Rice and Wheat
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA630559 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11744500_1.fastq.gz | Fastqsanger.gz | |||
| SRR11744500_2.fastq.gz | Fastqsanger.gz | |||
| SRR11744600_1.fastq.gz | Fastqsanger.gz | |||
| SRR11744600_2.fastq.gz | Fastqsanger.gz | |||
| SRR11748500_1.fastq.gz | Fastqsanger.gz |
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Project description:Global expression analysis of transcripts in response to salt treatment was carried out for common wheat using oligo-DNA microarrays. Microarrays have been designed from unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of common wheat were treated with 150 mM NaCl for 1, 6 and 24 hours and their roots and shoots were separately subjected to microarray analyses. Consequently, 5996 genes showed changes in expression of more than two-fold, and were classified into 12 groups according to correlations in gene expression patterns. These salt-responsive genes were assigned functions using Gene Ontology (GO) terms. Genes assigned to transcription factor, transcription-regulator activity and DNA binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data on gene expression suggest that multiple signal transduction pathways in response to salt treatment exist in wheat. Salt-responsive transcription factors (TFs), namely AP2/EREBP, MYB, NAC and WRKY, were selected and their expression patterns compared with those of rice. Most showed different expression patterns in wheat and rice in response to salt treatment. Furthermore, comparing the microarray data for wheat and rice, only a small number of genes were up- or down-regulated in common in response to salt treatment. These findings suggest that salt-responsive mechanisms distinct from rice might be present in wheat, and wheat genes can contribute to providing novel gene resources for breeding of salt-tolerant crops. Keywords: time cource, stress response
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Project description:Endophytes from rice and wheat Targeted loci cultured
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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:Global expression analysis of transcripts in response to salt treatment was carried out for common wheat using oligo-DNA microarrays. Microarrays have been designed from unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of common wheat were treated with 150 mM NaCl for 1, 6 and 24 hours and their roots and shoots were separately subjected to microarray analyses. Consequently, 5996 genes showed changes in expression of more than two-fold, and were classified into 12 groups according to correlations in gene expression patterns. These salt-responsive genes were assigned functions using Gene Ontology (GO) terms. Genes assigned to transcription factor, transcription-regulator activity and DNA binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data on gene expression suggest that multiple signal transduction pathways in response to salt treatment exist in wheat. Salt-responsive transcription factors (TFs), namely AP2/EREBP, MYB, NAC and WRKY, were selected and their expression patterns compared with those of rice. Most showed different expression patterns in wheat and rice in response to salt treatment. Furthermore, comparing the microarray data for wheat and rice, only a small number of genes were up- or down-regulated in common in response to salt treatment. These findings suggest that salt-responsive mechanisms distinct from rice might be present in wheat, and wheat genes can contribute to providing novel gene resources for breeding of salt-tolerant crops. Microarray hybridization was performed by a competitive two-color method including color-swap experiments. Chinese Spring wheat was grown for two weeks and treated with 150mM NaCl for 0, 1, 6 and 24 hours. RNA samples were extracted from roots and shoots.
2007-10-02 | E-GEOD-8064 | biostudies-arrayexpress
Project description:Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. However, we recently constructed the first physical map of a wheat chromosome (3B). But gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridized to a barley Agilent 15K expression microarray. This led to the identification of 738 barley genes with a homolog on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.
2010-12-02 | E-TABM-1011 | biostudies-arrayexpress
Project description:The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects.
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Project description:The Affymetrix GeneChip Wheat Genome Array currently provides the most comprehensive coverage of the wheat genome for a microarray. In addition to using this resource for transcript expression studies and hybridization-based DNA marker discovery, we endeavored to use the GeneChip to discover the expression of natural antisense transcript (NAT) pairs. By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. To enable maximum discovery, five different tissue types were selected for assay, and the wheat cultivar ‘Chinese Spring’ was used considering that most of the GeneChip probe sequences were based on sequencing of this genome. [PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tristan Coram. The equivalent experiment is TA21 at PLEXdb.]
2009-06-11 | GSE12528 | GEO
Project description:Rhizoctonia solani is a nectrotrophic fungal pathogen that causes billions of dollars of damage to agriculture worldwide and infects a broad host range including wheat, rice, potato and legumes. In this study we identify wheat genes that are differentially expressed in response to the R. solani isolate, AG8-1, using microarray technology. A significant number of wheat genes identified in this screen were involved in ROS production and redox regulation. Levels of ROS species were increased in wheat root tissue following R. solani infection as determined by NBT, DAB and titanium sulphate measurements/stainings. Pathogen/ROS related genes from R. solani were also tested for expression patterns upon wheat infection. TmpL, a R. solani gene homologous to a gene associated with ROS regulation in Alternaria brassicicola, and OAH, a R. solani gene homologous to oxaloacetate acetylhydrolase which has been shown to produce oxalic acid in Sclerotinia sclerotiorum, were highly induced in R.solani when infecting wheat. We speculate that the wheat germin-like protein (GLP) is induced to inactivate the oxalic acid that is produced by the R. solani OAH.
2015-11-04 | GSE74671 | GEO
Project description:Powdery mildew is a very common plant disease and only few plants are immune. Host interactions have been identified and characterized for the pathosystems barley-B. graminis f. sp. tritici (Bgt) and wheat-B. graminis f. sp. hordei (Bgh), whereas no data are reported about powdery mildew and nonhost plants, such as rice. On the other hand rice nonhost resistance is widely unexploited and only few expression data are available. To characterize rice response during nonhost interaction with Bgh, a global expression analysis was performed by using the GeneChip® Rice Genome Array. To describe rice gene expression profiles during nonhost interaction, 2 week-old rice plantlets were inoculated with Bgh. Treated (inoculated) and control (mock) samples were collected 24 hours post-inoculation for GeneChip® Rice Genome Array hybridization.
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