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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis - 70mer

ABSTRACT: Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series Expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for nine different genotypes; B37, B73, B84, Mo17, Oh43, B37xB73, B84xB73, Oh43xB73 and Oh43xMo17.

ORGANISM(S): Zea mays

SUBMITTER: Robert Stupar

PROVIDER: E-GEOD-10542 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.

Stupar Robert M RM Gardiner Jack M JM Oldre Aaron G AG Haun William J WJ Chandler Vicki L VL Springer Nathan M NM

BMC plant biology 20080410

<h4>Background</h4>Heterosis is the superior performance of F1 hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.<h4>Results</h4>We observed th ...[more]

PMID: 18402703

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Gene expression variation among eight maize inbreds - 70mer oligo array

Project description:Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10237). Keywords: Genotype comparison series Expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for eight different inbred lines; B37, B73, B84, Mo17, Oh43, B14a, Wf9 and W22.

2008-02-22 | E-GEOD-10543 | biostudies-arrayexpress

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Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range. These findings indicate that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. Experiment Overall Design: Affymetrix expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for nine different genotypes; B37, B73, B84, Mo17, Oh43, B37xB73, B84xB73, Oh43xB73 and Oh43xMo17.

2008-06-11 | E-GEOD-10236 | biostudies-arrayexpress

Transcription profiling of maize inbred strains

Project description:Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. Many genes exhibit presence-absence variation among the inbred lines. Experiment Overall Design: Affymetrix expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for eight different inbred lines; B37, B73, B84, Mo17, Oh43, B14a, Wf9 and W22.

2008-06-11 | E-GEOD-10237 | biostudies-arrayexpress

Transcription profiling of maize inbred lines B73 and Mo17 leads to additive expression - seedling data

Project description:Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns. Experiment Overall Design: Affymetrix expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for four different genotypes; B73, Mo17, B73xMo17 and Mo17xB73.

2008-06-17 | E-GEOD-8174 | biostudies-arrayexpress

Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series

2008-02-22 | GSE10542 | GEO

2008-01-26 | GSE10236 | GEO

Comparative transcription profiling of heritage maize lines

2012-08-16 | GSE40107 | GEO

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

Project description:Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence. RNA deep sequencing of shoot tissue from four inbreds (B73, B97, Mo18W and M162W) in three conditions 24h control (non-submerged), 24h submerged and 72h submerged.

2015-01-01 | E-GEOD-63429 | biostudies-arrayexpress

Comparative transcription profiling of heritage maize lines

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2012-08-16 | E-GEOD-40107 | biostudies-arrayexpress

Transcription profiling of maize segmental aneuploid to study phenotypic and gene expression changes associated with aneuploidy

Project description:ABSTRACT: BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSIONS: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions. Experiment Overall Design: There are four biological replicates of pooled wild-type siblings and four biological replicates of pooled DpDf plants. The DpDf plants are segmental aneuploids that contain three copies of the short arm of chromosome 5. These plants are all in the B73 inbred genetic background.

2008-06-11 | E-GEOD-10243 | biostudies-arrayexpress

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