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Setaria viridis

ABSTRACT: Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

PROVIDER: PRJNA391704 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5750472.fastq.gz	Fastqsanger.gz
	SRR5750473.fastq.gz	Fastqsanger.gz
	SRR5750474.fastq.gz	Fastqsanger.gz
	SRR5750475.fastq.gz	Fastqsanger.gz
	SRR5750476.fastq.gz	Fastqsanger.gz

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The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis

Project description:Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture. Here, we show that a single mutation in a gene encoding an AP1 A-class MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis.

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Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

Project description:RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.

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Leaf transcriptome analysis of Setaria viridis MPA1 RNAi plants

Project description:This experiment was conducted to investigate the effect of RNAi of MPA1 on the global leaf transcriptome of Setaria viridis.

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A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics

Project description:Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

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Setaria viridis (A10.1) circadian expression after light or temperature entrainment

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Pleiotropic and Non-redundant Effects of an Auxin Importer in Setaria and Maize

Project description:Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

2022-01-13 | GSE193344 | GEO

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Project description:Setaria viridis (green millet) is gaining popularity as a model C4 monocot due to its small size, rapid life cycle, and compact, sequenced genome. To analyze the structure and regulation of genes throughout development, the transcriptomes of 13 tissues at different stages of development were determined by RNA sequencing, and transcription start sites were mapped. Genes were identified that are differentially expressed in different developmental stages within the leaf, as well as in the apical meristem before and after the transition from vegetative to reproductive growth, and in panicles before and after anthesis. In a majority of genes, transcription initiated at the sequence YR within a narrow peak 20 – 40 nt downstream of a TATA box. Genes expressed in multiple tissues generally use the same transcription start site across all tissue types. Several introns were identified that increase gene expression. These results will increase understanding of plant development, improve the annotation of the Setaria genome, and provide tissue-specific or constitutive promoters for use in transgenic applications.

2017-11-14 | GSE89855 | GEO

High Light and High Temperature Reduce Photosynthetic Efficiency via Different Mechanisms in the C4 Model Setaria viridis

Project description:C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour HL or HT treatment at the photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in HL- or HT-treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to HL and HT. We provide a systematic analysis of HL and HT responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.

2021-08-01 | GSE178320 | GEO

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