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Rice developing ovary at 10 days after flowering

ABSTRACT: Proteome analysis of developing grain in indica rice "Naba" (S1) and "Puluik Arang" (S2). Ovary samples at 10 days after flowering were used.

ORGANISM(S): Oryza Sativa

SUBMITTER: Naoki Hirotsu

PROVIDER: PXD015105 | JPOST Repository | Fri Oct 18 00:00:00 BST 2019

REPOSITORIES: jPOST

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Dataset's files

Source:

			Action	DRS
	S1.MGF	Mgf
	S1.mzid	Mzid
	S1.raw	Raw
	S2.MGF	Mgf
	S2.mzid	Mzid

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1 - 5 of 6

Publications

Expression regulation of myo-inositol 3-phosphate synthase 1 (INO1) in determination of phytic acid accumulation in rice grain.

Perera Ishara I Fukushima Ayaka A Akabane Tatsuki T Horiguchi Genki G Seneweera Saman S Hirotsu Naoki N

Scientific reports 20191016 1

Phytic acid (PA) is the primary phosphorus (P) storage compound in the seeds of cereals and legumes. Low PA crops, which are considered an effective way to improve grain nutrient availability and combat environmental issues relating to seed P have been developed using mutational and reverse genetics approaches. Here, we identify molecular mechanism regulating PA content among natural rice variants. First, we performed genome-wide association (GWA) mapping of world rice core collection (WRC) acce ...[more]

PMID: 31619750

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Transcriptomes of developing rice ovules

Project description:We aimed to reveal transitions of gene expression profile in developing female gametophytes of rice in this study. The developmental process of rice female gametophyte, from megaspore mother cell at pre-meiotic stage to mature embryo sac, was separated into six stages. Developing ovules at each stage were separated from surrounding sporophyte tissues and collected using LMD. RNA samples extracted from them were subjected to microarray analysis. Dynamic gene expression profiles during female gametogenesis were revealed. Comparison of transcriptome in developing female gametophytes with those of male gametophyes revealed both conserved and diverged features between male and female gametogenesis. A lot of characteristic genes, such as a subset of transposable elements, auxin responsive genes and transcription factor genes, which showed dynamic expression profiles during female gametogenesis, were identified in this study. We believe that our transcriptome data will serve as a backbone of further focused biological analysis to understand the molecular basis in female gametogenesis of plant.

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Transcriptomes of developing rice ovules

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Gel-free/label-free proteomic analysis of developing rice grains under heat stress

Project description:High temperature markedly reduces the yields and quality of rice grains. To identify the mechanisms underlying heat stress-induced responses in rice grains, proteomic technique was used. Khao Dawk Mali 105 rice grains at the milky, doughy, and mature stages of development after flowering were treated at 40 °C for 3 days. Aromatic compounds were decreased in rice grains under heat stress. The protein abundance involved in glycolysis and tricarboxylic acid cycle, including glyceraldehyde 3-phosphate dehydrogenase and citrate synthase, was changed in milky and doughy grains after heat treatment; however, no changes in mature grains. The abundance involved in amino acid metabolism was increased in doughy grains, but decreased in milky grains. In addition, the abundance involved in starch and sucrose metabolism, such as starch synthase, ADP-glucose pyrophosphorylase, granule-bound starch synthase, and alpha amylase, was decreased in milky grains, but increased in doughy grains. A number of redox homeostasis-related proteins, such as ascorbate peroxidase and peroxiredoxin, were increased in developing rice grains treated with heat stress. These results suggest that in response to heat stress, the abundance of numerous proteins involved in redox homeostasis and carbohydrate biosynthetic pathways may play a major role in the development of KDML105 rice grains.

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Protein acetylation landscape of developing rice anthers

Project description:Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification, playing important biological roles in many organisms.Here, we reported results from a proteomic investigation to detect KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during rice anther development and meiosis. We identified a total of 1,354 KAC sites in 676 proteins.

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RNA-seq analysis of developing rice seeds under combined heat and drought stress

Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.

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Deep Transcriptional Profiling of Rice Using Illumina's Sequencing By Synthesis Technology

Project description:Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like ‘massively parallel signature sequencing (MPSS)’ and ‘Sequencing by Synthesis’ (SBS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). Illumina’s SBS technology can generate large amounts of sequence data in a short time at low cost compared to traditional Sanger sequencing based methods. Using the MPSS technology, we previously analyzed the transcriptomes of 72 rice tissues. To validate the sequencing results from MPSS technology, we employed SBS technology and constructed SBS libraries from 32 rice tissues (47 libraries including replications). For SBS library construction, we used the same mRNA samples and same restriction enzyme (DpnII) that were used for the construction of the MPSS libraries. These libraries include six abiotic-stress libraries, eight pathogen-infected libraries, five insect-damaged libraries, three developing seed libraries, and 10 untreated rice tissue libraries. This study was carried out with the following objectives; a) Identification and quantification of expressed genes in rice at all developmental stages of plant growth, response to biotic and abiotic stresses, and developing seeds; b) Compare SBS signatures with rice genomic sequence to identify novel transcripts; c) To validate the transcriptional data obtained through MPSS technology; and To create query and analysis tools to facilitate public use of and access to rice MPSS and SBS data and to display abundance and chromosomal locations of rice MPSS and SBS signatures. The SBS data will be available at http://mpss.udel.edu/rice_sbs/.

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