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APETALA2‐like transcription factor in shoot architecture and perennial traits

ABSTRACT: 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.

ORGANISM(S): Arabis alpina

PROVIDER: GSE145718 | GEO | 2021/01/26

REPOSITORIES: GEO

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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 | GSE145716 | GEO

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

2021-01-26 | GSE145715 | 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

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

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)

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2020-03-01 | GSE126944 | GEO

RNA-Seq analysis of adventitious rooting zone of Arabis alpina main stem during extended cold exposure.

Project description:Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximise fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4 °C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4 °C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developingin specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.

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Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

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2012-12-31 | E-GEOD-38894 | biostudies-arrayexpress

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

Project description:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found the BSs that were conserved in both species, and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

2018-01-01 | GSE89889 | GEO

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Project description:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 17% of their BSs were conserved in both species and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

2018-01-01 | GSE89638 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsPEP1 Ri1 transgenic line in response to exogenous PEP1 Transcriptomes

Project description:We used the NGS techonoly to compare the gene’s transcripts at rice whole genome levels of the WT (XS134) and OsPEP1 Ri1 transgenic line in response to the exogenous PEP1 signal. We found that the expgenous PEP1-mediated signal were blocked in OsPEP1 Ri1 transgenic line, but the application of exogenous PEP1 could restore this PEP1-mediated signal to the WT (XS134) level.

2021-12-31 | GSE173487 | GEO

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