Bringing Genomics to Bear on
World Crop Problems

The complete sequencing of the human genome caught the imagination of the scientific community as well as the public at large. The implications are enormous: a world in which many of our most dreaded diseases can be detected and perhaps ameliorated in life’s earliest stages; greater knowledge of how our genes interact with one another and the environment to shape our beings; and a fresh appreciation for how closely we are related to other organisms that inhabit the earth. Recent developments in plant genomics are equally revolutionary.

Functional plant genomics will provide a complete picture of the roles and functions of plant genes of interest and how they interact with one another and the environment to produce an individual plant type. Comparative genomics will make it possible to apply knowledge about the genome of one species to another species. These areas of study hold the key to creating crops with built-in resistance to major diseases and insect pests, as well as tolerance for the scourges of drought, high soil acidity, and low nitrogen. In this fast-changing research arena, CIMMYT’s Applied Biotechnology Center (ABC) has been quick to lay the groundwork for applying genomic approaches to improve farm productivity in developing countries.

Most recently, in April 2001, the ABC hosted a strategic planning workshop on the Cereal Genomics Initiative, a major collaboration proposed by CGIAR centers and US Land Grant universities aimed at harnessing crop genomics for the betterment of developing world agriculture. Underwritten by the Rockefeller Foundation, the workshop brought together about 50 experts in cereal genomics and researchers with first-hand experience in developing world agriculture.

“CIMMYT was selected to host the planning workshop because it is a recognized center of excellence for cereal improvement for developing countries,” says Robert Zeigler, one of the workshop organizers and director of the Plant Biotechnology Center at Kansas State University (in addition to his role as head of the Department of Plant Pathology). “To embark on a bold venture like this requires credibility, and there is no one with greater credibility than CIMMYT, with its years of adapting biotechnology to cereal improvement and long track record of partnering with advanced research institutions.”

From Common Origins, Uncommon Opportunities

Cereals, Zeigler explains, offer a unique opportunity among plants to produce rapid benefits from molecular research, because they all belong to the family of grasses and share a common origin. An understanding of how genes for a desirable trait, such as drought tolerance, work in one species can help breeders improve their function in other species. Similarity among cereal species also implies that when genes are moved from one cereal species into another, they will tend to work well and in the same way, with minimal genetic engineering. For instance, knowledge about the genetics of rice (which is almost completely sequenced) can be applied to maize and wheat, thereby accelerating research and genetic engineering.

Four principal areas of work and associated technologies were identified by workshop participants: alleviating abiotic stresses,  alleviating biotic stresses, adding value to cereals, and improving yield potential, specifically by modifying photosynthesis. The group also identified approaches to reach these goals, including a comprehensive genomics-based evaluation and characterization of the genetic resources available for improving cereals; coordinated development of molecular tools based on these resources; mechanisms to assure free and cost-effective access to tools; freely available data storage, manipulation, and analysis tools; and databases specifically designed for this program.

The scientists’ diverse backgrounds contributed to a productive research planning environment, says ABC director David Hoisington. A ten-year initiative was proposed to capture the technological strengths of the US scientific community, where nearly US$80 million have been invested in this area over the past decade, and wed them to the genetic resources, knowledge, and international scope of the CGIAR centers to solve high-priority problems affecting basic food crops.

The first five years of the proposed research would lay the  foundation for large-scale manipulation of the cereal genome. Scientists would generate a knowledge base to better understand the cereal genome and create tools to make the most of existing diversity. Relatively straightforward traits would be manipulated, and novel resistance to formerly invulnerable diseases and pests and tolerance to salinity would be moved into species requiring these traits. Towards the end of this first phase, commercial cultivars would be nearly ready for release. In the second phase, research partners would apply knowledge gained in the first phase to particularly complex traits such as tolerance to drought and extreme temperatures, cereal chemistry and nutritional quality, and photosynthesis.  Both phases of the research would include major training programs, as scientists from national agricultural research systems participate as students and postdoctoral fellows at CGIAR centers and US universities.

Hoisington, Zeigler, and workshop co-organizer Jeff Bennetzen, the H. Edwin Umbarger Professor of Genetics, Department of Biological Sciences at Purdue University, met with US officials and legislators in July to pursue funding for the initiative, which has received strong support from the National Corn Growers Association (NCGA), the American Farm Bureau Association, and the American Society of Plant Physiologists.  Although it might seem unusual that these groups would support research aimed primarily at developing world farmers, NCGA representative Gary Davis, speaking on behalf of the initiative to a US House of Representatives subcommittee, declared, “When scientists solve these problems in poor countries, they not only help people feed themselves and move up from poverty, they help ensure safe harvests across our own country.”

Zeigler meanwhile believes that the initiative will be picked up in some form by an interested party. “I am an incurable optimist,” he says, “especially when it comes to such an obviously good idea. Who can argue with applying the most powerful tools in plant biology to some of the most intractable problems facing humanity today?”

While Hoisington would welcome the opportunity to move ahead with the Cereal Crop Genome Initiative, he is pleased with progress CIMMYT has made on other genomics activities and partnerships. Much of this work focuses on the development of drought tolerance for maize and other cereals. The Rockefeller Foundation has funded an initial two-year project aimed at better understanding the response of maize to drought and the development of molecular approaches that complement conventional breeding for drought tolerance in cereals. The ABC also works with the International Rice Research Institute (IRRI) to discover key drought tolerance genes and mechanisms. CIMMYT has made progress on optimizing RNA extraction protocols and quantifying gene expression in segregating germplasm—two technical building blocks for functional genomics.

Most recently, CIMMYT and Pioneer Hi-Bred initiated a two-year collaboration aimed at utilizing functional genomics, specifically genomics tools called microarrays, to identify genes and pathways associated with drought tolerance, and to learn more about their interactions. This is a straightforward exchange, says CIMMYT molecular geneticist Jean-Marcel Ribaut. “They provide what they’ve learned about genes involved in stress tolerance, as well as the microarray technology, and we provide well-characterized germplasm and considerable field and lab work. Both sides benefit, and we are free to use and distribute the information we obtain to our clients. Productive arrangements like this one clearly show that we can work with the private sector without compromising our freedom to operate. It’s exciting.”

Finally, an agreement has been established with the project team developing the International Maize Database (MaizeDB) at the University of Missouri, for CIMMYT to serve as its first mirror site, with the intention of exploring avenues for making the information available to developing country partners.

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For more information: David Hoisington (d.hoisington@cgiar.org)

Published on October 2001

August, 2004

Annual Report 00-2001