Juvenility and Vegetative Phase Transition in Tropical/Subtropical Tree Crops.
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ABSTRACT:
PROVIDER: PRJNA540425 | ENA |
REPOSITORIES: ENA
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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
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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:Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under water deficit stress condition.<br><br>
2014-10-11 | E-MEXP-3992 | biostudies-arrayexpress
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
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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:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
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Project description:To identify transcriptomic signatures for the age-related resistance during vegetative phase change.
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