Rice Master Genomes: Improving the Mapping Efficiency and Providing New References for Genome Sequencing

The domesticated Asian rice, Oryza sativa, is known to have a complex population structure, and the history of rice domestication is inscribed within the genomes of these subpopulations. The species is one of the most prominent monocot model plants in academic biology research, while it is also an invaluable staple crop for global food security, being widely grown around the world, mostly in Asian countries. The whole-genome sequence of the Oryza sativa ssp. japonica cv. Nipponbare, revealed by the International Rice Genome Sequencing Project (IRGSP) in 2004 has been extensively used for fundamental and applied research in the last decade. Nowadays in the NGS era, an increasing number of genome sequences of cultivated rice have been published. Nevertheless, all these genome sequences were mapped against the Nipponbare reference genome, which lacks several aspects present in the other rice subpopulations.  Here we describe the construction of a more localized and specialized reference genome for each of the five rice subpopulations (indica, temperate japonica, tropical japonica, aus and aromatic). We assembled these Master Genomes using a large number of the publicly available rice genomic data. The use of these five Master Genomes in NGS re-sequencing analyses of rice varieties by other members of the rice community will greatly improve our knowledge on rice research. The efficiency and advantage of these Master Genomes in rice re-sequencing analyses will be discussed.