Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and OsNF-YB1 RNAi plants Transcriptomes
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE72185 | GEO | 2016/12/16
SECONDARY ACCESSION(S): PRJNA293280
REPOSITORIES: GEO
Similar Datasets
Project description:OsNF-YB1 is a transcription factor that plays important roles during rice grain filling. OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and OsNF-YB1 RNAi lines showed retardation in grain filling and produced small grains with chalky endosperm as well as the altered starch quality. To reveal the transcriptional regulatory framework of OsNF-YB1, we determined OsNF-YB1 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 933 binding peaks distributed 743 neighbor genes. OsNF-YB1 directly regulates genes involved in nutrient transport including sugar and amino acids, and interestingly, different from the reported binding site of NF-Y complex, the GCC-box (a binding motif of ERF transcription factors) was enriched in the binding peaks of OsNF-YB1.
2016-12-16 | GSE72186 | GEO
Project description:Grain development is a key life cycle stage of many plants. The development of seeds is the basis of agriculture and the primary source of calories consumed by humans. Here, we employ laser micro dissection (LMD) combined with shotgun proteomics to generate a cell-type proteome atlas of developing wheat endosperm at the early and late grain filling stages. We identified 1803 proteins from four different cell layers (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE), and endosperm transfer cells (ETCs)) of developing endosperm at 15 Days after anthesis (DAA) and 26 DAA. Sixty-seven differentially expressed proteins in the aleurone, 31 in the sub-aleurone, 27 in the starchy endosperm, and 50 in the endosperm transfer cells were detected between these two-time points. The results revealed highly distinguishable proteome dynamics in the different cell layers of endosperm over the time course. We observed high general metabolic activity of the grain with regard to carbohydrate metabolism, defence against oxidative stress, and signalling in the different cell layers during the grain filling process. Cell-specific identification of SUT and GLUT transporters suggest a grain filling model via nucellar projections and endosperm transfer cells (ETCs) initiating starch biosynthesis in the starchy endosperm (SE). The identification and regulation dynamics of proteins in the different cell layers demonstrate a functional switch of the proteome from the early to the late grain filling stage. Based on these data, we proposed a model for sugar loading and starch biosynthesis in wheat developing endosperm, including an abundance switch of cell-type-specific key proteins.
2024-12-11 | PXD035848 | Pride
Project description:Heat stress occurrence during endosperm development and seed filling forms chalky portion in the limited zone of starchy endosperm of rice grains. In this study, isolation of aleurone, dorsal, central and lateral tissues of developing endosperm by laser-microdissection (LM) coupled with gene expression analysis of 44K microarray was performed to identify key regulatory genes involved in the formation of milky-white (MW) and white-back (WB) chalky grains during heat stress. Gene regulatory network analysis classified the genes changed under heat stress into five modules. the modules of genes changed in developing starchy endosperm corresponding to MW and WB portion under heat stress suggested different regulatory genes involved in each type of grain chalk. The most distinct expression pattern was observed in a M1 and M2 modules where most of the small heat shock proteins and cellular organisation genes being upregulated under heat stress in dorsal aleurone cells and dorsal starchy endosperm zones The histological observation supported the significant increase in cell number and size of dorsal aleurone cells in WB grains. With regard to the central zone of starchy endosperm, preferential downregulation of high molecular weight heat shock proteins (HMW HSPs) including a prominent member encoding for endoplasmic reticulum (ER) chaperones by heat stress were observed, while expression of starch-biosynthesis genes remained unaffected. Characterization of transgenic plants supressing endosperm lumenal binding protein (BiP1), an ER chaperone preferentially downregulated at MW portion under heat stress, showed an evidence of forming the chalky grains without disturbing the expression of starch-biosynthesis genes. The present LM-based comprehensive expression analyses provides novel inferences that HMW HSPs play important role in controlling the redox, nitrogen and amino aicd metabolism in endosperm leading to the formation of MW and WB chalky grains.Keywords ; developing endosperm, gene expression, grain chalkiness, heat stress, laser-microdissection, Oryza sativa.
2018-12-10 | GSE122115 | GEO
Project description:Aleurone layer differentiation completes by 9 DAF, and most of the nutrient filling occurs between 6-21 DAF, (Wu et al., 2016a, 2016b), so we decided to use 10 DAF time point for collection of pericarp, aleurone, embryo and endosperm tissues for RNA-Seq analysis. Since aleurone is mostly single layer, and it’s almost impossible to separately collect pure pericarp and aleurone layers manually, so firstly we developed a method to collect different tissue types of developing grain through LCM and RNA extraction and Sequencing
2021-10-28 | GSE149118 | GEO
Project description:Favorable grain filling ability is crucial for seed development and plant yield1, with less fertilizer applying is the most urgent goals to meet the growing demands of green and safe food. However, the balance mechanism between grain filling and nutrient elements is still unclear so far. Here, we describe a gene GAF1, specially expressed in endosperm aleurone layer, encoding a phosphate transporter, positively controls rice grain filling and seed development and also contributes to phosphate balance was mapped in our study. To study the regulation pattern of GAF1, we performed the RNA-seq analysis of NIL-GAF1 and NIL-gaf1 at middle grain filling stage in seeds. The data shows that many pathways related to starch and sugar metabolism were enriched, and many starch synthesis related genes and phosphate response genes were up-regulated or down-regulated. These data further support that seed specific expressed GAF1 plays a key role in regulating both phosphate homeostasis and seed development. More importantly, overexpression of GAF1 can significantly improve grain filling and thus yield enhanced plant production in field.
2021-02-02 | GSE149101 | GEO
Project description:Hordeum vulgare (barley) hordoindolines (HINs), HINa, HINb1 and HINb2, are orthologous proteins of wheat puroindolines (PINs) that are small, basic, cysteine-rich seed-specific proteins and responsible for grain hardness. Grain hardness, is, next to its protein content, a major quality trait. In barley, HINb is most highly expressed in the mid-stage developed endosperm and is associated with both major endosperm texture and grain hardness. However, data required tounderstand the spatio-temporal dynamics of HIN transcripts and HIN protein regulation during grain filling processes are missing. Using reverse transcription quantitative PCR (RT-qPCR) and proteomics we analyzed HIN transcript and HIN protein abundance from whole seeds (WSs) at four ((6 days after pollination (dap), 10 dap, 12 dap and ≥ 20 dap)) as well as from aleurone, subaleurone and starchy endosperm at two (12 dap and ≥ 20 dap) developmental stages. At the WS level, results from RT-qPCR, proteomics and western blot showed a continuous increase of HIN transcript and HIN protein abundance across these four developmental stages. Miroscopic studies revealed HIN localization mainly at the vacuolar membrane in the aleurone, at protein bodies (PBs) in subaleurone and at the periphery of starch granules in the starchy endosperm. Laser microdissetion (LMD) proteomic analyses identified HINb2 as the most prominent HIN protein in starchy endosperm at ≥ 20 dap. Additionally, our quantification data revealed a poor correlation between transcript and protein levels of HINs in subaleurone during development. Here, we correlated data achieved by RT-qPCR, proteomics and microscopy that reveal different expression and localization pattern of HINs in each layer during barley endosperm development. This indicats a contribution of each tissue to the regulation of HINs during grain filling. The effect of the high protein abundance of HINs in the starchy endosperm and their localization at the periphery of starch granules at late development stages at the high end-product quality is discussed. Understanding the spatio-temporal regulated HINs is essential to improve barley quality traits for high end-product quality, as hard texture of the barley grain is regulated by the ratio between HINb/HINa.
2018-07-02 | PXD009708 | Pride
Project description:Exogenous spermidine promotes starch sugar metabolism in wheat grains, thereby promoting grain filling
2019-08-14 | GSE135536 | 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:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Keywords: time course
2007-12-20 | GSE9365 | GEO
Project description:Barley (Hordeum vulgare) is one of the major food sources for humans and forage source for animal livestock. Barley endosperm is structured into three distinct cell layers: the starchy endosperm, which acts essentially as storage tissue for starch, the subaleurone, which is characterized by a high accumulation of endoplasmic reticulum (ER)-derived seed storage proteins (SSP) and finally the aleurone beside the seed coat with a prominent role during seed germination. Prolamins account for more than 50% of the total protein amount in mature seeds. Together with other seed storage proteins (SSPs) they are important for both grain quality and flour quality. Prolamins are synthesized on the rough ER, translocated into the ER lumen and accumulate in distinct, ER-derived protein bodies (PBs) that are most abundant in the SE. PB formation is regulated by the protein disulfide isomerase (PDI) that is involved in the disulfide transfer pathway. Here, we used laser microdisection (LMD) to characterize spatio-temporal molecular and morphological differences of the ER during barley endosperm development. We revealed by nanoLC-MS/MS proteomic analyses performed on whole seeds and collected tissues at different seed development stages that the protein level of the protein disulfide isomerase HvPDIL1-1 is spatio-temporally regulated in developing barley endosperm. Our microscopic studies showed that HvPDIL1-1 preferentially accumulates in SE, especially at 12 days after pollination (dap). HvPDIL1-1 re-localized from PBs to the protein matrix at the periphery of starch granules along grain filling process. Detailed analysis of SE proteome dynamics identified clusters of proteins with similar expression pattern as HvPDIL1-1, which were analysed in a protein-protein network. It revealed a strong functional interconnection between transcription and translation, protein folding and amino acid synthesis with sucrose and starch metabolism. Our data indicate a role of HvPDIL1-1 in the coordination of protein synthesis and prolamins deposition during grain filling processes in developing barley endosperm. These results are discussed in relation to the putative role of HvPDIL1-1 for cereal food end-product quality and recombinant protein production in cereal seeds.
2018-10-01 | PXD009710 | Pride