R I C E
A National Rice Genomics Initiative
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R I C E |
Currently, the U.S. produces about 7.5 million metric tons of rice per year resulting in $1.7 billion in annual income. Over two-thirds of the rice produced in the U.S. is sold to overseas markets primarily in Asia and Latin America, thus making the U.S. the third largest exporter of rice worldwide. Furthermore, the high quality of U.S. rice means that producers are able to command three to five times more per bushel than crops such as wheat or corn. With the ever-increasing world population particularly in countries where rice is the staple food, the potential market for U.S. grown rice is enormous. In order to realize these emerging opportunities, the U.S. rice industry must continue to support the development of rice varieties that serve as the foundation for its success. As advances in biotechnology are changing the process by which new varieties are and can be created, the way the rice community interacts to take fullest advantage of these developments needs to be examined.
Unlike corn or cotton, 99% of rice varieties grown in the U.S. today are due to the efforts of public breeding programs. As a result, growers and other members of the rice industry have benefited tremendously from the free-flow of germplasm resources and information that is the cornerstone of public sector breeding. Currently, most variety development occurs in the 5 major rice-growing states (Arkansas, Louisiana, Mississippi, Texas and California) and is based largely on traditional crossing and selection strategies. With the recent advent of successful applications of agricultural biotechnology such as the use of genetic engineering to create herbicide and insect resistant crops, the landscape that breeders and producers operate in is rapidly changing. This change brings with it opportunities as well as challenges that must be addressed in order for the U.S. to retain its place as a major player the global agricultural marketplace. The introduction of genetically engineered herbicide resistant rice and recent commercialization of hybrid rice varieties in China and India are just two examples of developments that will impact U.S. and global rice production. It is critical that U.S. rice breeders and growers act now to position themselves to take advantage of the new tools and strategies of biotechnology to remain competitive in today's market.
Plant breeding and variety development involves the manipulation and selection of combinations of agronomic traits that yield a superior cultivar. These traits are governed by genes in a manner that is based on how the products of those genes (i.e. proteins) interact with each other and with their environment. Traditionally, rice breeders have had to compare thousands of genetically distinct plants (i.e. each having its own combination of genes) in multiple environments to select superior plants in a process that requires many years. Given the time-consuming and labor-intensive nature of traditional methods, the use of new approaches that streamline the breeding process and increase its productivity will greatly enhance the variety development that is required to meet the current and future needs of the rice industry.
During the past decade, a new scientific discipline called genomics has taken shape and is changing the manner in which biological research is conducted. Genomics refers to the mapping, sequencing, and subsequent analysis of an organism's genome, i.e. its complete set of genes and chromosomes (DNA). Since the mid-1980s, genomics efforts have resulted in the complete DNA sequence of dozens of microorganisms including H. influenzae, E. coli, and S. cerevisiae (baker's yeast). With this sequence information, researchers have been able to identify all the genes that govern the physical characteristics of these organisms.
Today even more ambitious, publicly supported efforts are under way to characterize the genomes of complex organisms. Most notable among these is the Human Genome Project, although a number of plant genomics efforts have also been initiated. At the forefront of plant genomics is the international effort to sequence the genome of Arabidopsis thaliana, a weedy dicot that has become the model system for plant molecular genetics. While Arabidopsis was chosen because of basic research considerations, the successes that have been achieved by this genome project have lent support to the application of genomics to crop species. In fact, the U.S. is currently considering undertaking a parallel effort to sequence the entire rice genome, however such a project will not move ahead unless there is strong support from the U.S. rice community.
The identification of all the genes of a given organism is an incredible resource that can be tapped to determine which genes are responsible for a character of interest (e.g. disease resistance genes). Having this information would also facilitate the study of more complex traits such as yield (i.e. grain number and weight) that might otherwise be too difficult to address. Identifying and isolating the genes governing agronomic traits opens the door to crop improvement methods involving gene modification and transfer to generate improved varieties. In addition, the basic discoveries that will undoubtedly come from these genomic resources are likely to find their way to applications that enhance the productivity of the U.S. rice industry.
A testament to the utility of the genomics approach can be found in the commitment of U.S. seed and life sciences companies (e.g. Pioneer Hi-Bred, Monsanto, Novartis, Dupont, and Dow Agrosciences) to the development of infrastructure and strategies geared towards exploiting genomics-based resources in various crops including rice.
Over the last 10 years, the rice research community here and abroad has generated an extensive set of tools that form the foundation for rice genomics and plant improvement. These tools include a high-density molecular genetic map of the rice genome consisting of over 3,000 publicly available DNA markers, representing the most comprehensive map of any crop species. These markers are being used in rice breeding projects around the world and have been instrumental in rice improvement through marker-assisted selection. In addition to speeding the introgression of valuable traits controlled by single genes, these markers have facilitated the identification of hundreds of quantitative trait loci (QTLs) which are largely responsible for agronomic traits.
With the mapping of the rice genome, the next phase of the rice genomics effort has begun. An international initiative aimed at sequencing the entire rice genome has been organized and work toward this objective has been initiated in Japan, China, the U.S., and the European Union. The data gained from this research together with the vast amount of classical genetic information, the enormous germplasm resources, and the development of agricultural biotechnology (e.g. genetic transformation of rice) will form the playing field as rice variety improvement moves into the new millennium.
The development of resources from genomics have direct applications to crop improvement. Chief among these applications has been the use of molecular markers in marker-assisted selection. This technology has gained wide acceptance and use in plant breeding of a number of crops including rice where efforts in China, India, Japan, as well as many Southeast Asian and Latin American countries are beginning to pay dividends. Furthermore, with the assistance of international research centers such as IRRI, CIAT, and WARDA, other countries that form the global marketplace for rice will have access to this tool. Notably, while the foundation for most of this effort was initiated in the U.S. over ten years ago, relatively little application of molecular marker technology has found its way to U.S. public sector rice breeding efforts.
As rice genomics moves into the era of sequencing, the genes that control important characteristics will be defined and become the ultimate resource for crop improvement. While the sequence of a gene in and of itself is of limited value, the information that has been collected from hundreds of years of rice breeding and classical genetic studies will be used in conjunction with the sequence data to unlock the full crop improvement potential of genomics. How this can be accomplished to the greatest benefit of the U.S. rice community and the roles that growers, breeders, and other members of the rice industry will play are two of the challenges that must be addressed in the near future.
Clearly the time is now for the U.S. rice industry to get involved in supporting rice genomics. Both Japan and China have already initiated national programs to sequence the rice genome and to use that information to address their own rice interests. While an international genomics initiative that includes the U.S. has been undertaken, the levels and sources of support for this effort need to be clarified. Furthermore, since the U.S.-based public sector interest in the international rice genomics initiative has primarily come from the basic plant research community, a role has yet to be defined for the U.S. rice community which stands to profit tremendously from the success of this effort.
Without a role in international or national rice genomics efforts, members of the U.S. rice industry who have benefited from variety development in the public sector face the possibility of becoming dependent on private sector concerns to remain competitive in the global marketplace. Emerging partnerships and agreements among the private sector may also further restrict the independence of U.S. rice producers, an autonomy that is based on the achievements of breeders and other scientists in the public sector.
In order to preserve the free-flow of information and the continuing development of superior rice cultivars in the public domain, we propose that members of the U.S. rice industry and public sector rice breeders actively seek involvement in shaping and supporting a national rice genomics initiative. The goal of the U.S. rice community should be to position itself in a way that will promote the most effective development and utilization of rice genomics resources.
* This paper is the result of a workshop co-sponsored by Dr. Susan McCouch and Dr. Steve Linscombe and held at Cornell University on November 11, 1998 to discuss the current state of rice genomics and the involvement of U.S. rice breeders and the rice community at large.