Abstract
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 materialThe online version of this article (doi:10.1186/s12284-016-0107-4) contains supplementary material, which is available to authorized users.
Highlights
The elucidation of the rice genome sequence is a major milestone in science as it paves the way for understanding the biology of a major cereal crop that feeds more than half of the world’s population (International Rice Genome Sequencing Project 2005)
The latest genome assembly was constructed as a joint effort of the Rice Annotation Project Database (RAPDB) of the National Institute of Agrobiological Sciences (NIAS) and the Michigan State University (MSU) Rice Genome Annotation Project to update and validate the reference International Rice Genome Sequencing Project (IRGSP) Nipponbare genome sequence and provide a unified set of pseudomolecules to the rice research community (Kawahara et al 2013)
In Japan, rice genomics has been a part of major research programs of the Ministry of Agriculture, Forestry and Fisheries (MAFF) that address various issues in sustainable food production and agriculture
Summary
The elucidation of the rice genome sequence is a major milestone in science as it paves the way for understanding the biology of a major cereal crop that feeds more than half of the world’s population (International Rice Genome Sequencing Project 2005). The complete rice genome sequence based on the cultivar Nipponbare led to the large-scale characterization of other japonica cultivars including the widely cultivated and elite cultivar Koshihikari (Yamamoto et al 2010) known for good eating quality.
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