Sequencing the Rice Genome: Gateway to Agricultural Development

Abstract

For 10,000 years, rice, the most important staple crop in the world, has played a central role in human nutrition and culture. Ensuring a stable supply of this crop to an ever-increasing global population in the face of climate change has become essential. The focus, therefore, has shifted on maximising rice productivity, yield potential and stability. This requires an in-depth understanding of the functional genomics of rice and its breeding pipeline. Spearheaded by the Rice Genome Research Program (Japan), with multinational contribution from ten countries and integration of draft sequences from private organisations, the International Rice Genome Sequencing Project (IRGSP) published a map-based, high-quality genome sequence for Oryza sativa ssp. japonica variety ‘Nipponbare’ in 2006. With the release of the first crop genome sequence data, the global rice community identified novel genes underlying agronomic traits, developed new tool sets for marker-assisted breeding and positional cloning and advanced towards sequencing other cereal genomes. Enhanced comparative and functional genomic studies delivered crucial insights into genome diversity and evolution, speciation and domestication. Integration of the whole-genome data into diverse omics data like transcriptome, protein-protein interaction network and metabolome allowed high-throughput analysis and orthologous gene identification. The rice genome sequence simultaneously laid the foundation for the international 3000 rice genomes resequencing effort and for identification of candidate loci that can be exploited to breed Green Super Rice. More than a decade later, this milestone continues to serve as an information platform for leveraging the genomics of agroecosystems.