Institute of Crop Science, NARO

Field Omics Research Unit

Great advancement of crop genomics study has led to the identification of a number of genes associated with agricultural important traits and more effective improvement of crop plants based on applied genomics approaches. However, many complicated traits that are controlled by multiple genetic factors have remained unclear. Omics analysis is a powerful tool to comprehensively analyze a molecular dynamics associated with a specific biological event and would enable us to evaluate a physiological phenomenon and an environmental response more accurately. Therefore, an approach based on the omics analysis would be useful for exploration of new technology in crop plant improvement. Field Omics Research Unit is performing researches with rice and soybean based on molecular genetics, genetics and biochemistry as well as omics analysis such as transcriptomics, proteomics, and metabolomics, and trying to clear the molecular mechanism on environmental stress resistance, response, and adaptation such as moisture resistance in soybean, nutrient usage and adjustment of flowering time in rice.


Unit Leader

Hironori ITOH

Unit Members

Name
Position
Research Topic
Yusaku UGA Senior Researcher
Yuko OGO Senior Researcher Rice, Flowering
Hinako TAKEHISA Researcher Rice, Transcriptome, Growth physiology, Molecular Genetics
Yutaka SATO Senior Researcher Rice, Transcriptome, Growth physiology, Molecular Genetics

Research Publications

  • Yin X, Komatsu S (2016) Nuclear proteomics reveals the role of protein synthesis and chromatin structure in root tip of soybean during the initial stage of flooding stress. J Proteome Res 15:2283-2298
  • Wang X, Komatsu S (2016) Gel-free/label-free proteomic analysis of endoplasmic reticulum proteins in soybean root tips under flooding and drought stresses. J Proteome Res 15:2211-2227
  • Yin X, Nishimura M, Hajika M, Komatsu S (2016) Quantitative proteomics reveals the flooding-tolerance mechanism in mutant and abscisic acid-treated soybean. J Proteome Res 15:2008-2025
  • Hossain Z, Mustafa G, Sakata K, Komatsu S (2016) Insights into the proteomic response of soybean towards Al(2)O(3), ZnO, and Ag nanoparticles stress. J Hazard Mater 304:291-305
  • Itoh J, Sato Y, Sato Y, Hibara K, Shimizu-Sato S, Kobayashi H, Takehisa H, Sanguinet K.A, Namiki N, Nagamura Y (2016) Genome-wide analysis of spatio-temporal gene expression patterns during early embryogenesis in rice. Development 143:1217-1227
  • Ogo Y, Mori T, Nakabayashi R, Saito K, Takaiwa F (2016) Transgenic rice seed expressing flavonoid biosynthetic genes accumulate glycosylated and/or acylated flavonoids in protein bodies. J Exp Bot 67:95-106
  • Li M, Yin X, Sakata K, Yang P, Komatsu S (2015) Proteomic analysis of phosphoproteins in the rice nucleus during the early stage of seed germination. J Proteome Res 14:2884-2896
  • Kamal AH, Komatsu S (2015) Involvement of reactive oxygen species and mitochondrial proteins in biophoton emission in roots of soybean plants under flooding stress. J Proteome Res 14:2219-2236.
  • Mustafa G, Komatsu S (2015) Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress. Front Plant Sci 5:627
  • Komatsu S, Tougou M, Nanjo Y (2015) Review-Proteomic techniques and management of flooding tolerance in soybean. J Proteome Res 14:3768-3778
  • Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S (2015) Review-Proteomics of important food crops in the Asia Oceania Region: Current status and future perspectives. J Proteome Res 14:2723-2744
  • Miyazaki S, Sato Y, Asano T, Nagamura Y, Nonomura K (2015) Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR. Plant Mol Biol 89:293-307
  • Takehisa H, Sato Y, Antonio B, Nagamura Y (2015) Coexpression network analysis of macronutrient deficiency response genes in rice. Rice 8:24
  • Wakasa Y, Takagi H, Watanabe N, Kitamura N, Fujiwara Y, Ogo Y, Hayashi S, Yang L, Ohta M, Thet Tin WW, Sekikawa K, Takano M, Ozawa K, Hiroi T, Takaiwa F (2015) Concentrated protein body product derived from rice endosperm as an oral tolerogen for allergen-specific immunotherapy--a new mucosal vaccine formulation against Japanese cedar pollen allergy. Plos One 10:e0120209
  • Oh M, Nanjo Y, Komatsu S (2014) Gel-free proteomic analysis of soybean root proteins affected by calcium under flooding stress. Front Plant Sci 5:559
  • Yin X, Sakata K, Komatsu S (2014) Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress. J Proteome Res 13:5618-5634
  • Khan MN, Sakata K, Hiraga S, Komatsu S (2014) Quantitative proteomics reveals that peroxidases play key roles in post-flooding recovery in soybean roots.J Proteome Res 13:5812-5828
  • Han C, Yang P, Sakata K, Komatsu S (2014) Quantitative proteomics reveals the role of protein phosphorylation in rice embryos during early stages of germination. J Proteome Res 13:1766-1782
  • Komatsu S, Kamal AH, Hossain Z (2014) Review-Wheat proteomics: proteome modulation and abiotic stress acclimation.Front Plant Sci 5:684
  • Ogo Y, Kakei Y, Itai RN, Kobayashi T, Nakanishi H, Nishizawa NK (2014) Tissue-specific transcriptional profiling of iron-deficient and cadmium-stressed rice using laser capture microdissection. Plant Signal Behav 9: e29427
  • Ogo Y, Wakasa Y, Hirano K, Urisu A, Matsuda T, Takaiwa F (2014) Generation of transgenic rice with reduced content of major and novel high molecular weight allergens. Rice 7:19
  • Ogo Y, Takahashi H, Wang S, Takaiwa F. (2014) Generation mechanism of novel, huge protein bodies containing wild type or hypoallergenic derivatives of birch pollen allergen Bet v 1 in rice endosperm. Plant Mol Biol 86:111-123
  • Ogo Y, Kakei Y, Itai RN, Kobayashi T, Nakanishi H, Takahashi H, Nakazono M, Nishizawa NK (2014) Spatial transcriptomes of iron-deficient and cadmium-stressed rice. New Phytol 201:781-794.
  • Nakano M, Yamada T, Masuda Y, Sato Y, Kobayashi H, Ueda H, Morita R, Nishimura M, Kitamura K, Kusaba M (2014) A green-cotyledon/stay-green mutant exemplifies the ancient whole-genome duplications in soybean. Plant Cell Physiol 55:1763-1771
  • Shinano T, Yoshimura T, Watanabe T, Unno Y, Osaki M, Nanjo Y, Komatsu S (2013) Effect of phosphorus levels on the protein profiles of secreted protein and root surface protein of rice. J Proteome Res 12:4748-4756
  • Komatsu S, Han C, Nanjo Y, Altaf-Un-Nahar M, Wang K, He D, Yang P (2013) Label-free quantitative proteomic analysis of abscisic acid effect in early-stage soybean under flooding. J Proteome Res 12:4769-4784
  • Nanjo Y, Nakamura T, Komatsu S (2013) Identification of indicator proteins associated with flooding injury in soybean seedlings using label-free quantitative proteomics. J Proteome Res 12:4785-4798
  • Hossain Z, Khatoon A, Komatsu S (2013) Review-Soybean proteomics for unraveling abiotic stress response mechanism. J Proteome Res 12:4670-4684
  • Komatsu S, Hossain Z (2013) Review Organ-specific proteome analysis for identification of abiotic stress response mechanism in crop. Front Plant Sci 4:71
  • Salavati A, Shafeinia A, Klubicova K, Bushehri AA, Komatsu S (2013) Review-Proteomic insights into intra- and intercellular plant-bacteria symbiotic association during root nodule formation. Front. Plant Sci 4:28
  • Afroz A, Zahur M, Zeeshan N, Komatsu S (2013) Review-Plant-bacterium interactions analyzed by proteomics. Front Plant Sci 4:21
  • Komatsu S, Yanagawa Y (2013) Review - Cell wall proteomics of crops. Front Plant Sci 4:17
  • Aghaei K, Komatsu S (2013) Review-Crop and medicinal plants proteomics in response to salt stress. Front Plant Sci 4:8
  • Hossain Z, Komatsu S (2013) Review-Contribution of proteomic studies towards understanding plant heavy metal stress response. Front Plant Sci 3:310
  • Nouri MZ, Komatsu S (2013) Review-Subcellular protein overexpression to develop abiotic stress tolerant plants. Front Plant Sci 4:2
  • Itoh H, Izawa T (2013) The coincidence of critical day length recognition for florigen gene expression and floral transition under long-day conditions in rice. Molecular Plant 6:635-649
  • Ogo Y, Ozawa K, Ishimaru T, Murayama T, Takaiwa F (2013) Transgenic rice seed synthesizing diverse flavonoids at high levels: a new platform for flavonoid production with associated health benefits. Plant Biotechnol J 11:734-746
  • Itai RN, Ogo Y, Kobayashi T, Nakanishi H, Nishizawa NK (2013) Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots. Rice 25:16
  • Kakei Y, Ogo Y, Itai RN, Kobayashi T, Yamakawa T, Nakanishi H, Nishizawa NK (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice. Rice 22: 22
  • Hirano K, Aya K, Morinaka Y, Nagamatsu S, Sato Y, Antonio B, Namiki N, Nagamura Y, Matsuoka M (2013) Survey of genes involved in rice secondary cell wall formation through a co-expression network. Plant Cell Physiol 54:1803-1821
  • Hirano K, Kondo M, Aya K, Miyao A, Sato Y, Antonio B, Namiki N, Nagamura Y, Matsuoka M (2013) Identification of transcription factors involved in rice secondary cell wall formation. Plant Cell Physiol 54:1791-1802
  • Tanaka N, Uraguchi S, Saito A, Kajikawa M, Kasai K, Sato Y, Nagamura Y, Fujiwara T (2013) Roles of pollen-specific boron efflux transporter, OsBOR4 in rice fertilization process. Plant Cell Physiol 54:2011-2019
  • Takehisa H, Sato Y, Antonio BA, Nagamura Y (2013) Global transcriptome profile of rice root in response to essential macronutrient deficiency. Plant Signal Behav 8:e24409
  • Yamatani H, Sato Y, Masuda Y, Kato Y, Morita R, Fukunaga K, Nagamura Y, Nishimura M, Sakamoto W, Tanaka A, Kusaba M (2013) NYC4, the rice ortholog of Arabidopsis THF1, is involved in the degradation of chlorophyll-protein complexes during leaf senescence. Plant J 74: 652-662
  • Kazama Y, Fujiwara MT, Takehisa H, Ohbu S, Saito H, Ichida H, Hayashi Y, Abe T (2013) Characterization of a heavy-ion induced white flower mutant of allotetraploid Nicotiana tabacum. Plant Cell Rep 32:11-19
  • Sato Y, Namiki N, Takehisa H, Kamatsuki K, Minami H, Ikawa H, Ohyanagi H, Sugimoto K, Itoh J, Antonio BA, Nagamura Y (2013) RiceFREND: a platform for retrieving coexpressed gene networks in rice. Nucleic Acids Res 41:D1214-D1221
  • Sato Y, Takehisa H, Kamatsuki K, Minami H, Namiki N, Ikawa H, Ohyanagi H, Sugimoto K, Antonio B.A, Nagamura Y (2013) RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome. Nucleic Acids Res 41:D1206-D1213
  • Yoshida A, Sasao M, Yasuno N, Takagi K, Daimon Y, Chen R, Yamazaki R, Tokunaga H, Kitaguchi Y, Sato Y, Nagamura Y, Ushijima T, Kumamaru T, Iida S, Maekawa M, Kyozuka J (2013) TAWAWA1, a regulator of rice inflorescence architecture, functions through the suppression of meristem phase transition. Proc Natl Acad Sci USA 110:767-772
  • Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu J, Matsumoto T, Takai T, Okuno K, Yano M (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45:1097-1102
  • Ogo Y, Ozawa K, Ishimaru T, Murayama T, Takaiwa F. (2013) Transgenic rice seed synthesizing diverse flavonoids at high levels: a new platform for flavonoid production with associated health benefits. Plant Biotechnol J 11:734-746
  • Ohyanagi H, Sakata K, Komatsu S (2012) Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics. Front Plant Sci 3:110
  • Nanjo Y, Skultety L, Uva?kova L, Klubicova K, Hajduch M, Komatsu S (2012) Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. J Proteome Res 11:372-385
  • Asano T, Hayashi N, Kobayashi M, Aoki N, Miyao A, Mitsuhara I, Ichikawa H, Komatsu S, Hirochika H, Kikuchi S, Ohsugi R (2012) A rice calcium-dependent protein kinase OsCPK12 oppositely modulates salt-stress tolerance and blast disease resistance. Plant J 69:26-36
  • Hossain Z, Nouri MZ, Komatsu S (2012) Review-Plant cell organelle proteomics in response to abiotic stress. J Proteome Res 11:37-48
  • Komatsu S, Hiraga S, Yanagawa Y (2012) Review-Proteomics techniques for the development of flood tolerant crops. J Proteome Res 11:68-78
  • Nagano AJ, Sato Y, Mihara M, Antonio BA, Motoyama R, Itoh H, Nagamura Y, Izawa T (2012) Deciphering and prediction of transcriptome dynamics under fluctuating field conditions. Cell 151:1358-1369
  • Kobayashi K, Yasuno N, Sato Y, Yoda M, Kimizu M, Yoshida H, Nagamura Y, Kyozuka J (2012) Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2, a SEPALLATA MADS box gene. Plant Cell 24:1848-1859
  • Kitomi Y, Inahashi H, Takehisa H, Sato Y, Inukai Y (2012) OsIAA13-mediated auxin signaling is involved in lateral root initiation in rice. Plant Sci 190:116-122
  • Takehisa H, Sato Y, Igarashi M, Abiko T, Antonio BA, Kamatsuki K, Minami H, Namiki N, Inukai Y, Nakazono M, Nagamura Y (2012) Genome-wide transcriptome dissection of the rice root system: Implication for developmental and physiological functions. Plant J 69:126-140
  • Ozawa K, Wakasa Y, Ogo Y, Matsuo K, Kawahigashi H, Takaiwa F (2012) Development of an efficient agrobacterium-mediated gene targeting system for rice and analysis of rice knockouts lacking granule-bound starch synthase (Waxy) and β1,2-xylosyltransferase. Plant Cell Physiol 53:755-761
  • Takahashi R, Ishimaru Y, Shimo H, Ogo Y, Senoura T, Nishizawa NK, Nakanishi H (2012) The OsHMA2 transporter is involved in root-to-shoot translocation of Zn and Cd in rice. Plant Cell Environ 35:1948-1957
  • Komatsu S, Yamamoto A, Nakamura T, Nouri MZ, Nanjo Y, Nishizawa K, Furukawa K (2011) Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. J Proteome Res 10:3993-4004
  • Ogo Y, Itai RN, Kobayashi T, Aung MS, Nakanishi H, Nishizawa NK (2011) OsIRO2 is responsible for iron utilization in rice and improves growth and yield in calcareous soil. Plant Mol Biol 75:593-605
  • Tanaka N, Itoh H, Sentoku N, Kojima M, Sakakibara H, Izawa T, Itoh J, Nagato Y (2011) The COP1 ortholog PPS regulates the juvenile-adult and vegetative-reproductive phase changes in rice. Plant Cell 23:2143-2154
  • Itoh H and Izawa T. (2011) A study of phytohormone biosynthetic gene expression using a circadian clock-related mutant in rice. Plant Signal Behav 6:1932-1936
  • Osugi A, Itoh H, Ikeda-Kawakatsu K, Takano M, Izawa T (2011) Molecular dissection of the roles of phytochrome in photoperiodic flowering in rice. Plant Physiol 157:1128-1137
  • Izawa T, Mihara M, Suzuki Y, Gupta M, Itoh H, Nagano AJ, Motoyama R, Sawada Y, Yano M, Yokota Hirai M, Makino A, Nagamura Y (2011) Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field. Plant Cell 23:1741-1755
  • Uraguchi S, Kamiya Y, Sakamoto T, Kasai K, Sato Y, Nagamura Y, Yoshida A, Kyozuka J, Ishikawa S, Fujiwara T (2011) OsLCT1 regulates cadmium transport into rice grains. Proc Natl Acad Sci USA 108:20959-20964
  • Bashir K, Ishimaru Y, Shimo H, Kakei Y, Senoue T, Takahashi R, Sato Y, Sato Y, Uozumi N, Nakanishi H, Nishizawa NK (2011) Rice phenolics efflux transporter 2 (PEZ2) plays an important role in solubilizing apoplasmic iron. Soil Sci Plant Nutr 57:803-812
  • Ishimaru Y, Kakei Y, Shimo H, Bashir K, Sato Y, Sato Y, Uozumi N, Nakanishi H, Nishizawa NK (2011) A rice phenolic efflux transporter is essential for solubilizing precipitated apoplasmic iron in the plant stele. J Biol Chem 286:24649-24655
  • Sato Y, Antonio BA, Namiki N, Motoyama R, Sugimoto K, Takehisa H, Minami H, Kamatsuki K, Kusaba M, Hirochika H, Nagamura Y (2011) Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC Plant Biol 11:10
  • Sato Y, Antonio BA, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y (2011) RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res 39:D1141-D1148

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