Using Metabolomic Approaches to Explore Chemical Diversity in Rice

Kusano, Miyako; Yang, Zhigang; Okazaki, Yuji; Nakabayashi, Ryo; Fukushima, Atsushi; Saito, Kazuki

doi:10.1016/j.molp.2014.11.010

Cited by 141 publications

(84 citation statements)

References 117 publications

(141 reference statements)

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“…Rice ( Oryza sativa L.) is one of the most important staple foods worldwide, providing almost one-quarter of the global dietary energy supply for humans12. The demand for food continues to rise as the population rapidly grows, necessitating the production of 40% more rice in 2030, and arable land is limited together with environmental degradation3.…”

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confidence: 99%

Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System

Zhou¹,

et al. 2016

Sci Rep

194

126

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Hybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and developed new “transgene clean” TGMS lines. We designed 10 target sites in the coding region of TMS5 for targeted mutagenesis using the CRISPR/Cas9 system and assessed the potential rates of on- and off-target effects. Finally, we established the most efficient construct, the TMS5ab construct, for breeding potentially applicable “transgene clean” TGMS lines. We also discussed factors that affect the editing efficiency according to the characteristics of different target sequences. Notably, using the TMS5ab construct, we developed 11 new “transgene clean” TGMS lines with potential applications in hybrid breeding within only one year in both rice subspecies. The application of our system not only significantly accelerates the breeding of sterile lines but also facilitates the exploitation of heterosis.

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confidence: 99%

Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System

Zhou¹,

et al. 2016

Sci Rep

194

126

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“…3) Rice accumulates bioactive specialized metabolites, 4) such as phenylpropanoids, [5][6][7][8][9] quinolone and pyridine alkaloids, 10,11) terpenoids, [12][13][14] and flavonoids (quercetin, kaempferol, tricin, and their glycosides). [15][16][17][18][19][20] Such metabolites exhibit properties beneficial to humans, including anti-tumor, 21) anti-inflammatory, 22) and anti-oxidant activities.…”

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confidence: 99%

Metabolome Analysis of <i>Oryza sativa</i> (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity

et al. 2016

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Oryza sativa L. (rice) is an important staple crop across the world. In the previous study, we identified 36 specialized (secondary) metabolites including 28 flavonoids. In the present study, a metabolome analysis using liquid chromatography-mass spectrometry was conducted on the leaf, bran, and brown and polished rice grains to better understand the distribution of these metabolites. Principal component analysis using the metabolome data clearly characterized the accumulation patterns of the metabolites. Flavonoids, e.g., tricin, tricin 7-O-rutinoside, and tricin 7-O-β-D-glucopyranoside, were mainly present in the leaf and bran but not in the polished grain. In addition, anti-inflammatory and anti-oxidant activity of the metabolites were assayed in vitro. Tricin 4′-O-(erythro-β-guaiacylglyceryl)ether and isoscoparin 2″-O-(6‴-(E)-feruloyl)-glucopyranoside showed the strongest activity for inhibiting nitric oxide (NO) production and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging, respectively. Key words Oryza sativa; rice; specialized metabolite; anti-inflammatory; anti-oxidantPlants produce a wide range of chemically and biologically diverse specialized (secondary) metabolites. These metabolites play an important role in human health because they have nutritional and medicinal aspects. 1) Rice (Oryza sativa L.) is one of the most important staple crops and provides more than a fifth of the total calories consumed across the world.2)The major nutrient of rice is starch; minor nutrients include protein, lipid, fiber, vitamins, and minerals.3) Rice accumulates bioactive specialized metabolites, 4) such as phenylpropanoids, 5-9) quinolone and pyridine alkaloids, 10,11) terpenoids, [12][13][14] and flavonoids (quercetin, kaempferol, tricin, and their glycosides). [15][16][17][18][19][20] Such metabolites exhibit properties beneficial to humans, including anti-tumor, 21) anti-inflammatory, 22) and anti-oxidant activities. 8) To improve the quality of rice plants, the organ-specific metabolic networks of primary and specialized metabolites were recently investigated using metabolite profiling based on liquid chromatography (LC)-MS.19,23-28) Metabolome-genome-wide association studies on rice have been increasingly attracting attention. 25,29) There are two primary types of rice grown in the world (i.e., the Indica and Japonica varieties). The Habataki cultivar is an Indica variety with higher yields, while the Koshihikari cultivar is a Japonica variety of better quality. In the previous study, 36 metabolites were isolated from the leaves of the Habataki cultivar.20) It is important to investigate organ specificity and benefits of the metabolites for application studies to improve the quality of rice plants. Here, to better understand the organ specificity of the metabolites and their benefits to humans, we performed the metabolite profiling of the leaf, bran, and brown and polished rice grains, using liquid chromatography-quadrupole time-of-flight (LC-QTOF)-MS. In addition, nitric oxide (NO) assay and 1,1-diphe...

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“…Glutamate is a precursor for arginine, spermine, and γ-amino-butyric acid which were related to plant defense (Gill and Tuteja 2010;Huang et al 2011;Kusano et al 2015). Threonine has been conferred as the amino acid that resistant to Hyaloperonospora arabidopsilis, presumably by altering the pathogen's ability to grow under that condition (Stuttmann et al 2011).…”

Section: Resultsmentioning

confidence: 99%

NMR metabolite comparison of local pigmented rice in Yogyakarta

Wijaya

Susanto

Purwestri

et al. 2018

Indones. J. Biotechnol.

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Pigmented rice may have a black or red color due to higher anthocyanin content in its grain. A natural an oxidant, many studies on anthocyanin have reported its posi ve effects on human health. This fact has spurred the development of pigmented rice as a func onal food. This study aimed to compare the metabolite profiles of black and red rice. Three black rice cul vars, namely Melik, Pari Ireng, and Cempo Ireng Sleman, and two red rice cul vars, Inpari 24 and RC 204, were used. A er husk removal, grain samples were ground in liquid nitrogen and dried with a freeze dryer. The dried samples were extracted using 50% MeOD4 (in a D 2 O phosphate buffer pH 6 containing 0.01% TSP as an internal standard). Metabolomic analysis was performed using 500 MHz NMR followed by mul variate data analysis. An orthogonal par al least squares-discriminant analysis (OPLS-DA) model a er PCA was constructed to discriminate between the five different cul vars. The resul ng OPLS-DA score plot revealed a clear separa on between black rice and red rice. The metabolites that could influence the separa on of red rice and black rice were valine, threonine, alanine, glutamate, galac nol, β-glucose, α-glucose, raffinose, and fumaric acid.

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Using Metabolomic Approaches to Explore Chemical Diversity in Rice

Cited by 141 publications

References 117 publications

Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System

Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System

Metabolome Analysis of <i>Oryza sativa</i> (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity

NMR metabolite comparison of local pigmented rice in Yogyakarta

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