RNA-Seq from zmknl1 and WT kernels at 14 DAP (day after pollination) with each two independent biological replicates
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PROVIDER: PRJNA511399 | ENA |
REPOSITORIES: ENA
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Project description:To further understand the basis of the phenotypic defects in the zmknl1 mutant, we performed RNA-Seq from zmknl1 and WT kernels at 14 DAP with each two independent biological replicates. Totally 555 significantly differentially expressed genes (DEGs) were identified according to these RNA-Seq data (q-value <0.05, log2(fold change) >= 1.5), with 317 down- and 238 up-regulated genes.
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Project description:Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced two pericarp cDNA libraries, D20 (20 DAP) of shading treatment, and L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000.
2018-03-30 | E-MTAB-6398 | biostudies-arrayexpress
Project description:Survey of post pollination events in a sexually deceptive orchid (Ophrys fusca): a transcriptional approach Pollination through deception is a widespread phenomenon in angiosperm, and is extremely common in Orchidaceae family. One of the most striking pollination mechanism in orchids is known as sexual deception, in which flowers lure pollinators by foraging chemical (sex pheromones), visual (e.g. labellum colour and/or shape) and tactile (e.g. labellum pilosity) cues of the female insect pollinator. Ophrys has been used as a model genus to study sexual deception mechanism, mainly regarding chemical analysis in plant-insect association. Study was focused on Ophrys fusca, a species widely distributed in Mediterranean Basin. The main objective rely on Ophrys fusca gene expression study after pollination, through a transcriptional approach using cDNA microarrays. In order to evaluate pollination enhanced events, two different time points were selected: 2 days and 4 days after pollination. Ophrys fusca plants were sampled from a Portuguese natural occurring population. Plants were covered with a white and inert net, built specially for preventing pollinator’s visits in both pollinated and unpollinated flowers. Cross- pollination was performed manually with a sterile plastic stick. Five biological replicates (5 plants in each replicate) from each condition (pollinated and unpollinated) were collected in each time-point Flowers that demonstrate strict pollination regulation, as orchids, provide an excellent model system to unravel pollination- elicited mechanisms (i.e. petal senescence, pigmentation changes, ovary growth). Therefore, this study aims to contribute to the overall knowledge on orchid pollination biology, which is still lacking.
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Project description:Transcriptome profiles of MATZ and BETL tissues are compared across three stages of development. Sugars and other nutrients unloaded from vascular tissues in the MATZ are imported by the BETL for utilization by the developing endosperm. Pronounced changes in gene expression occur in both tissues during kernel development. RNAseq data were obtained from duplicate tissue samples isolated by cryomicrodissection of developing maize kernels at three developmental time points; 8 days post-pollination (DAP), 14 DAP and 20 DAP.
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Project description:Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis; The fresh kernel samples of each inbred line were collected on DAP 24, DAP 35 days, respectively. Mature kernel samples were harvested after all the plants turned yellow. Three biological replicates of each sample were collected, and total RNA with high quality was pooled and sent for sequencing. Total RNA of high quality was pooled for transcriptome analysis, and raw RNA-seq data of DAP 24, DAP35 and mature kernels for both two inbred lines were obtained. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, ρ-ABA branch, serine/THF/5-M-THF cycle and the conversion of tetrahydrofolate monoglutamate to tetrahydrofolate polyglutamate; The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.
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Project description:In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. We observed a gradual increase of paternal gene mRNAs in the 3- and 5-DAP kernels. In the 7-DAP endosperm, the majority of the tested genes reached a ratio of 2m:1p suggesting that paternal genes were nearly fully activated by 7 DAP. A total of 116, 234 and 63 imprinted genes exhibiting parent-specific expression were identified in the 7-, 10-, and 15-DAP endosperms, respectively. The highest amount of paternally expressed genes (PEGs) was found at 7 DAP mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP which were primarily attributed to the sharply increased expression levels compared to the other stages. GO enrichment analysis of the imprinted genes indicated the 10-DAP-specific MEGs were involved in the nutrient uptake and allocation through auxin signaling pathway in the maize endosperm coincident with the endosperm developmental stage associated with the beginning of starch and storage protein accumulation The unpollinated kernels (0 DAP), the kernels of 3, 5 DAP and endosperms of 7 10, 15 DAP from the B73 and Mo17 reciprocal crosses were used to perform high-throughput sequencing using the Illumina HiSeq2000 platform
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Project description:Kernel development is accompanied by complex gene networks. Expression quantitative trait loci (eQTL) analysis is an efficient way to detect the regulatory elements of genes, especially the trans-eQTLs help to construct the regulatory networks of genes and contribute to a better understanding of the intrinsic mechanisms of biological processes. Till now, the 15 DAP (day after pollination) eQTL has been elucidated in maize kernel, but little is known about the early stage. Here, we conduct eQTL analysis for 5 DAP maize kernel using 318 maize inbred lines. The results will provide insights into the genetic basis of early kernel development.
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