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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent

ABSTRACT: Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes (‘paternal excess’) associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants. Six biological samples: 2xX2x, 2xX4x, 2xX6x, 6xX2x, 4xX2x and fis1X2x. Each non-2xX2x cross was co-hybridised with 2xX2x to a two-colour array (5 arrays). Dyes were then swapped and the hybridisations repeated using an additional 5 arrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Reiner Schulz

PROVIDER: E-GEOD-20006 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix

Project description:Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes (‘paternal excess’) associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants. Two biological replicate samples each of 2xX2x, 2xX4x, 2xX6x, 6xX2x, 4xX2x and fis1X2x and a single sample of msi1. Each sample was hybridised to a separate array.

2010-08-26 | E-GEOD-20005 | biostudies-arrayexpress

Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent

2010-08-26 | GSE20006 | GEO

Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix

2010-08-26 | GSE20005 | GEO

Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds.

Project description:Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. Interploidy crosses disrupt the genome balance in endosperm and alter seed size. Specifically, paternal-excess crosses (2 M-CM-^W 4) delay endosperm cellularization (EC) and produce larger seeds, whereas maternal-excess crosses (4 M-CM-^W 2) promote precocious EC and produce smaller seeds. The mechanisms for responding to the parental genome dosage imbalance and for gene expression changes in endosperm are unknown. In plants, RNA polymerase IV (PolIV or p4) encoded by NRPD1a is required for biogenesis of a major class of 24-nt small interfering RNAs (also known as p4-siRNAs), which are predominately expressed in developing endosperm. Here we show that p4-siRNA accumulation depends on the maternal genome dosage, and maternal p4-siRNAs target transposable elements (TEs) and TE-associated genes (TAGs) in seeds. The p4-siRNAs correlate negatively with expression levels of AGAMOUS-LIKE (AGL) genes in endosperm of interploidy crosses. Moreover, disruption of maternal NRPD1a expression is associated with p4-siRNA reduction and AGL up-regulation in endosperm of reciprocal crosses. This is unique genetic evidence for maternal siRNAs in response to parental genome imbalance and in control of transposons and gene expression during endosperm development. 8 samples: 2x X 2x seed,leaf; 4x X 4x seed,leaf; 2x X 4x seed,leaf; 4x X 2x seed,leaf.

2011-11-11 | E-GEOD-25280 | biostudies-arrayexpress

Seed development

Project description:Reciprocal crosses of a diploid Arabidopsis with different ploidies results in different endosperm development patterns and phenotype. Typically if the ploidy is higher on the maternal side, there are fewer endosperm cells which cellularize early, and conversely, if the paternal ploidy is higher, there is more number of endosperm cells which cellularize late. Crosses involving diploid and tetraploid Arabidopsis (C24) are viable, whereas crosses involving the diploid and hexaploid, even though exhibit the above mentioned directional trend in endosperm development, abort (Scott et al 1998). The 'maternalised' and 'paternalised' development of endosperm is also observed in crosses involving some Arabidopsis mutants. Mutants in the fis class of genes, e.g. fis1-medea, when crossed with a diploid Arabidopsis (pollen parent) show endosperm development-seed development similar to a diploid (seed parent) crossed with hexaploid pollen parent. Reciprocal crosses of homozygous met1 and diploid Arabidopsis also exhibit reciprocal trends in endosperm development, where a homozygous met1 mutant (seed parent) crossed with diploid is similar in phenotype to a diploid (seed parent) - tetraploid cross. Endosperm development in the reciprocal cross has phenotypic similarity to the tetraploid (seed parent)-diploid cross (Adams et al 2000). We are interested in understanding gene profiles and trends in expression underlying the endosperm development in the interploidy crosses as well as the fis and met1 mutant.

2010-01-09 | GSE19259 | GEO

Seed development

2010-01-09 | E-GEOD-19259 | biostudies-arrayexpress

Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds.

Project description:Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. Interploidy crosses disrupt the genome balance in endosperm and alter seed size. Specifically, paternal-excess crosses (2 × 4) delay endosperm cellularization (EC) and produce larger seeds, whereas maternal-excess crosses (4 × 2) promote precocious EC and produce smaller seeds. The mechanisms for responding to the parental genome dosage imbalance and for gene expression changes in endosperm are unknown. In plants, RNA polymerase IV (PolIV or p4) encoded by NRPD1a is required for biogenesis of a major class of 24-nt small interfering RNAs (also known as p4-siRNAs), which are predominately expressed in developing endosperm. Here we show that p4-siRNA accumulation depends on the maternal genome dosage, and maternal p4-siRNAs target transposable elements (TEs) and TE-associated genes (TAGs) in seeds. The p4-siRNAs correlate negatively with expression levels of AGAMOUS-LIKE (AGL) genes in endosperm of interploidy crosses. Moreover, disruption of maternal NRPD1a expression is associated with p4-siRNA reduction and AGL up-regulation in endosperm of reciprocal crosses. This is unique genetic evidence for maternal siRNAs in response to parental genome imbalance and in control of transposons and gene expression during endosperm development.

2011-11-11 | GSE25280 | GEO

Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana

Project description:This SuperSeries is composed of the following subset Series: GSE20005: Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix GSE20006: Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent Refer to individual Series

2010-08-26 | E-GEOD-20007 | biostudies-arrayexpress

Rice interploidy crosses disrupt epigenetic regulation, gene expression, and seed development

Project description:Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures. Here we report that the defective endosperm was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt siRNAs were enriched in the 5’ and 3’ flanking sequences of nonadditively expressed genes in the interploidy crosses and negatively associated with the expression of imprinted genes. Furthermore, some PRC2 gene family members and the genes for DNA methylation including OsMET1b and OsCMT3a were upregulated in the 2X4 cross but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes including starch metabolic and storage protein genes during grain filling were associated with DNA methylation or H3K27me3 and repressed in both 2X4 and 4X2 crosses. WUSCHEL homeobox2 (WOX2)-like (WOX2L), an endosperm-preferred gene, was expressed specifically in the rice endosperm, on contrary to WOX2 expression in the Arabidopsis embryo. CRISPR/Cas9 editing of WOX2L in transgenic rice blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.

2018-08-31 | GSE65149 | GEO

DNA hypomethylation bypasses the interploidy hybridization barrier in Arabidopsis

Project description:Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes are causal for the response to interploidy hybridizations, revealing an epigenetic basis of this phenomenon. In this study we present evidence that paternal hypomethylation can bypass the interploidy hybridization barrier by alleviating the requirement of the epigenetic Polycomb Repressive Complex 2 (PRC2) in the endosperm. Bypass of the barrier is mediated by suppressed expression of imprinted genes. We show that hypomethylated pollen causes redistribution of CHG methylation to PRC2 target genes, revealing that different epigenetic modifications can functionally substitute for each other. Our work presents a method and the underlying mechanism for the generation of viable triploids, providing an impressive example for the potential of epigenome manipulations for plant breeding. Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen, and gene expression in seeds

2014-09-22 | E-GEOD-53642 | biostudies-arrayexpress

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