Where’s My Rice? Securing the Future of Rice

4 Feb 2019 2:05 PM

By Jelina Tetangco

Excerpts from this article were taken from the Nature-published paper entitled “Genomic variation in 3,010 diverse accessions of Asian-cultivated rice”, with permission from the International Rice Research Institute.


Almost half of humanity is sustained by rice, according to the Food and Agriculture Organization (FAO). Asian cultivated rice (Oryza sativa L.) is grown worldwide as half the world’s staple food. Asian rice cultivation and yield is affected not only by climatic factors, but by genetic erosion due to rice farming practices, and human disturbance.

By the year 2035, the FAO says that an additional 112 million metric tons of rice must be produced with less land and water under more fluctuating climates, requiring that future rice cultivars be higher yielding and resilient to multiple abiotic and biotic stresses. The foundation to continued improvement of rice is the rich genetic diversity within its populations and wild relatives.

The International Rice Research Institute (IRRI) leads rice research to ensure the long-term preservation of rice biodiversity as a part of the global strategy for the conservation of rice genetic resources. A research
team from IRRI, led by Dr. Ramil Mauleon, together with collaborators from the Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences (CAAS), BGI-Shenzhen, and 13 other partner institutions embarked on the 3,000 Rice Genome (3kRG) Project to analyze genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice genomes. The results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that show correlation with geographic location.

The research team identified 29 million single nucleotide polymorphisms (SNPs) and 2.4 million small indels, and over 90,000 structure variation (SVs), which contribute to within and between population variation. Pan-genome analyses identified more than 10,000 novel full length protein-coding genes and a high number of presence absence variations (PAVs). The complex patterns of introgression observed in domestication genes are consistent with multiple modes of rice domestication. The public availability of data from the 3k RG project provide a resource for rice genomics research and breeding.


As a community, the next challenge will be to examine associations of the 3k genetic variation with agriculturally relevant phenotypes measured under multiple field and laboratory environmental conditions; this will guide and accelerate rice breeding by identifying genetic variation that will be useful in breeding efforts and future sustainable agriculture.

The DOST-ASTI contributed to this important research through the Computing and Archiving Research Environment (COARE) facility, which provided the computational processing, data storage, distribution and access service platform requirements.