Oryza sativa
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PROVIDER: PRJNA162671 | ENA |
REPOSITORIES: ENA
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Project description:Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars
| PRJNA215708 | ENA
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari. Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biological replicate in each small open top chamber - seed; pooled) were used, and dye-swaped.
2013-08-20 | E-GEOD-49963 | biostudies-arrayexpress
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2012-05-01 | GSE37650 | GEO
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2013-08-20 | GSE49963 | GEO
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2012-04-30 | E-GEOD-37650 | biostudies-arrayexpress
Project description:Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage. Ozone induced gene expression in rice inflorescence meristem was measured at 6 month after exposure to dose of 43.7 nL L-1 (ambient air) and 85.7 nL L-1 (2-fold concentration compared to ambient air) (12 hours mean). The two culticars, Sasanishiki and Habataki, were used for each experiment.
2015-01-31 | E-GEOD-65465 | biostudies-arrayexpress
Project description:Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage.
2015-01-31 | GSE65465 | GEO
Project description:As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.
2012-02-19 | GSE31077 | GEO
Project description:As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment. Whole plants of two rice cultivars Zhonghua11 (low temperature sensitive) and Hanfeng (low temperature tolerance) were treated at 14°C for 2 days during seed development stage. The plants without treatment serve as controls. Rice seeds were harvested for RNA extraction.
2012-02-19 | E-GEOD-31077 | biostudies-arrayexpress
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq. Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays. Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy. Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-05-07 | GSE174017 | GEO