Rice Genomics in Japan

Takashi Matsumoto
Agrogenomics Research Center
National Institute of Agrobiological Sciences
Tsukuba, Japan

The completion of the high-quality map-based sequence of the reference Nipponbare genome paved the way for successive efforts in deeper understanding of the structure of specific regions of the genome, comprehensive profiling of the transcriptome, characterization of many agronomic traits traits across various cultivars, and map-based cloning of many agronomic traits. Continuous efforts on gap-filling of the pseudomolecules led to characterization of the centromere regions, telomeres and nucleolar-organizing regions. Using these additional sequences, an optical map of rice, and next-generation sequencing data, a unified genome assembly now referred to as Os-Nipponbare-Reference-IRGSP-1.0 was constructed in 2012 in a joint effort with the MSU Rice Genome Annotation Project. We have performed a series of comparative genomic analysis within or among the species in Oryza genus by focusing on a number of domestication or adaptation related genes in rice. In Japan, the cultivar Koshihikari developed in 1953 is the most popular cultivar representing almost 80 percent of Japanese rice production. The genome sequence of cultivar Koshihikari identified SNPs with Nipponbare and other relevant information on various landraces and pedigree haplotype blocks involved in the breeding process. Analysis of the rice transcriptome has been pursued by microarray and RNA-seq strategies. Gene expression profiling has been performed in organs and tissues at various developmental stages, various hormonal treatments as well as abiotic/biotic conditions to provide the platform for deciphering gene functions of all rice genes. Combining the massive field transcriptomic data and meteorological information with statistical model construction, we have also succeeded in predicting fluctuation of gene expression, or transcriptome dynamics that will lead to precise assumption of crop production, disease resistance and resilience to stress. Recent innovative rice breeding strategies have now been highly facilitated by the genome sequence that brings marker assisted selection as a routine procedure most notably in map-based cloning of QTLs underlying many agronomically important traits in rice. As a result many QTLs have been detected in rice, including those responsible for increased yield, resistance to various insect pests and diseases, resistance to abiotic stress such as drought, salinity and submergence, good eating quality etc. The list of publications and databases below provide a summary of our achievements in the last 10 years.

Major Publications

Mizuno H, Wu J, Matsumoto T (2014) Characterization of chromosomal ends on the basis of chromosome-specific telomere variants and subtelomeric repeats in rice (Oryza sativa L.). Subtelomeres 10: 187-194.

Oono Y, Yazawa T, Kawahara Y et al. (2014) Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice. PLoS One 9:e96946.

Sakai H, Kanamori H, Arai-Kichise Y et al. (2014) Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res. 21: 397-405.

Takai T, Adachi S, Taguchi-Shiobara F et al. (2013) A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Sci. Rep. 3: 2149.

Uga Y, Sugimoto K, Ogawa S et al. (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat. Genet. 45: 1097-1102.

Ishimaru K, Hirotsu N, Madoka Y et al. (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat. Genet. 45: 707-711.

Kanamori H, Fujisawa M, Katagiri S et al. (2013) A BAC physical map of aus rice cultivar ‘Kasalath’, and the map-based genomic sequence of ‘Kasalath’ chromosome 1. Plant J. 76: 699-708.

Kawahara Y, de la Bastide M, Hamilton J et al. (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4.

Oono Y, Kawahara Y, Yazawa T et al. (2013) Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles. Plant Mol. Biol. 83: 523-537.

Ogiso-Tanaka E, Matsubara K, Yamamoto S et al. (2013) Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice. PLoS One 8:e75959

Matsubara K, Ogiso-Tanaka E, Hori K et al. (2013) Natural variation in Hd17, a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flowering. Plant Cell Physiol. 53: 709-716.

Hori K, Ogiso-Tanaka E, Matsubara K et al. (2013) Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response Plant J. 76:36-46.

Nagano AJ, Sato Y, Mihara M et al. (2012) Deciphering and prediction of transcriptome dynamics under fluctuating field conditions. Cell 151: 1358-1369.

Kawahara Y, Oono Y, Kanamori H et al. (2012) Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS One 7-11 e49423.

Yang CC, Sakai H, Numa H, Itoh T (2011) Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison. Gene 477: 53-60.

Oono Y, Kawahara Y, Kanamori H et al. (2011) mRNA-seq reveals a comprehensive transcriptome profile of rice under phosphate stress. Rice 4: 50-65.

Mizuno H, Kawahara Y, Wu J et al. (2011) Asymmetric distribution of gene expression in the centromeric region of rice chromosome 5. Front. Plant Sci. 2: 16.

Sakai H, Ikawa H, Tanaka T et al. (2011) Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis. Plant J. 66: 796-805.

Sato Y, Antonio B, Namiki N et al. (2011) Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC Plant Biol. 11:10.

Matsubara K, Yamanouchi U, Nonoue Y et al. (2011) Ehd3, encoding a plant homeodomain finger-containing protein, is a critical promoter of rice flowering. Plant J. 66: 603-612.

Sugimoto K, Takeuchi Y, Ebana K et al. (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc. Natl. Acad. Sci. USA 107: 5792-5797.

Mizuno H, Kawahara Y, Sakai H et al. (2010) Massive parallel sequencing of mRNA in identification of unannotated salinity, stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics 11:683.

Yamamoto T, Nagasaki H, Yonemaru J et al. (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11: 267.

Wu J, Fujisawa M, Tian Z et al. (2009) Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure. Plant J. 60: 805-819.

Takahashi Y, Teshima KM, Yokoi S et al. (2009) Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proc. Natl. Acad. Sci. USA 106: 4555-4560.

Fukuoka S, Saka N, Koga H et al. (2009) Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325: 98-101.

Hattori Y, Nagai K, Furukawa S et al. (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460: 1026-1030.

Wu J, Mizuno H, Sasaki T, Matsumoto T (2008) Comparative analysis of rice genome sequence to understand the molecular basis of genome evolution. Rice 1: 119-126.

Shomura A, Izawa T, Ebana K et al. (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 40: 1023-1028.

Fujino K, Sekiguchi H, Matsuda Y et al. (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice Proc. Natl. Acad. Sci. USA 105: 12623-12628.

Komiya R, Ikegami A, Tamaki S et al. (2008) Hd3a and RFT1 are essential for flowering in rice. Development 135: 767-774.

Mizuno H, Wu J, Katayose Y et al. (2008) Characterization of chromosome ends on the basis of the structure of TrsA subtelomeric repeats in rice (Oryza sativa L.). Mol. Genet. Genomics 280: 19-24.

Mizuno H, Wu J, Katayose Y et al. (2008) Chromosome-specific distribution of nucleotide substitutions in telomeric repeats of rice (Oryza sativa L.). Mol. Biol. Evol. 25: 62-68.

Rice Annotation Project (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36: D1028-1033.

Shimono M, Sugano S, Nakayama A et al. (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19: 2064-2076.

Konishi S, Izawa T, Lin SY et al. (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1 392-1396.

Fujisawa M, Yamagata H, Kamiya K et al. (2006) Sequence comparison of distal and proximal ribosomal DNA arrays in rice (Oryza sativa L.) chromosome 9S and analysis of their flanking regions. Theor. Appl. Genet. 113: 419-428.

Mizuno H, Wu J, Kanamori H et al. (2006) Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S. Plant J. 46: 206-217.