Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA301135 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes. We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-changeââ¥â2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down).
2015-08-30 | E-MTAB-4195 | biostudies-arrayexpress
Project description:In the current study, we characterized an miRNA, OsmiR397, which was found to be associated with increased grain size, more rice panicle branching and higher grain productivity. We also elucidated the molecular mechanisms by which OsmiR397 increased grain yield. This miRNA downregulated the expression of its target gene, OsLAC, which then affected the sensitivity of plants to brassinosteroids. These results should be useful for breeding high-yield crops through genetic engineering. We performed RNA-seq on the young panicles of the wild-type, OXmiR397b and OXLAC plants and found that lots of brassinosteroid-related genes were differentially expressed between the three samples
2013-07-17 | E-MTAB-4429 | biostudies-arrayexpress
Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
2015-08-02 | E-MTAB-4291 | biostudies-arrayexpress
Project description:Differentially expressed genes from different developmantal stages in rice
| PRJNA99403 | ENA
Project description:Differentially expressed genes under different stress conditions in rice
| PRJNA99405 | ENA
Project description:Identification of rice genes differentially expressed upon virulent infection by Magnaporthe grisea
| PRJNA98011 | ENA
Project description:In this study, we investigated novel rice genes that are expressed in aleurone cells by RNA-seq. RNA-seq was performed on four samples: a control sample, and samples treated with ABA, GA, and a mixture of the two hormones.
2013-11-14 | E-MTAB-4443 | biostudies-arrayexpress
Project description:Gibberellins control a wide range of aspects of plant growth and development. Although a series of mutant of the signaling pathway has been identified, the global regulatory network underlying gibberellin signal transduction has not been revealed. To address this issue, we performed microarray analysis with rice gibberellin signaling mutants, gid1, gid2, slr, and the parental cultivar Taichung 65.
2009-04-21 | GSE15046 | GEO
Project description:Cellularization is a key event during the development of the endosperm. Our understanding of the developmental regulation of cellularization has been limited for plants other than Arabidopsis. We found that the activation of OsbZIP76 coincided with the initiation of cellularization of rice. Either knockdown or knockout of OsbZIP76 led to precocious cellularization. Many genes involved in endosperm development or starch biosynthesis were prematurely activated in the caryopsis at two days after fertilization. The results implied that OsbZIP76 is involved in the regulation of cellularization in rice. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity. However, it was able to interact with OsNF-YB9 and OsNF-YB1, two nuclear factor Y (NF-Y) family transcription factors, both in yeast and in planta. OsbZIP76 and OsNF-YB9 showed similar endosperm-preferential expression patterns and the transiently expressed proteins were colocalized in the epidermal cells of tobacco. As with osnf-yb1 mutants, the osbzip76 mutants showed reduced seed size and reduced apparent amylose content of the seeds. We also confirmed that OsbZIP76 is an imprinted gene in rice, the expression of which depended on the genetic background. Our results suggested that OsbZIP76 is an endosperm-expressed imprinted gene to regulate development of the endosperm in rice.
2019-12-28 | GSE139445 | GEO
Project description:DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development. Bisulfite sanger sequencing and qRT-PCR of six differentially methylated genes revealed extensive occurrence of DNA hypomethylation triggered by double fertilization at IAP compared with IBP, suggesting that DNA demethylation might be a key mechanism to activate numerous maternal controlling genes. These results presented here not only greatly expanded the rice methylome dataset, but also shed novel insight into the regulatory roles of DNA methylation in rice seed maternal integument development.
2017-10-10 | GSE95107 | GEO