-
Above: The output of a high-throughput gene sequencer at CIMMYT's new facility. Eight hundred base pairs of 27 genes (lanes indicated by the blue diamonds at top) are depicted. DNA sequences are indicated by color, with red indicating "T"; blue, "C"; yellow, "G"; and green, "A." Sophisticated bioinformatics tools are used to derive useful information from such data.
Designer crop plants that carry specifically selected genes with traits that allow them to thrive in particular environments or produce valued consumer characteristics are now only a few years in the future.
Functional genomics is a major force behind this imminent revolution. Simply defined, functional genomics is a scientific approach that seeks to identify and define the function of genes, and uncover when and how genes work together to produce traits. Current structural genomic approaches (i.e., mapping) generally focus on traits controlled by one or only a few genes, and often they only provide information regarding the location of a gene or genes.
Although obtaining location information is a critical first step, functional genomics goes further to examine the interrelationships and interactions between thousands of genes to determine when and why certain traits are expressed, which sets of genes are specifically responsible for that expression, and under what conditions. This information equips scientists to create varieties with exact combinations of traits. If they can develop varieties that yield as well as possible under any given set of conditions, we will come much closer to meeting the global demand for food.
Global Advances
Recent developments, within and outside of CIMMYT, are bringing functional genomics to the fore. In the global arena, the public release of the gene sequences of wild mustard (Arabidopsis thaliana) and rice has made a wealth of information available to scientists. Because the genes that code for scores of plant traits and processes are quite similar across many species, this knowledge can be applied to genetic research on wheat, maize, and other crops. Furthermore, rapid improvements in innovations, such as microarray technology, enable scientists to generate information on thousands of genes and expressed sequences (so-called "expressed sequence tags" or ESTs) in their search for a trait, as opposed to looking at just a few specific "candidate genes."
Analyzing the mountains of data generated by such technologies falls into the realm of bioinformatics. It requires powerful computational capabilities and highly sophisticated software, networking, and database packages and the human resources to run them. Such resources, while expensive, are now available.
CIMMYT Advances, Applications, and Challenges
Developments within CIMMYT mirror those in the outside world. During the past year, a unit devoted to bioinformatics was created and incorporated into the Applied Biotechnology Center. On another front, the International Crop Information System (ICIS, developed through the work of national research programs, seven CGIAR centers, and other advanced agricultural research institutes) was released on CD-ROM in early 2000. This product is the foundation for more comprehensive crop data systems.
A gene sequencing facility was established at CIMMYT as well. This facility enabled CIMMYT to contribute more than 1,000 ESTs to the International Triticeae EST Consortium (ITEC, a group of 20 private and public labs, including CIMMYT), which publicly released at least 20,000 wheat gene sequences in July 2000. Whereas a few years ago public institutes had only a handful of sequences to work with, they will now have an abundance. These sequences are the raw material for predicting the possible function of a gene, which can then be substantiated in DNA microarrays. These arrays, in turn, can provide data on when and under what conditions ESTs (or genes) express themselves. Mutagenesis and genetic engineering technology also employ ESTs to further define the function of a particular gene.
The task of tackling a genome is too large for any single institution. Through partnerships and other arrangements with public and private research groups, CIMMYT has gained access to data, expertise, and technologies that enhance its ability to pursue functional genomics.
In 1999, CIMMYT and the International Rice Research Institute (IRRI) launched the "Maize-Rice Functional Genomics Project," with some initial financial support from the CGIAR's Technical Advisory Committee. The project seeks to discover the key genes responsible for drought tolerance and to produce molecular tools that will enhance breeding for the requisite trait(s). Another significant step in this direction was the Strategic Planning Workshop on Molecular Approaches for the Genetic Improvement of Cereals in Water Limited Environments.
Whether the ultimate goal is improved drought tolerance, enhanced nutritional composition, or higher yield potential, functional genomics will play an increasingly importantly role in helping scientists achieve their aims. CIMMYT is committed to harnessing this powerful new approach to provide resource-poor farmers the means to produce not just more food, but better food.
For more information:
David Hoisington (d.hoisington@cgiar.org)
Jean-Marcel Ribaut (j.ribaut@cgiar.org)
Published on October 2000.
August, 2004