The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size
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ABSTRACT:
PROVIDER: PRJNA478446 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7450892_1.fastq.gz | Fastqsanger.gz | |||
| SRR7450892_2.fastq.gz | Fastqsanger.gz | |||
| SRR7450893_1.fastq.gz | Fastqsanger.gz | |||
| SRR7450893_2.fastq.gz | Fastqsanger.gz | |||
| SRR7450894_1.fastq.gz | Fastqsanger.gz |
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Project description:The APETALA2-like transcription factor SUPERNUMERARY BRACT confers seed shattering by positively regulating qSH1 and SH5, while altering seed size by modulating longitudinal cell elongation in rice glumes.
2018-06-29 | GSE116422 | GEO
Project description:The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size
2020-04-01 | E-GEOD-116422 | ExpressionAtlas
Project description:The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in theArabidopsis thalianaecotypes Col-0 and C24. These CNS lines differ only in the nuclear genome (imprinting) or in the cytoplasm. The CNS reciprocal hybrids with the same cytoplasm display a ∼20% seed size difference as observed in the conventional hybrids. However, seed size is similar between the reciprocal cybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection have identified 104 maternally expressed genes (MEGs) and 90 paternally-expressed genes (PEGs). These imprinted genes are involved in pectin catabolism and cell wall modification in the endosperm.HDG9, an epiallele and one of 11 cross-specific imprinted genes, controls seed size. In the embryo, a handful of imprinted genes is found in the CNS hybrids but only one is expressed higher in the embryo than endosperm.AT4G13495encodes a long-noncoding RNA (lncRNA), but no obvious seed phenotype is observed in the lncRNA knockout lines.NRPD1, encoding the largest subunit of RNA Pol IV, is involved in the biogenesis of small interfering RNAs. Seed size and embryo is larger in the cross usingnrpd1as the maternal parent than in the reciprocal cross. In spite of limited ecotypes tested, these results suggest potential roles of imprinting andNRPD1-mediated small RNA pathway in seed size variation in hybrids.
2024-06-05 | GSE249562 | GEO
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
2023-10-16 | GSE203310 | GEO
Project description:Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) encodes a membrane protein that links the ethylene perception to transcriptional regulation. Interestingly, during seed development EIN2 is maternally-expressed in Arabidopsis and maize, but the role of EIN2 in seed development is unknown. Here we show that EIN2 is expressed specifically in the endosperm, and the maternal-specific EIN2 expression affects temporal regulation of endosperm cellularization. As a result, seed size increases in the genetic cross using the ein2 mutant as the maternal parent or in the ein2 mutant. The maternal-specific expression of EIN2 in the endosperm is controlled by DNA methylation but not by H3K27me3 or by ethylene and several ethylene pathway genes tested. RNA-seq analysis in the endosperm isolated by laser-capture microdissection show upregulation of many endosperm-expressed genes such as AGAMOUS-LIKEs (AGLs) in the ein2 mutant or when the maternal EIN2 allele is not expressed. EIN2 does not interact with DNA and may act through ETHYLENE INSENSITIVE3 (EIN3), a DNA binding protein present in sporophytic tissues, to activate target genes like AGLs, which in turn mediate temporal regulation of endosperm cellularization and seed size. These results provide mechanistic insights into endosperm and maternal-specific expression of EIN2 on endosperm cellularization and seed development, which could help improve seed production in plants and crops.
2022-10-12 | GSE147587 | GEO
Project description:Comparison of gene expression profiles of wild-type and apetala2 inflorescences. This series contains the data for three replicate experiments performed with three sets of biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wild type-Cy5 mutant-Cy3 Set 2: wild type-Cy3 mutant-Cy5 Set 3: wild type-Cy5 mutant-Cy3 Keywords: repeat sample
2004-05-02 | GSE1266 | GEO
Project description:Comparison of gene expression profiles of wild-type and apetala2 inflorescences. This series contains the data for four replicate experiments performed with four sets of biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wild type-Cy3 mutant-Cy5 Set 2: wild type-Cy5 mutant-Cy3 Set 3: wild type-Cy3 mutant-Cy5 Set 4: wild type-Cy5 mutant-Cy3 Keywords: repeat sample
2004-05-02 | GSE1271 | GEO
Project description:Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size
| PRJNA839397 | ENA
Project description:Arabidopsis APETALA2 (AP2) encodes a member of the AP2/EREBP (ethylene responsive element binding protein) class of transcription factors and is involved in the specification of floral organ identity, establishment of floral meristem identity, suppression of floral meristem indeterminancy, and development of the ovule and seed coat. Here, we show that loss-of-function ap2 mutations cause an increase in seed mass relative to that of wild-type seeds. Analysis of an allelic series of ap2 mutations showed that increases in seed mass corresponded with the severity of defects in flower structure, indicating that AP2 activity directly influences seed mass. Experiments with male-sterile plants and deflowered wild-type plants showed that reduced fertility of ap2 mutant plants due to abnormal flower structure accounted for only part of the increase in seed mass caused by strong ap2 mutant alleles. Reciprocal cross experiments showed that AP2 acts maternally to control seed mass. The maternal effect of AP2 on seed mass involves the regulation of both embryo cell number and cell size. We show further that ap2 mutations cause changes in the ratio of hexose to sucrose during seed development, opening the possibility that AP2 may control seed mass through its effects on sugar metabolism. Together, these results identify a role for AP2 in controlling seed mass.
| S-EPMC549491 | biostudies-literature
Project description:microRNA172 targets APETALA2 to regulate anthocyanin biosynthesis
| PRJNA725146 | ENA