The 3000 Rice Genome Project

The majority of the world’s population, especially the poor in rural Asia, depends on rice for their sustenance and livelihood.  While current yields have kept abreast with the increase in population, yield increases need to be maintained through development of improved varieties that will also cope with environmental extremes wrought by climate change.  Hence, the identification of novel alleles from diverse germplasm through the application of next-generation sequencing technology is one step in this direction.  IRRI, the Chinese Academy of Agricultural Sciences (CAAS) and BGI-Shenzhen have undertaken re-sequencing of an extensive collection of rice genetic resources to uncover allelic variation.  Three thousand and twenty-four types of rice coming from the International Rice Gene Bank (IRG), the China National Crop Gene Bank and CAAS working collections were sequenced at an average depth of 13X (ranging from about 5X to over 50X depth).  Reference-based alignment to the japonica Nipponbare genome identified variants at over tens of millions loci by stringent criteria.  Variant calling using other reference genomes for rice is currently underway with other partners.  Seed from the sequenced entries is being made available through the IRG and CAAS so that detailed phenotyping for high priority traits for breeding can be accomplished.  This phenotyping data will enable genome-wide association studies as well as genetic, physiological and biochemical studies.  The development of a rice information portal under the International Rice Informatics Consortium will serve as one entry point to the variant calls and annotations.