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A comparative transcriptome analysis of hybrid necrosis-showing plants in diploid and hexaploid wheat

ABSTRACT: We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in two types of hybrid necrosis-showing plants; one was derived from interspecific crosses of two diploid wheat species Triticum monococcum ssp. aegilopoides and Triticum urartu, and another from intraspecific hybrids of common wheat. Of the up-regulated genes, defense-related and carbohyfrate metabosim-related genes were frequently found, whereas photosythesis-related genes down-regulated in the hybrid necrosis-showing plants. These observations strongly suggests that autoimmune responses might be triggered by Ne1-Ne2 interaction in common wheat and by Ned1-Ned2 interaction in the wild diploid wheat, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in other wheat hybrid necrosis such as type III necrosis in the ABD wheat triploids crossed between tetraploid wheat and Aegilops tauschii.

ORGANISM(S): Triticum aestivum Triticum monococcum subsp. aegilopoides x Triticum urartu

PROVIDER: GSE64342 | GEO | 2014/12/19

SECONDARY ACCESSION(S): PRJNA270772

REPOSITORIES: GEO

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A comparative transcriptome analysis of hybrid necrosis-showing plants in diploid and hexaploid wheat

Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in two types of hybrid necrosis-showing plants; one was derived from interspecific crosses of two diploid wheat species Triticum monococcum ssp. aegilopoides and Triticum urartu, and another from intraspecific hybrids of common wheat. Of the up-regulated genes, defense-related and carbohyfrate metabosim-related genes were frequently found, whereas photosythesis-related genes down-regulated in the hybrid necrosis-showing plants. These observations strongly suggests that autoimmune responses might be triggered by Ne1-Ne2 interaction in common wheat and by Ned1-Ned2 interaction in the wild diploid wheat, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in other wheat hybrid necrosis such as type III necrosis in the ABD wheat triploids crossed between tetraploid wheat and Aegilops tauschii. Expression patterns were compared between a wild-type wheat hybrid plant (as a reference) and a hybrid necrosis-showing hybrid plant in each of common and wild diploid wheat. Total RNA samples were isolated from leaf tissues. Two independent experiments were conducted in each expriment.

2014-12-19 | E-GEOD-64342 | biostudies-arrayexpress

mRNA-Seq for homoeologous gene expression analysis in hexaploid bread wheat

Project description:Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoalleles, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ânullisomic-tetrasomicâ lines) with next generation deep sequencing of gene transcripts (RNA-seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative homoeoallelic contribution to gene expression. We obtained mRNA-Seq datasets from non-normalized cDNA libraries created from shoot and root tissues of the euploid bread wheat cultivar Chinese Spring, from which the nullitetra lines are derived, from complete sets of chromosome 1 and 5 nullitetras, and from extant relatives of the diploid A (Triticum urartu) and D (Aegilops tauschii) genome donors, herein referred to as A and D genome diploids

2014-04-22 | E-MTAB-4223 | biostudies-arrayexpress

Expression profiling of hybrid necrosis in triploid hybrids crossed between tetraploid wheat and Aegilops tauschii

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. Expression patterns were compared between the two synthetic hexaploid lines showing the wild-type phenotype (as a reference) and hybrid necrosis. Total RNA samples were isolated from the 3-week-old seedling leaves. Two independent experiments were conducted.

2010-05-16 | E-GEOD-19613 | biostudies-arrayexpress

Expression profiling of cold-induced hybrid necrosis in triploid hybrids crossed between tetraploid wheat and Aegilops tauschii.

Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in cold-induced hybrid necrosis lines, 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 in the leaves and shoot apical meristem (SAM) of type II necrosis line with low temperature. On the other hand, cell cycle-related genes were highly down-regulated in SAM of type II necrosis line under low temperature. To validate the microarray data, RT-PCR and quantitative RT-PCR analyses for 37selected genes were performed in total. Of the examined 21 up-regulated and 16 down-regulated genes, more than 75% of expression pattern were consistent with the microarray data. Together with cytological analysis of the necrotic tissues, the microarray analysis strongly suggests that an autoimmune response-like reaction and repression of cell division might be triggered by intergenomic incompatibility between the AB and D genomes in type II necrosis. Expression patterns were compared between the two synthetic hexaploid lines showing the wild-type phenotype (as a reference) and cold-induced hybrid necrosis. Total RNA samples were isolated from the 3-week-old seedling leaves. In addition, total RNA were also extracted from the seedling leaves and shoot meristem with 12- and 6-weeks of low temperature, respectively. Two independent experiments were conducted in each exprement.

2010-10-07 | E-GEOD-24566 | biostudies-arrayexpress

Expression profiling of hybrid necrosis in triploid hybrids crossed between tetraploid wheat and Aegilops tauschii

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

[hexa-] Transcriptomic changes in synthetic hexaploid wheat

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

Dysfunction of mitotic cell division at shoot apices triggered severe growth abortion in interspecific hybrids between tetraploid wheat and Aegilops tauschii Coss.

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

[hexa-] Transcriptomic changes in synthetic hexaploid wheat

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 GeneChipÂ® 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

A comparative transcriptome analysis of hybrid necrosis-showing plants in diploid and hexaploid wheat

Project description:A comparative transcriptome analysis of hybrid necrosis-showing plants in diploid and hexaploid wheat

| PRJNA270772 | ENA

Expression profiling of grass-clump dwarf in syntheitic hexaploids from triploid hybrids crossed between tetraploid wheat and Aegilops umbellulata.

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

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