Tetraploid wheat NLRs
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ABSTRACT:
PROVIDER: PRJEB34907 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a quantitative proteomic analysis of immature spikes harvested from tetraploid near-isogenic lines of wheat with normal spikelete (NSs), FRSs, and RSs and investigated the molecular mechanisms of lateral meristem differentiation and development. This work provides valuable insight into the underlying functions of the lateral meristem and how it can produce differences in the branching of tetraploid wheat spikes.
2018-10-19 | PXD008910 | Pride
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype.
2016-03-02 | GSE78784 | GEO
Project description:Wheat is a cereal grain and one of the world’s major food crops. Recent advances in wheat genome sequencing are by now facilitating genomic and proteomic analyses of this crop. However, little is known about the protein levels of hexaploid versus tetraploid wheat cultivars, and knowledge on phosphorylated proteins still limited. Using our recently established (phospho)proteomic workflow, we performed a parallel analysis of the proteome and phosphoproteome on seedling leaves from two hexaploid wheat cultivars (Pavon 76 and USU-Apogee) and a tetraploid wheat (Senatore Cappelli). This revealed that a large portion of proteins and phosphosites can be quantified in all cultivars. Our shotgun proteomics data revealed a high similarity between hexaploid and tetraploid varieties with respect to protein abundance. However, we could identify a set of proteins that were differentially abundant between hexaploid and tetraploid cultivars. In addition, already at seedling stage, a small set of proteins were differential between the small (USU-Apogee) and larger hexaploid wheat cultivar (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.
2017-04-03 | PXD005437 | Pride
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in a grass-clump dwarf line, which is a synthetic hexaploid line from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon) and a diploid wheat relative Aegilops umbellulata (KU-4052). Up-regulation of metabolic and catabolic processes-related genes for cell wall-associated molecules was observed, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf line. Unusual expression of the branching-related SPLs and flowering time regulation-related MADS-box genes could explain the grass-clump dwarf phenotype.
2017-01-24 | GSE93969 | GEO
Project description:Common wheat is an allohexaploid species, derived through endoreduplication of an inter-specific triploid hybrid produced from a cross between cultivated tetraploid wheat and the wild diploid relative Aegilops tauschii Coss. Hybrid incompatibilities, including hybrid necrosis, have been observed in triploid wheat hybrids. A limited number of Ae. tauschii accessions show hybrid lethality in triploid hybrids crossed with tetraploid wheat due to developmental arrest at the early seedling stage, which is termed severe growth abortion (SGA). Despite the potential severity of this condition, the genetic mechanisms underlying SGA are not well understood. We conducted comparative analyses of gene expression profiles in crown tissues to characterize developmental arrest in triploid hybrids displaying SGA. A number of defense-related genes were highly up-regulated, whereas many transcription factor genes, such as the KNOTTED1-type homeobox gene, which function in shoot apical meristem (SAM) and leaf primordia, were down-regulated in the crown tissues of SGA plants. Transcript accumulation levels of cell cycle-related genes were also markedly reduced in SGA plants, and no histone H4-expressing cells were observed in the SAM of SGA hybrid plants. Our findings demonstrate that SGA shows unique features among other types of abnormal growth phenotypes, such as type II and III necrosis.
2011-11-01 | GSE33357 | GEO
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype. Expression patterns were compared between the three synthetic hexaploid lines showing the wild-type phenotype (as a reference) and grass-clump dwarf. Total RNA samples were isolated from crown tissues of the plants grown at 24°C under long day (18-h light and 6-h dark) condition for 8 weeks. Two independent experiments were conducted in each exprement.
2016-03-02 | E-GEOD-78784 | biostudies-arrayexpress
Project description:Hybrid chlorosis, one of the hybrid incompatibilities, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In our previous study, hybrid chlorosis was observed in the wheat triploids between a tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we performed cytological and comparative gene expression analyses in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis symptom. In addition, disease resistance was comparatively assessed. A number of carbohydrate metabolism- and defense-related genes were markedly up-regulated in the hybrid chlorosis lines, and abnormal chloroplasts were formed in the mesophyll cells before the leaves turned to be yellowish. The mild chlorosis plants showed increased resistance to a wheat blast fungus, although little significant differences of agricultural traits were found between the wild-type and mild chlorosis-showing plants. These observations suggest that the senescence processes might be accelerated in the hybrid chlorosis lines of wheat synthetics. Moreover, the negative effects on biomass can be minimized and the substantial fitness may be obtained under pathogen-polluted conditions in the mild chlorosis-showing wheat synthetics.
2014-08-12 | GSE59640 | GEO
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in hybrid necrosis-showing plants, which are triploid hybrids crossed between tetraploid wheat and diploid wheat progenitor Aegilops tauschii. Of the up-regulated genes, defense-related genes were most frequently found, whereas photosythesis-related genes down-regulated in the type I necrosis line. To validate the microarray data, RT-PCR and quantitative RT-PCR analyses for 22 selected genes were performed. Of the examined 15 up-regulated and 7 down-regulated genes, the expression pattern of only one down-regulated gene was inconsistent with the microarray data. Together with cytological analysis of the necrotic tissues, the microarray analysis strongly suggests that an autoimmune response might be triggered by intergenomic incompatibility between the AB and D genomes in type I necrosis, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in Arabidopsis intraspecific and Nicotiana interspecific hybrids.
2009-12-23 | GSE19613 | GEO
Project description:Allopolyploidy, entailing whole genome duplication (WGD) of merged divergent genomes of different species, often instigates transcriptome shock, whereby both total gene expression level and homeolog expression partitioning can be disrupted and remodeled. Little is known about the extent to which the parental expression-conserved genes will be disrupted/remodeled by allopolyploidization, nor the evolutionary relevancy of shock-induced expression repatterning. Here, by microarray-based gene expression profiling and gene-specific cDNA-pyrosequencing, we assessed transgenerational transcriptome shock in a synthetic allotetraploid wheat (AT2) with karyotype and basic morphology mimicking those of natural tetraploid wheat, Triticum turgidum. We show that the transcriptome shock in AT2 is exceptionally strong that it disrupted intrinsically conserved parental gene expression, and resulted in extensive expression nonadditivity in the newly formed allotetraploid plants. At total expression level, a substantial proportion of shock-induced novel expression, especially over-transgressive expression, was rapidly stabilized already in early generations of AT2. Extensive remodeling of homeolog expression occurred in AT2, including those genes that showed additive total expression, and which generated subgenome expression dominance, a pattern that mirrors T. turgidum. Thus, the shock-induced new patterns of gene expression at both the total expression level and subgenome homeolog partitioning showed evidence of evolutionary persistence. Complex relationships between homeolog expression remodeling and nonadditive total expression were observed in a tissue-specific manner.
2016-02-12 | GSE65844 | GEO
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in SGA plants, which are triploid hybrids crossed between tetraploid wheat and a diploid wheat relative Aegilops umbellulata. Of the up-regulated genes, cell death and carboxy-lyase activity-related genes were the most frequently found in crown tissues of SGA plants. On the other hand, photosynthesis-related genes were highly down-regulated in crown tissues of SGA plants. In addition, transcript accumulation levels of shoot apical meristem (SGA)-related genes such as knotted-1 like homeobox (Knox) genes were also repressed in SGA plants. The microarray analysis strongly suggests that an autoimmune response-like reaction might be triggered by intergenomic incompatibility between the AB and U genomes in SGA. In addition, SAM-related and cell cycle-related genes were dramatically down-regulated in crown tissues of SGA, indicating that abnormalities of SAM are associated with the abnormal growth phenotypes in SGA.
2017-01-24 | GSE93943 | GEO