Transcriptome study of age-related resistance associated with vegetative phase change in Arabidopsis
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PROVIDER: PRJNA860564 | ENA |
REPOSITORIES: ENA
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Project description:To identify transcriptomic signatures for the age-related resistance during vegetative phase change.
2022-07-27 | GSE208657 | GEO
Project description:Vegetative phase change is the developmental transition from the juvenile phase to the adult phase during which a plant becomes competent for sexual reproduction. Gain of ability to flower is often accompanied by changes in patterns of differentiation in newly forming vegetative organs. In maize, juvenile leaves differ from adult leaves in morphology, anatomy, and cell wall composition. Whereas the normal sequence of juvenile followed by adult is repeated with every sexual generation, this sequence can be altered in maize by the isolation and culture of the shoot apex from an adult phase plant; an “adult” meristem so treated reverts to forming juvenile vegetative organs. To investigate the molecular differences between the juvenile and adult phases in maize comparisons among two juvenile samples, leaf 4 and culture-derived leaf 3 or 4, and an adult sample (leaf 9) were made using cDNA microarrays. All samples were leaf primordia at plastochron 6. A gene was scored as “phase specific” if it was up- (or down-) regulated in both juvenile samples compared to the adult sample with at least a twofold-change in gene expression at P-value less than or equal to 0.005. Some 221 ESTs up-regulated in juvenile and 28 ESTs up-regulated in adult were identified. Altered patterns of expression of selected ESTs in the phase change mutants Tp2, d1 and gl15 further confirmed these genes as being phase-specific and allowed us to position these genes in the known genetic hierarchy regulating phase change. Keywords: Transcript profiling among seed-derived juvenile leaf 4 and adult leaf 9 and culture-rejuvenated leaf 3 or 4 in maize
2008-09-01 | GSE9430 | GEO
Project description:Vegetative phase change is the developmental transition from the juvenile phase to the adult phase during which a plant becomes competent for sexual reproduction. Gain of ability to flower is often accompanied by changes in patterns of differentiation in newly forming vegetative organs. In maize, juvenile leaves differ from adult leaves in morphology, anatomy, and cell wall composition. Whereas the normal sequence of juvenile followed by adult is repeated with every sexual generation, this sequence can be altered in maize by the isolation and culture of the shoot apex from an adult phase plant; an âadultâ meristem so treated reverts to forming juvenile vegetative organs. To investigate the molecular differences between the juvenile and adult phases in maize comparisons among two juvenile samples, leaf 4 and culture-derived leaf 3 or 4, and an adult sample (leaf 9) were made using cDNA microarrays. All samples were leaf primordia at plastochron 6. A gene was scored as âphase specificâ if it was up- (or down-) regulated in both juvenile samples compared to the adult sample with at least a twofold-change in gene expression at P-value less than or equal to 0.005. Some 221 ESTs up-regulated in juvenile and 28 ESTs up-regulated in adult were identified. Altered patterns of expression of selected ESTs in the phase change mutants Tp2, d1 and gl15 further confirmed these genes as being phase-specific and allowed us to position these genes in the known genetic hierarchy regulating phase change. Keywords: Transcript profiling among seed-derived juvenile leaf 4 and adult leaf 9 and culture-rejuvenated leaf 3 or 4 in maize To identify juvenile or adult specific ESTs, total RNA from leaf primordia at plastochron 6 (P6) was isolated from leaves 4 (L4) and 9 (L9) from seed-derived plants and leaf 3 or 4 (RL3/4) from culture-derived plants. For each of six biological replications, each of the three pairwise comparisons of P6-staged leaf primordia from L4, L9 and RL3/4 was made on one slide. With six biological replications and three slides per replication (L4 vs. L9, L9 vs. RL3/4, RL3/4 vs. L4), this replicated loop design used a total of 18 slides. To ensure dye balance, each of the 18 target samples was measured once with Cy3 labeling and once with Cy5 labeling.
2010-06-20 | E-GEOD-9430 | biostudies-arrayexpress
Project description:In plants, juvenile to adult phase transition is regulated by the sequential activity of two microRNAs: miR156 and miR172. A decline in miR156 and increase in miR172 abundance is associated with phase transition. There is very limited information on phase transition in economically important horticultural tree crops, which have a significantly long vegetative phase affecting fruit bearing. Here we profiled various molecular cues known to be involved in phase transition and flowering, including the microRNAs miR156 and miR172, in three horticultural tree crops avocado (Persea americana), mango (Mangifera indica) and macadamia (Macadamia integrifolia). We observed that miR156 expression decreases as these trees age and can potentially be used as a juvenility marker. Consistent with findings in annual plants, we also observed conserved regulation of the miR156-SPL3/4/5 regulatory module in these genetically distant tree crops, suggesting that this pathway may play a highly conserved role in vegetative identity. Meanwhile, the abundance of miR172 and its target AP2-like genes, as well as the accumulation level of SPL9 transcripts, were not related with plant age in these crops except in avocado where miR172 expression increased steadily. Finally, we demonstrate that various floral genes, including AP1 and SOC1 were upregulated in the reproductive phase and can be used as potential markers for the reproductive phase transition. Overall, this study provides an insight into the molecular associations of juvenility and phase transition in horticultural trees where crop breeding and improvement is encumbered by long juvenile phases.
2019-05-01 | GSE130476 | GEO
Project description:SVP is a key MADS-box transcription factor for Arabidopsis development since it acts both during vegetative and reproductive phases where it plays different roles probably by interacting with different partners to regulate specific sets of target genes. In fact, whereas SVP functions as a repressor of floral transition during the vegetative phase, it works as floral meristem gene during reproductive phase. We studied the behavior of SVP during two distinct developmental phases: the vegetative and reproductive phase. The aim of these studies is to identify subsets of genes that are regulated by SVP by means of Arabidopsis Tiling 1.0R Arrays (Affymetrix) during the two distinct phases of development.
2013-04-23 | GSE32397 | GEO
Project description:The embryonic temporal regulator FUSCA3 (FUS3) plays major roles in the establishment of embryonic leaf identity and regulation of developmental timing. Loss-of-function mutations of this B3-domain transcription factor result in replacement of cotyledons with leaves and precocious germination, while constitutive misexpression causes the conversion of leaves into cotyledon-like organs and delays vegetative and reproductive phase transitions. To identify downstream targets of FUS3 involved in vegetative phase transitions, we performed microarray analysis on seedlings that transiently activate FUS3 using the AtML1:FUS3-GR-DEX inducible system. Using this construct, FUS3 is ectopically expressed in the ML1 or epidermal layer and becomes activated upon addition of dexamethasone. We found that activation of FUS3 after germination dampens the expression of genes involved in the biosynthesis and response to the plant hormone ethylene, while a loss-of-function fus3 mutant shows many phenotypes consistent with increased ethylene signaling. This FUS3-dependent regulation of ethylene signaling also impinges on timing functions outside of embryogenesis. Loss of FUS3 function results in accelerated vegetative phase change and this is again partially dependent on functional ethylene action. This alteration in vegetative phase transition is dependent on both embryonic and vegetative FUS3 function, suggesting that this important transcriptional regulator controls both embryonic and vegetative developmental timing. This study indicates that the embryonic regulator FUS3 not only regulates the embryonic-to-vegetative phase transition through hormonal regulation, but also functions postembryonically to modulate vegetative phase transitions by negatively regulating ethylene action.
2011-12-11 | E-MEXP-3465 | biostudies-arrayexpress
Project description:In mammals, it is well known that DNA methylation has important roles during aging. However, age-related DNA methylation changes during phase transitions largely remain unclear in plants. Moso bamboo needs a very long time to transition from vegetative to floral phase. To comprehensively investigate the influence of DNA methylation on aging, we present here a distinctive single-base-resolution DNA methylation profile using both high-throughput bisulfite sequencing (BS-Seq) and single-molecule nanopore-based DNA sequencing, which covers the long period of vegetative growth and transition to flowering of moso bamboo’s development. We discovered that CHH methylation gradually accumulated from vegetative to reproductive growth in a time-dependent fashion. Importantly, DMR (differential DNA methylation) correlating with chronological aging occurred preferentially at both transcription start sites (TSS) and transcription termination sites (TTS). Genes with CG methylation changes showed enrichment of gene ontology (GO) categories in ‘vegetative to reproductive phase transition of meristem’. In addition, In combination with mRNA sequencing (RNA-Seq) revealed that DNA methylation in promoter, intron, and exon has different roles in regulating gene expression. Finally, circular RNA sequencing (circRNA-Seq) revealed that flanking introns of circRNAs show hypermethylation. Further analysis revealed that these flanking introns were enriched in LTR-retrotransponsons. Together, observations in this study provide insights about dynamic DNA methylation and circRNAs landscape with chronological ages, which paves the way to further study the impact of epigenetic factors on flowering in moso bamboo.
2021-04-30 | GSE139217 | GEO
Project description:SVP is a key MADS-box transcription factor for Arabidopsis development since it acts both during vegetative and reproductive phases where it plays different roles probably by interacting with different partners to regulate specific sets of target genes. In fact, whereas SVP functions as a repressor of floral transition during the vegetative phase, it works as floral meristem gene during reproductive phase. We studied the behavior of SVP during two distinct developmental phases: the vegetative and reproductive phase. The aim of these studies is to identify subsets of genes that are regulated by SVP by means of Arabidopsis Tiling 1.0R Arrays (Affymetrix) during the two distinct phases of development. Arabidopsis thaliana seedlings and inflorescences were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. To evaluate the amount of SVP expression in the vegetative phase we used svp-41 single mutant and wild-type seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark); for the reproductive phase we used wild-type and svp-41 agl24-2 ap1-12 triple mutant inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.
2013-04-23 | E-GEOD-32397 | biostudies-arrayexpress
Project description:Many plants dramatically elongate their vegetative stems following flowering, yet it is unclear how this response is linked to the reproductive phase. We show that microRNA (miRNA) control of a deeply conserved phase change transcription factor, APETALA (AP2), is required for rapid and complete elongation of stem internodes in barley, especially of the final 'peduncle' internode directly underneath the inflorescence. Disrupted miR172-targeting of AP2 causes leads to short peduncles in the Zeo barley mutant due to reduced cell number and late stage cell expansion, which was associated with lower mitotic activity, delayed growth dynamics and premature lignification. In agreement, multiple, stage and tissue specific comparative transcriptomics revealed decreased expression of proliferation-associated genes, and ectopic expression of maturation-related genes in Zeo1.b. In addition, Zeo1.b peduncles showed persistent, elevated expression of genes associated with jasmonate (JA) and stress responses. Reproductive development including stem elongation in Zeo1.b was hypersensitive to inhibition by methyl JA (MeJA) but less responsive to promotion via gibberellin (GA). Based on these data, we propose that miR172- restriction of AP2 during flowering may release JA-associated vegetative growth restraint in order to facilitate GA-promoted stem growth in the reproductive phase. Microarray experiment M1. Comparison of control Bowman (Bw) and mutant (Zeo1.b) lines in peduncle initials tissue.
2019-05-01 | E-MTAB-7229 | biostudies-arrayexpress
Project description:Many plants dramatically elongate their vegetative stems following flowering, yet it is unclear how this response is linked to the reproductive phase. We show that microRNA (miRNA) control of a deeply conserved phase change transcription factor, APETALA (AP2), is required for rapid and complete elongation of stem internodes in barley, especially of the final 'peduncle' internode directly underneath the inflorescence. Disrupted miR172-targeting of AP2 causes leads to short peduncles in the Zeo barley mutant due to reduced cell number and late stage cell expansion, which was associated with lower mitotic activity, delayed growth dynamics and premature lignification. In agreement, multiple, stage and tissue specific comparative transcriptomics revealed decreased expression of proliferation-associated genes, and ectopic expression of maturation-related genes in Zeo1.b. In addition, Zeo1.b peduncles showed persistent, elevated expression of genes associated with jasmonate (JA) and stress responses. Reproductive development including stem elongation in Zeo1.b was hypersensitive to inhibition by methyl JA (MeJA) but less responsive to promotion via gibberellin (GA). Based on these data, we propose that miR172- restriction of AP2 during flowering may release JA-associated vegetative growth restraint in order to facilitate GA-promoted stem growth in the reproductive phase. Microarray experiment MS. Comparison of control Bowman (Bw) and mutant (Zeo1.b) lines in spike (developing flower) tissue at 21 days post-anthesis.
2019-05-01 | E-MTAB-7228 | biostudies-arrayexpress