Uncovering Genetic Diversity of Rice Varieties Could Improve Nutritional Value, Productivity of World’s Greatest Food Source

Colorado State University, The Institute for Genomic Research, Perlegen Sciences, Inc. and the International Rice Research Institute are joining forces to unlock the genetic secrets of rice, information that could improve rice crops and help address hunger and malnutrition for millions of people. Rice is the world’s top food crop and the principal source of nourishment for nearly half the world’s population, particularly people in the poorest but fastest growing nations.  

The study will focus on the genetic basis underlying important agricultural traits such as the nutritional value and disease resistance of 21 diverse lines, or varieties, of rice, by identifying and comparing differences in DNA sequences. This information will accelerate development of hardier, more productive types of rice. The U.S. Department of Agriculture’s Cooperative State Research, Education and Extension Service – National Research Initiative competitive grants plant genome program provided $715,000 for the U.S. group’s contribution to the collaboration. Additional funding for international collaboration will be provided by other sources.   

"This collaboration will produce a powerful resource to investigate the patterns of molecular variation across the rice genome, assess evolutionary forces shaping rice and discover genes controlling important traits such as disease resistance, drought tolerance and nutritional value," said Jan Leach, the lead U.S. researcher on the study and a professor of bioagricultural sciences and pest management at Colorado State University. "In the long term, this information will be used to improve rice, and it will also help scientists better understand how to improve other crop plants."

As populations boom in countries with limited availability of productive land, the need for additional information about agriculture and crops that can improve production and nutritional values have become key in preventing hunger and malnutrition. Much of the information scientists need may reside in the genomes of wild species of rice.

DNA sequence variation accounts for many differences between individual plants and different varieties of the same plant, such as how the plant develops, how much a crop plant yields, the nutritional value and how well the plant tolerates stresses such as drought or exposure to diseases. Much of the variation in genomes is represented by single nucleotide polymorphisms, known as SNPs, which are changes at single base positions in DNA.

This collaboration will identify SNPs from across the whole genome of 21 rice strains using methodologies developed by Perlegen Sciences. Wild species of rice are a rich resource of diverse traits, and analysis of their genomic variations may provide valuable information regarding phenotypic variation between different rice strains.

SNPs are a marker of genetic variation between individuals of a species, and they allow scientists to identify regions of genetic variation that may be linked to traits. By identifying differences in SNPs among major rice varieties, the study will help uncover the genetic basis behind important agricultural traits.

"In addition to their importance in understanding genome evolution, studying the SNPs of rice is valuable for several reasons," Leach said. "First, it reveals DNA variation among different varieties of rice, which provides information for developing better varieties. It also provides the ultimate anchor to relate the study of rice and other crops."

The International Rice Research Institute is a non-profit agricultural research and training center that was established to improve the wellbeing of present and future generations of rice farmers and consumers, particularly those with low incomes. It helps farmers in developing countries produce more food on limited land, using less water, labor and chemicals. The institute has helped to develop about 1,000 modern varieties of rice, which has increased the availability of rice to populations in need and reduced the price.

Affymetrix Inc. is supporting this important research effort and providing the GeneChip microarray technology that will enable the group to identify SNPs from across the genomes of 21 rice strains. Perlegen will perform the microarray experiments. Perlegen uses microarray technology to quickly assess DNA variations and compare whole genomes in an effort to identify those variations associated with human diseases and to explain and predict the efficacy and adverse effects of prescription drugs.

"Rice is an important crop for world agriculture and an excellent candidate for DNA variation study," said Kelly Frazer, vice president of genomic biology at Perlegen. "The combination of the methodologies and experience our company can provide and the initial genomic research that has been conducted by the International Rice Research Institute will give scientists the opportunity to improve the quality of one of the most critical human food sources in the world."