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RNAseq analysis of Arabis alpina buds in the dormant zone (V2) and buds in the growing zone (V3) at the end of vernalization (+0) and 5 days later (+5d)

ABSTRACT: Arabis alpina, similar to woody perennials, has a complex architecture with a zone of axillary vegetative branches and a zone of dormant buds that serve as perennating organs. We show that floral development during vernalization is the key for shaping the dormant bud zone by facilitating a synchronized and rapid growth after vernalization and thereby causing an increase in auxin transport, response and endogenous indole-3-acetic acid (IAA) levels in the stem. Floral development during vernalization is associated with the development of axillary buds in subapical nodes. Our transcriptome analysis indicated that these buds are not dormant during vernalization but only reach sustained growth after the return to warm temperatures. Floral and subapical vegetative branches grow after vernalization and inhibit the development of the buds below. Dormancy in these buds is regulated across the A. alpina life cycle by low temperatures and by apical dominance in a BRANCHED 1 dependent mechanism.

ORGANISM(S): Arabis alpina

PROVIDER: GSE126944 | GEO | 2020/03/01

REPOSITORIES: GEO

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Keep a distance to be different: axillary bud initiating at a distance to the shoot apical meristem are crucial for the perennial life style of Arabis alpina

Project description:Purpose: In higher plants, perennialism is achieved through axillary buds and side-shoots that stay vegetative. This work aims to analyze the pattern of axillary bud (AB) formation in the perennial model plant Arabis alpina and to study the role of LATERAL SUPPRESSOR (AaLAS) gene in this process. Methods: This study combines stereomicroscopic analysis with RNA sequencing to monitor how patterns of AB formation and gene expression correlate. The role of AaLAS was studied using an RNAi approach. Results: During vegetative development, ABs initiate at a distance to the SAM, whereas after induction of flowering ABs initiate adjacent to the SAM. Dormant buds are established before onset of vernalization. Transcript profiles of ABs initiated at a distance were different from that of the SAM, whereas transcript patterns of buds initiated in close proximity were similar to the corresponding SAM. Knock-down of AaLAS leads to loss of both dormant buds and vegetative side-shoots, strongly compromising perennial life style. Conclusions: AB formation is regulated differently during vegetative and reproductive development. New meristems that show gene expression profiles different from the SAM are established at a distance to the SAM. AaLAS plays an essential role in perennial life cycle modulating the establishment of dormant buds and vegetative side-shoots.

2020-03-03 | GSE140316 | GEO

Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina

Project description:Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone ehxibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth.

2020-06-14 | GSE152417 | GEO

RNAseq analysis of Arabis alpina buds in the dormant zone (V2) and buds in the growing zone (V3) at the end of vernalization (+0) and 5 days later (+5d)

Project description:RNAseq analysis of Arabis alpina buds in the dormant zone (V2) and buds in the growing zone (V3) at the end of vernalization (+0) and 5 days later (+5d)

| PRJNA523826 | ENA

Transcriptomic analysis implicates ABA signalling and carbon supply in the differential outgrowth of petunia axillary buds

Project description:Shoot branching of flowering plants exhibits phenotypic plasticity and variability. This plasticity is determined by the activity of axillary meristems, which in turn is influenced by endogenous and exogenous cues such as nutrients and light. In many species, not all buds on the main shoot develop into branches despite favorable growing conditions. In petunia, basal buds (buds 1-3) typically do not grow out to form branches, while more apical buds (buds 6 and 7) are competent to grow. The genetic regulation of buds was explored using transcriptome analyses of petunia axillary buds at different positions on the main stem. To suppress or promote bud outgrowth, we grew the plants in media with differing phosphate (P) levels. Using RNA-seq, we found many (>5000) differentially expressed genes between bud 6 or 7, and bud 2. In addition, more genes were differentially expressed when we transferred the plants from low P to high P medium, compared with shifting from high P to low P medium. Buds 6 and 7 had increased transcript abundance of cytokinin and auxin-related genes, whereas the basal non-growing buds (bud 2 and to a lesser extent bud 3) had higher expression of strigolactone, abscisic acid, and dormancy-related genes, suggesting the outgrowth of these basal buds was actively suppressed. Consistent with this, the expression of ABA associated genes decreased significantly in apical buds after stimulating growth by switching the medium from low P to high P. Furthermore, comparisons between our data and transcriptome data from other species suggest that the suppression of outgrowth of bud 2 was correlated with a limited supply of carbon to these axillary buds. Candidate genes that might repress bud outgrowth were identified by co-expression analysis.

2023-07-26 | GSE237985 | GEO

Total proteome of germinative and dormant axillary buds of the sugarcane cultivar RB867515

Project description:Sugarcane is the raw material for the production of ethanol and sugar, and its by-products are used in cogeneration of energy in addition to various industrial processes. The cane field establishment is dependent of the axillary buds sprouting. The present study aimed to catalog the total proteome of germinative axillary bud and dormant axillary buds, and to identify important budding proteins, which are differentially expressed in these types of axillary buds. The proteome was obtained by extraction of total proteins using the TCA acetone method adapted for axillary buds. The experiment was carried out in biological triplicate. Protein samples were submitted to denaturing polyacrylamide gel electrophoresis (SDS-PAGE) and stained with comassie blue. Each lane of the polyacrylamide gel was fractionated (11 slice) and treated for purification and isolation of the polypeptides. Tryptic digestion was performed on each fragment with subsequent UPLC separation (Nano Acquity). The polypeptides were analyzed on Waters® Micromass® ESI-Q-Tof micro ™ mass spectrometer. Protein samples from the germinative and dormant axillary buds showed distinct bands patterns in the SDS-PAGE gel. Mass spectrometry data were analyzed by MASCOT tool (http://www.matrixscience.com).

2019-08-04 | PXD008008 | JPOST Repository

Beyond flowering time: diverse roles of an APETALA2‐like transcription factor in shoot architecture and perennial traits

Project description:Polycarpic perennials maintain vegetative growth after ﬂowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) inArabis alpina regulates ﬂowering and contributes to polycarpy in a vernalisation-dependent pathway. pep1 mutants do not require vernalisation to ﬂower and have reduced return to vegetative growth as all of their axillary branches become reproductive. To identify additional genes that regulate ﬂowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping-by-sequencing, we cloned a mutant (enhancer of pep1-055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild-type allele. eop055 ﬂowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)-like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a ﬂoral repressor and acts upstream of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 5 (AaSPL5). In the wild-type background, which requires cold treatment to ﬂower, AaTOE2 regulates the age-dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing ﬂowering of axillary buds before and during cold exposure. We conclude that AaTOE2 is instrumental in ﬁne tuning different developmental traits in the perennial life cycle of A. alpina.

2021-01-26 | GSE145715 | GEO

APETALA2‐like transcription factor in shoot architecture and perennial traits

2021-01-26 | GSE145718 | GEO

Beyond flowering time: diverse roles of an APETALA2‐like transcription factor in shoot architecture and perennial traits

2021-01-26 | GSE145716 | GEO

Photoperiod induction of endodormancy in Vitis riparia axillary buds.

Project description:This study compares age matched V. riparia axillary buds at one time point during long photoperiod (paradormancy maintenance) and short photoperiod (endodormancy induced). Keywords: endodormancy, photoperiod, paradormancy, grape, axillary bud

2005-08-05 | GSE3052 | GEO

Discovering differentially expressed genes in early floral buds of SlREVRis overexpression line and wild type in tomato

Project description:Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato. 1-2 mm floral buds at stage 6-8 were sampled from three individual plants of 35S::REVRis-1 and corresponding WT control. Three aliquots of RNA from transgenic or WT plants were pooled. Then, the digital expression profile were generated by Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.).

2014-06-10 | E-GEOD-58305 | biostudies-arrayexpress

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