, and chart their distribution in time and space within cells and whole plants. In addition to identifying these molecules, Salk scientists will determine how they interact to form a robust molecular network of metabolic pathways. This will require untangling the complex web of genetic and epigenetic regulation, understanding the stability and distribution of proteins, and discerning how the dynamics of these networks vary from species to species and from one climate to another.

Discovering enzymes and metabolites and explaining their functions will produce new targets for enhancing crop growth and production and for developing crops that are more nutritious. For instance, characterizing the enzymes involved in the production of seed oils may allow for the development of improved crops that yield higher qualities and quantities of oils—products important for both biofuels and human nutrition. This research also will help explain how metabolism is coordinated in all organisms, since many of the biochemical pathways and enzymes found in plants are also found in other organisms, including humans. Identifying the players in these pathways, such as enzymes, hormones and other signaling molecules, will provide new targets for the development of drugs against a range of human diseases.

SYSTEMS AND COMPUTATIONAL BIOLOGY
Plants and other organisms, including humans, can be thought of as a complex collection of nested biological machines. Interconnected molecular pathways within cells process nutrients, expel wastes and orchestrate the myriad of functions necessary to maintain a life-sustaining chemical balance. In turn, cells and organs communicate among themselves to allow for growth, reproduction, disease resistance and so on. In the past, scientists focused on identifying the individual players in this biochemical and physiological symphony. With new technologies at their disposal, they now are working to explain how these elements work together as a dynamic system. Next-generation sequencing machines, which track biochemical fluctuations in cells in real time, and powerful computers and statistical modeling approaches, which allow this information to be integrated and analyzed, are driving this new area of research.

The Plant Science Initiative will allow Salk plant biologists to integrate studies on particular molecules and cellular pathways with analysis of genetic and epigenetic variation among plants from different environments. It will allow them to produce and refine mathematical models that simulate the complexity of plants’ biological systems. This research promises to help explain how different environments select for different kinds of molecular “machines” in plants, generating a diversity that has allowed them to spread across the planet. This will, in turn, explain precisely how these biochemical pathways fit together, what configurations of molecular machines work best for certain environments and how we might use this information to help plants – both agricultural and wild—cope with changing climates.

The excellence of Salk’s plant biology research is unparalleled. Thomson Reuters’s ScienceWatch ranked Salk first internationally in plant biology programs and Salk plant scientists have made a number of seminal discoveries:

Joanne Chory discovered how plants grow to escape shade, a finding that could lead to higher yielding crops for food, biofuels and biorenewable chemicals and make farmland use more efficient. Chory’s lab showed that plants utilize steroid hormones to control cell growth, organism size and homeostasis and that plants utilize a different mechanism than animals to respond to steroids.

Joseph R. Ecker led a multinational project that sequenced the genome of Arabidopsis thaliana, a modest weed that has become the primary model organism for the study of plant genetics. He and his collaborators revolutionized plant biology and greatly enhanced research on plant growth regulators and signaling.

Julie A. Law employs genetic, biochemical and genomics approaches to expand current knowledge of epigenetic gene regulation in plants and increase scientists' ability to understand and control the expression of existing and newly introduced genes—research that has broad implications in both agriculture and gene therapy.

Joseph P. Noel discovered the engineering rules governing families of plant enzymes that produce substances important for animal and human nutrition, biorenewable chemicals and biofuels. His work deciphering the 3-D structures of plant enzymes has clarified their precise biological functions and led to plants with higher nutritional value or capable of providing valuable biorenewable products.

Salk plant biologists have been honored by appointments as Howard Hughes Medical Institute investigators and elections to the U.S. National Academy of Sciences, American Academy of Arts and Sciences, the Royal Society, the German National Academy of Science and the French Academy of Sciences. Scientific American magazine has named Chory and Ecker as Research Leaders in Agriculture.