Transcriptomic analysis of maize developing earshoot, B73 X Mo17 hybrid
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE17932 | GEO | 2010/01/14
SECONDARY ACCESSION(S): PRJNA119869
REPOSITORIES: GEO
Similar Datasets
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. B73 X Mo17 is a model maize hybrid. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology. B73 X Mo17 hybrid_developing earshoot microarray data: Technical replicates, no biological replicates
2010-01-13 | E-GEOD-17932 | biostudies-arrayexpress
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. Intermated B73 X Mo17 recombinant inbred lines (IBMRIL) belong to a predominantly used mapping population. Illinois high protein (IHP) line is a metabolic extreme with respect to nitrogen mebolism with around 30% seed protein. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology. IBMRIL population was crossed to IHP to find the allelic interaction related to nitrogen metabolism. Microarray experiment was conducted using the developing earshoots from IBMRIL X IHP1 lines that deffered in their grain yield significantly. Keywords: Yield response
2010-02-04 | GSE17953 | GEO
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. Intermated B73 X Mo17 recombinant inbred lines (IBMRIL) belong to a predominantly used mapping population. Illinois high protein (IHP) line is a metabolic extreme with respect to nitrogen mebolism with around 30% seed protein. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology. IBMRIL population was crossed to IHP to find the allelic interaction related to nitrogen metabolism. Microarray experiment was conducted using the developing earshoots from IBMRIL X IHP1 lines that deffered in their grain yield significantly. Keywords: Yield response Technical replicates, dye swaps, technical replicates of dye swaps, no biological replicates
2010-02-03 | E-GEOD-17953 | biostudies-arrayexpress
Project description:We aim to examine defense transcript changes in maize stems following elicitation with heat-killed Fusarium hyphae in B73 and Mo17.
2020-07-08 | GSE138962 | GEO
Project description:Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. To investigate the allele-specific DNA methylation pattern of maize endosperm on a genome-wide scale, we performed MethylC-seq for shoot, embryo, and endosperm tissue 12 d after pollination (DAP) of inbred B73, and the endosperm tissue 12 DAP of reciprocal crosses B73 Ã Mo17 (BM) and Mo17 Ã B73 (MB). We also performed additional RNA-seq for samples from 12-DAP and 10-DAP endosperm of both reciprocal crosses between inbreds B73 and Mo17
2013-10-17 | E-MTAB-4206 | biostudies-arrayexpress
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 immature ear tissue from maize. Three biological replicates were performed for four different genotypes; B73, Mo17, B73xMo17 and Mo17xB73.
2008-06-16 | E-GEOD-8176 | biostudies-arrayexpress
Project description:Following the domestication of maize over the past 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.
2009-11-20 | GSE16938 | 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. Experiment Overall Design: Affymetrix expression profiling was used to study gene expression in 19 day after pollination embryo tissue of maize. Three biological replicates were performed for four different genotypes; B73, Mo17, B73xMo17 and Mo17xB73.
2008-06-16 | E-GEOD-8179 | biostudies-arrayexpress
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: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