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Transcriptomic analyses indicate that ligule initiation recapitulates gene expression patterns that occur at lateral branching

ABSTRACT: Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.

ORGANISM(S): Zea mays

PROVIDER: GSE61333 | GEO | 2014/09/12

SECONDARY ACCESSION(S): PRJNA260793

REPOSITORIES: GEO

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Transcriptomic analyses indicate that ligule initiation recapitulates gene expression patterns that occur at lateral branching

Project description:Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia. In this study, we analysed the transcriptome associated with ligule formation using laser microdissection RNA-sequencing (LM-RNAseq). We quantified transcript accumulation in the PLB and adjacent pre-blade and pre-sheath regions of wild-type leaf primordia in order to identify candidate genes involved in proximal-distal patterning at the blade-sheath boundary. We also compared transcript accumulation in lg1-R mutants and wild-type siblings to identity genes acting downstream of LG1.

2014-09-12 | E-GEOD-61333 | biostudies-arrayexpress

Spatio-temporal transcriptional profiling of leaf development in rice

Project description:Rice leaves consist of three distinct regions along a proximal-distal axis, namely, the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, however,but the genetic programs underlying the development of each region are poorly understood. To capture the entire picture of rice leaf development and to discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages.

2020-10-06 | GSE159047 | GEO

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy

Project description:Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit âKranzâ anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.

2013-07-29 | E-MTAB-4134 | biostudies-arrayexpress

Genome-wide gene expression profiling of rice Zhonghua11 and ila1 lamina joint

2012-05-01 | GSE33361 | GEO

Arabidopsis thaliana strain:Landsberg erecta Transcriptome or Gene expression

Project description:To study cell type-specific gene expression in the leaf boundary region in the genome scale, we employed the TRAP-seq approach recently implemented. In brief, we introduced a reporter line carrying the fusion of the large subunit ribosomal protein L18 with N-terminal His and FLAG epitope tags (HF-RPL18) under the control of the pOp promoter into driver lines expressing the chimeric TF LhG4 under the control of the LATERAL SUPPRESSOR (LAS) promoter, and under the control of the ASYMMETRIC LEAVES1 (AS1) promoter. These driver lines were chosen because pLAS::LhG4 has boundary region-specific activity (Goldshmidt et al, 2008), and pAS1::LhG4 drives pOp reporter expression throughout emerging leaf primordia, but not in the SAM. Cell type-specific expression of HF-RPL18 can efficiently incorporate epitope tags into polysomes for immunopurification of all translating cellular mRNAs. We immunopurified polysomes from seedlings at 7 days after germination (DAG), to isolate translating mRNA in the LAS-expressing organ boundary cells and AS1-expressing leaf primordia and cotyledon cells. Then, we used deep sequencing to map and quantify these mRNA samples.

2015-02-07 | E-MTAB-4423 | biostudies-arrayexpress

Setaria viridis small RNAs from panicle tissues

Project description:A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).

2018-07-28 | GSE111490 | GEO

Genome-wide gene expression profiling of rice Zhonghua11 and ila1 lamina joint

Project description:The leaf lamina joint joins the rice leaf blade and sheath, contributing significantly to the leaf angle trait. A more erect leaf facilitates the penetration of sunlight, enhancing photosynthetic efficiency and occupying less space in dense planting. Genetic screening found a mutant increased leaf angle1, ila1 from rice T-DNA insertional mutants library. We used microarrays to detail the transcriptional profile changes in the mutant ila1 lamina joint. Two biological replicate sample of leaf lamina joints from the ila1 and wild-type plants at tillering stage were collected for RNA extraction. Total RNAs were isolated from each replicate via the TRIzol method (Invitrogen) and used in target synthesis for the Rice Genome Array from Affymetrix. The microarray analyses were performed through following standard protocols (Affymetrix).

2012-04-30 | E-GEOD-33361 | biostudies-arrayexpress

Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice

Project description:An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting. A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.

2011-01-13 | E-GEOD-21396 | biostudies-arrayexpress

Transcriptome sequencing of the developing internode and ligular region of maize mutant Sdw3

Project description:The reduced plant height and enlarged leaf angle of Sdw3 are mainly attributed to a reduction in longitudinal cell elongation in the internode and an increase in the auricle. To investigate the transcriptome changes during internode and auricle development in Sdw3 versus N18, we performed RNA sequencing analysis.

2020-07-08 | GSE127448 | GEO

ZmDCT2 has a major role in the photosynthetic development of maize

Project description:We sequenced mRNA from from four segments along a developing 9 day old third maize leaf of WT W22 accession and ZmDCT2 KO (in W22 background - dct2-1::Ac) plants, to identify changes in gene expression in dct2-1::Ac as a response to the loss of ZmDCT2 function. The segments were referenced relative to the position of the ligule of leaf 2 as this point represents the source-sink boundary in a wild-type leaf and the transition from shaded leaf tissue to fully light exposed. Segment -4 was isolated at the base of the leaf blade that is photosynthetically inactive, -1, defined as the sink to source transition zone (just below the point of leaf emergence from the whorl), segment +4, from a fully light exposed and photosynthetically active region in the mid-leaf (maturation zone), and +10, the tip of the leaf and the terminally differentiated tissue

2015-08-30 | E-GEOD-67722 | biostudies-arrayexpress

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