The genome of a plant, animal or microbe is the totality of its genetic information including all the genes and the non-transcribed sections of the DNA - basically all the genes that an organism has. Genomics is the study of this complete genetic content of an organism.

The Rice Genome is the worlds first complete genome of a crop plant, rice. The sequence contains all of the genetic information that determines the makeup of rice. This includes the DNA sequence of every gene, the regulatory DNA sequences that surround the genes, the linear order of the genes along every chromosome, and the correspondence between the genome map and the plant breeders map of inherited traits.

Rice is the largest commercial crop in the world, nourishing over half of the Worlds population. There is tremendous potential to improve the worlds ability to feed its people through improving yields and reducing the rice plants dependence upon fertilizer and pesticides. The Syngenta research also demonstrated the similarity between rice and other cereal crops such as corn and wheatin which Syngenta has a strong commercial interest.

The Rice Genome Map was made using a shotgun sequencing strategy. This is the same strategy that revolutionized the Human Genome Project. Shotgun sequencing enables full coverage of the genome in a fraction of the time required for the alternative BAC sequencing approach.

The Syngenta draft sequence analysis identified between 32,000-50,000 genes and a total of 420 million base pairs of nucleotides, present within rices 12 chromosomes. This analysis covers 99% of the rice genome at an accuracy level of 99.8%.

The Syngenta draft sequence is 99.8% accurate. Finishing the sequence to a completion and accuracy level of 99.99% is essential, however, for scientists to capture the full value of the rice genome.

The rice sequence was completed to better than 6x coverage in approximately 14 months. Although enhancements to the system mean that it runs faster all the time, it was running at approximately 12 million base pairs of DNA per day as the genome was completed. 6x coverage means that the genome was sequenced the equivalent of six times over, or approximately 2.6 billion base pairs in total.

Plant breeders will use the rice genome map to precisely select the best progeny from plant breeding crosses. This will accelerate the improvement of rice varieties. The map will also be used by biotechnologists to snip out and transfer single genes from one rice variety to another, so that discrete improvements can be made without mixing together all of the genes from both varieties.

The rice genome sequence will be useful as a research tool to understand how crops resist stress or how they confer health benefits to food. Because of the considerable genetic similarity between rice and other cereals such as wheat and maize, the rice genome map is a virtual map of all cereal species. Therefore, the rice genome sequence could accelerate the improvement of all cereal species.

The similarity between the rice genome and the genomes of other cereal crops and Arabidopsis (the first completed plant genome) is one of the most significant findings. With this knowledge, scientists will be able to move faster in developing genome sequence data for other cereal crops such as corn and wheat. This will accelerate our ability to improve crops through both conventional plant breeding and biotechnology.

Since announcing completion of the rice genome map and sequence last year, Syngenta has undertaken a more in-depth analysis of the sequence. The analysis published in Science provides essential information about the physical location of genes on individual chromosomes and how these genes function. The information gained from this analysis will be critical to accelerate plant breeding that can enhance rice and other cereal crops.

Completing the draft sequence analysis was a critical step in developing information important to the scientific community. When we had completed this analysis, Science magazine invited us to publish our findings in their magazine. The peer review process for such a publication takes time.

Public Benefits

Translating this knowledge into practical applications that benefit consumers should begin to occur over the next three to five years. The information from the rice genome will help scientists understand how a plant responds to the environment and which genes control various functions of the plant. With this knowledge, plant breeders can, using biotechnology and conventional breeding, more selectively develop plants that resist drought, disease, pests, and other environmental threats.

Syngenta also hopes to use this information to improve the nutritional value of todays crops, enhance crop yields, and improve the processing characteristics of the major commodities within the food chain. The rice genome sequence will also be a useful in identifying plant-specific genes that can be potential herbicide targets. This knowledge will help Syngenta develop new crop protection products for rice as well as other cereal crops.

Understanding cereal genomes and proteins will accelerate scientists ability to breed crops with stable yields by improving seed quality, resistance to pests and diseases and plant hardiness. Crop plants could also be made more nutritious. Another benefit could be increased environmental protection. The greatest threat to the environment in many areas is the excessive use of land and water for agriculture. Understanding cereal genomes will accelerate the ability to breed crops with increased yield and hardiness, thus reducing the agricultural need for land and water.

Agricultural research in developing countries is often focused on rice. The rice genome will create opportunities for the improvement of rice.