Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1025149 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26315400_1.fastq.gz | Fastqsanger.gz | |||
| SRR26315400_2.fastq.gz | Fastqsanger.gz | |||
| SRR26315401_1.fastq.gz | Fastqsanger.gz | |||
| SRR26315401_2.fastq.gz | Fastqsanger.gz | |||
| SRR26315402_1.fastq.gz | Fastqsanger.gz |
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Project description:OsPSTOL1 confers phosphorus (P)-deficiency tolerance in rice through enhancement of early root growth. The larger root surface area at early stage provides the plants an advantage for nutrient uptake. We conducted microarrays to determine the genes which are constitutively regulated by OsPSTOL1, independent of P supply and developmental stage. For Affymetrix microarrays, root RNA samples from IR64 35S::OsPSTOL1 plants (transgenic: T) and Nulls (non-transgenic: NT) grown in P-deficient soil +/- application of P fertilizer were used. Plants were at the reproductive/heading stage (- P treatment) and at mid-tillering (+P treatment), respectively.
2012-09-01 | E-GEOD-38871 | biostudies-arrayexpress
Project description:Objective: In order to study the change law of Chinese fir gene expression caused by fertilization, it provides scientific basis for Chinese fir fertilization theory and practice. Method: Using Illumina HiSeq4000 high-throughput sequencing technology, sequencing sequences of four different fertilizer treatment materials (control CK1, nitrogen treatment N1, phosphorous treatment P1, and phosphorous and nitrogen mixture treatment NP1, each with three biological repeats) were obtained, and a series of comparative analysis of the differences were conducted. The experimental material was the 1-year clone cuttings of Chinese fir K62. At the end of 2017year, sand culture experiment was carried out in the plastic greenhouse of research institute of subtropical forestry,CAF. Because it was transcriptome sequencing without reference genome , sequencing reads need to be spliced into de novo, unigene and transcripts are assembled, and then functional annotation, differential expression and other project analysis are conducted. Result: In 12 samples, transcriptome sequencing produced clean reads5.0E+07nt to 7.1E+07nt, and the total splicing length was 724,341,090nt. BLASTX analysis was performed on clean reads in six databases (Nr, Swiss-prot,eggNOG, ,KEGG, Pfam, GO), and 74,288 genes were generated；The Venn diagram reveals the general overview of the gene response of different fertilization treatments: in the N1-VS-CK1 comparison group, NH4NO3 stimulation induced the opening expression of 3,295 genes, and CK1 produced 2,944 genes resistant to nitrogen; Similar results were obtained for other comparison groups. Chinese fir fertilization turns on and up-regulates the expression of some genes while shutting down or down regulating some genes of expression; Analysis of gene differential expression revealed that :720 differentially expressed genes were screened out in the N1-VS-CK1 comparison group, and 3,694 genes were found to be silenced by nitrogen application. Similar results were obtained in the other five groups: a number of differentially expressed genes were screened out, and a number of genes were silenced by nitrogen and phosphorus fertilizer; The results of the heatmap clustering graph of the six comparison groups were revealed that the genes between the same treatment and the same comparison group are basically distributed in blocks: either high expression or low expression, and vice versa. The gene distribution between different treatments in the same comparison group was complementary. To fertilize Chinese fir, it is better to mix fertilizer with different types of fertilizers; The GO enrichment and functional classification has three major categories, namely, biological process BP, cell component CC and molecular function MF, with 50 small categories; Fertilization, whether single fertilizer or multiple fertilizers, has the greatest impact on the GO terms of Chinese fir: chloroplasts, cytoskeleton, cell membrane, nucleus and cytoplasm. secondly molecular function, protein binding and biological process are affected. These results revealed that nitrogen and phosphorus can promote the absorption and metabolism of themselves and each other; KEGG enrichment analysis was performed in 6 comparison groups, and the most significant first 5 Pathway KEGG terms were selected in each comparison group, the comprehensive analysis results showed that after fertilizing Chinese fir, the most significant KEGG term was photosynthesis, nitrogen metabolism, carbon fixation and carbon metabolism, plant hormone signal transduction, plant-pathogen interaction, phenylpropanoid biosynthesis, pentose-phosphate pathway, porphyrin and chlorophyll metabolism, arginine biosynthesis and ect. Based on the above studies, the significantly up-regulated or down-regulated genes in important terms obtained by GO enrichment and classification and KEEG enrichment can be studied, and the results can guide the diagnosis of Chinese fir fertilization. Conclusion: Illumina HiSeq4000 transcriptome sequencing is a quick and cheap way to study the molecular mechanisms of non-model plants, including coniferous trees with large genomes. Chinese fir fertilization can not only turn on some genes, but also turn off some genes. The growth and development of Chinese fir will be regulated in a way that is favorable for its adaptation to the environment, competitive resources and growth and development.
2019-01-12 | GSE121245 | GEO
Project description:Improvement of phosphorus (P) uptake by crops is a prerequisite for sustainable agriculture. Rice (Oryza sativa L.) PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) increases root growth and total P uptake. Here, a biogeographic survey of rice demonstrates OsPSTOL1 loss in a subset of japonica rice after the temperate-tropical split and frequent absence in paddy varieties of east Asia. OsPSTOL1 absence or loss-of-function alleles prevail in landraces from regions with fertilizer use and controlled irrigation, suggesting it is an adaptive genetic variant in low nutrient rainfed ecosystems. OsPSTOL1 is a truncated member of a family of multi-module kinases associated with microbial interactions. We demonstrate that ectopic expression of OsPSTOL1 in wheat (Triticum aestivum L.) increases shoot and root growth under low P conditions, promotes root plasticity, and hastens induction of the low P response pathway. OsPSTOL1’s influence on adaptive root development in wheat validates its potential for broad utilization in crop improvement.
2023-08-30 | GSE185875 | GEO
Project description:Chinese fir (Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus (LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity, proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups (CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software, 607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.
2020-12-20 | GSE113410 | GEO