The 3,000 Rice Genomes Project

International Rice Research Institute (IRRI), Chinese Agricultural Academy of Sciences (CAAS) and Beijing Genomics Institute (BGI) have come together to sequence the genomes of 3000 rice accessions. A report of this unprecedented sequencing effort and access to the sequence information was recently published in the Journal GigaScience (Jia-Yang Li, Jun Wang, and Robert S Zeigler GigaScience May 2014, 3:8).

The 3000 rice genomes sequenced originate from 89 countries worldwide, while the sequenced germplasm come from the collections of IRRI (2,466 accessions) and CAAS (534 accessions). These accessions encompass: parental lines of popular varieties including many landraces; genome wide introgression lines established for molecular breeding programs; selected mapping populations; the so called mega varieties of rice which are grown in large scale throughout Asia; and at least one of the recently developed Sub-1 introgressed cultivars.

The resulting sequence information contain an average of 14X coverage for the 3000 genomes with 92-94% mapping rate (when aligned against the japonica variety) and reveal 18.9 million single nucleotide polymorphisms (SNPs: indicating the depth of allelic diversity). The significance of this study is not only the diversity of the germplasm sequenced and the quality of genome coverage but the accessibility of the sequence information for the research community to further analyze and mine this data to accelerate their own research output.

The rich genetic diversity within the rice germplasm collections throughout the world has always provided the basis for rice breeding. The sequence information from the 3000 rice genomes project, on the other hand, provide the initial step in building a platform to integrate the genetic/molecular information of this diversity with functional genomics, which can link allelic variation to metabolic and regulatory networks and the resulting phenotypic traits. A process by which, desirable but genetically complex traits may be effectively incorporated to the genomics based breeding programs. The recently initiated International Rice Informatics Consortium is expected to provide a portal for rice researchers to interphase with such an integrated platform to develop high yielding, low input, stress tolerant cultivars of this plant that feeds half the world.