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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

ABSTRACT: We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents. Examination of sRNA populations from two-week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal hybrids.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Michael Groszmann

PROVIDER: E-GEOD-25022 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor.

Groszmann Michael M Greaves Ian K IK Albertyn Zayed I ZI Scofield Graham N GN Peacock William J WJ Dennis Elizabeth S ES

Proceedings of the National Academy of Sciences of the United States of America 20110125 6

Intraspecific hybrids between the Arabidopsis thaliana accessions C24 and Landsberg erecta have strong heterosis. The reciprocal hybrids show a decreased level of 24-nt small RNA (sRNA) relative to the parents with the decrease greatest for those loci where the parents had markedly different 24-nt sRNA levels. The genomic regions with reduced 24-nt sRNA levels were largely associated with genes and their flanking regions indicating a potential effect on gene expression. We identified several exa ...[more]

PMID: 21266545

Similar Datasets

sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

Project description:We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents.

2011-01-12 | GSE25022 | GEO

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq

Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of small RNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.

2011-12-22 | E-GEOD-34656 | biostudies-arrayexpress

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq

Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of mRNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.

2011-12-22 | E-GEOD-34655 | biostudies-arrayexpress

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq

Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of DNA methylation by Bisulfite sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.

2011-12-22 | E-GEOD-34657 | biostudies-arrayexpress

Alterations to hormone regulated defense and stress response networks contribute to the greater growth of Arabidopsis F1 hybrids

Project description:Heterosis, or hybrid vigor, has been exploited in agriculture to deliver increases in crop yields for over a century, yet the molecular basis is not well understood We have studied the transcriptomes of 15 day old seedlings from intraspecific Arabidopsis hybrids with varying levels of heterosis and their parental lines in order to identify drivers of heterosis. The patterns of altered gene expression in the hybrids point to a reduction in basal defense levels that could reflect the antagonism between plant immunity and plant growth. Associated with this theme are changes to the salicylic acid and auxin regulated networks which are known to control abiotic and biotic defense responses as well as being important regulators of plant growth. Increased auxin response correlates with the heterotic phenotype of greater leaf cell numbers, whereas reduced salicylic acid levels and response promotes increased leaf cell size in hybrids involving C24. By manipulating salicylic acid levels in each of our hybrid systems, we can alter levels of heterosis, promote additional growth in the hybrids, and generate increased growth in the parents, especially C24. Aerial tissues of 15 days after sowing seedlings from C24, Ler, Col and their reciprocal hybrid offspring. In total 7 biological replicates for both the C24 and Ler parents, 2 biological replicates for Col, 10 biological replicates for C24/Ler and 4 biological replicates for both C24/Col and Col/Ler were sequenced and analysed. Each replicated consisted of a pools of 5-15 seedlings (see publication for more details)

2015-10-01 | E-GEOD-64475 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

| PRJNA134395 | ENA

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq

2011-12-22 | GSE34657 | GEO

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq

2011-12-22 | GSE34656 | GEO

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq

2011-12-22 | GSE34655 | GEO

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids

Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series

2011-12-22 | E-GEOD-34658 | biostudies-arrayexpress

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