Gene expression variation among eight maize inbreds
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE10237 | GEO | 2008/01/26
SECONDARY ACCESSION(S): PRJNA108413
REPOSITORIES: GEO
Similar Datasets
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
2008-02-22 | GSE10543 | GEO
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
Project description:Genome-wide transcriptomics experiment (RNA-seq) on proliferative tissue of eight maize inbred lines (A632, B73, B96, F7, H99, HP301, Mo17, W153R). These inbreds are used as parents in a funnel breeding design to generate an advanced recombinant maize population.
2015-06-29 | E-MTAB-3173 | biostudies-arrayexpress
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
Project description:Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection. Methylation profiles in seedling tissue of the maize inbred lines B73 and Mo17. Each genotype was compared for three biological replications using a gene-focused custom 2.1M NimbleGen array.
2011-11-21 | E-GEOD-29099 | biostudies-arrayexpress
Project description:Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection.
2011-11-21 | GSE29099 | GEO
Project description:Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize. meDIP-chip analysis of four maize tissues identifed few tissue-specific DNA methylation variable regions (tDMRs), whereas hundreds of genotype-specific DMRs were identified that were conserved across tissues.
2012-08-27 | GSE38503 | GEO
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. Keywords: genotype comparison
2007-06-21 | GSE8179 | GEO
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. Keywords: genotype comparison
2007-06-21 | GSE8174 | GEO
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. Keywords: genotype comparison
2007-06-21 | GSE8176 | GEO