Expression profiles of synthetic wheat lines and their parents during amphidiploidization
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ABSTRACT:
PROVIDER: PRJNA236393 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression levels of newly synthetic triploid wheat (ABD), its chromosome-doubled hexaploid (AABBDD), stable synthetic hexaploid (AABBDD), and their parents, Triticum turgidum (accession KU124, AABB) and Aegilops tauschii (accession KU2074, DD) were compared to understand genome-wide change of gene expressions during the course of amphidiploidization and genome stabilization. Stable synthetic hexaploid which were maintained through self-pollinations for 13 generations using the same combinations of the parents for production of synthetic common wheat.
2014-11-30 | GSE54398 | GEO
Project description:Expression profiles of allopolyploids and their parents lines during allopolyploidization
| PRJNA272397 | ENA
Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway. Expression patterns were compared between a synthetic wheat line which treated 24M-bM-^DM-^C and 4M-bM-^DM-^C. Total RNA samples were respectively isolated from leaves and crown tissues of the synthetic line grown at normal temperature for 3 weeks and then at 4M-BM-0C for 12 and 6 weeks. Two independent experiments were conducted in each exprement.
2014-10-10 | E-GEOD-61621 | biostudies-arrayexpress
Project description:RNA-seq data for synthetic hexaploid wheat lines and their corresponding tetraploid and diploid parents
| PRJNA905376 | ENA
Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway.
2014-10-10 | GSE61621 | GEO
Project description:We profiled genome-wide gene expression changes in newly hybridized triploids (ABD), its genome-duplicated hexaploid (AABBDD), stable synthetic hexaploid (AABBDD) and T. turgidum (AABB) and Ae. tauschii (DD) parental lines of two independent crosses to reconstruct the events of allopolyploidization and genome stabilization. Gene expression levels of newly hybridized triploids (ABD), its chromosome-doubled hexaploids (AABBDD), stable synthetic hexaploid (AABBDD) which were selfed during 4 and 13 generations, and their parents, Triticum turgidum (AABB) and Aegilops tauschii (DD) were compared. Total RNA of each line was extracted from three biological replicates of two leaves seedlings except for triploids.For newly hybridized triploids, biological duplicates of two leaves seedlings were used.
2015-08-01 | E-GEOD-64883 | biostudies-arrayexpress
Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison
2010-02-18 | GSE20169 | GEO
Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison 18 arrays - wheat
2010-02-21 | E-GEOD-20169 | biostudies-arrayexpress
Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels.
2011-12-08 | GSE28023 | 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.
2016-03-02 | GSE78784 | GEO