Whole genome fine map of rice completed and published

After publishing a draft sequence of the Chinese hybrid rice genome as a cover article in the journal of Science (2002, Vol. 296 Issue 5565 ), Beijing Genomics Institute (BGI) of the Chinese Academy of Sciences (CAS) published the fine map of the rice genome in another top international scientific journal “Public Library of Science Biology” (2002, Vol.3 Issue 2).

The efficiency and data quality of the fine maps of two strains of rice, Indica and Japonica, are better than the draft sequence published in 2002. The fine maps were assembled with whole genome shortgun approach. Through searches of 19079 full length cDNA, 97.7% of complete genes were found in the two genomes. After adjusting for residual errors of predictions with EST data, the number of genes is estimated to be between 30000 to 40000. Among them, Only 2-3% genes are unique to any one of the two strains.

Even though the genetic difference between the two strains is small, there are large differences in intergenic regions. The study also analyzed the duplication history of the rice genome. Eighteen pairs of apparent duplications were discovered, covering 65.7% of the genome. Among them, 17 pairs happened before the divergence of the grasses from other flowering plants. More importantly, the on-going duplications of single genes provided a unlimited source of raw materials for gene genesis, creating differences among the grass family.

The Chinese Superhybrid Rice Genome Project, initiated by BGI in 2000, focused on the hybrid rice “Liang You Pei Jiu” as the basic research object. The hybrid was developed by the famous Chinese rice expert Longping Yuan. The goal of the Chinese Superhybrid Rice Genome Project was to reveal the molecular mechanism of the hybridization advantages, thus providing the theoretical basis for improving output and selecting better strains of agriculture crops. The current publication provided a completed fine map for the paternal strain“93-11”(indica), and its comparison with the genome sequence of the Japonica.

It is reported that BGI will finish whole genome assembly and analysis for the maternal strain “PeiAi 64” (its main genetic background being Japonica, as well as a mixture of Indica and Japonica genes ). This would further help discovering distribution of the hybrid genes in F1 and the changes of physiological traits, thus revealing the source of the hybridization advantage in hybrid rice.

Rice is an important staple crop. The successful cultivation of hybrid rice made fundamental contribution towards the food production in China. The completion of the fine maps of the rice genome sequences laid foundation for studying the differences among strains of rices and shed insight into mechanisms of hybrid advantages at a new level. Rice is a model species for the grass family. Through the study of rice genome, a blueprint for study the grass family is built. And a foundation for comparative genomics and evolution studies has been firmly planted.

Source: Crop Biotech Update

Scientists led by Gane Ka-Shu Wong from the Beijing Institute of Genomics reported a “much improved, near complete genome analysis of the indica and japonica subspecies of Oryza sativa” in an article published in PLoS Biology. They used the combined DNA sequence data from the two subspecies to facilitate the sequence assembly. This resulted in an almost 1,000-fold increase in contiguity for the two genome sequences relative to the existing sequence data.

In their article “The genomes of Oryza sativa: a history of duplications,” Wong and colleagues mentioned that they used their improved genome sequence to investigate the evolutionary history of rice. They noted that there is evidence in the rice DNA sequences for a whole-genome duplication event just before the grasses diverged from other flowering plants, about 55–70 million years ago. This genome duplication may have played a role in the origin of the grasses, which then spread rapidly across the world.

The individual gene duplications provide a continuous source of raw material for gene genesis. The challenge is thus to use the rice sequence to develop improved strains of rice and other important food crops.

The article is available online at http://www.plosbiology.org. Contact Gane Ka-Shu Wong at gksw@genomics.org.cn