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The map-based genome sequence of the  japonica  rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.   Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0107-4) contains supplementary material, which is available to authorized users.

The Nipponbare genome and the next-generation of rice genomics research in Japan