Optimization of Phenotyping Assays for the Model Monocot Setaria viridis

Choudhury, Swarup Roy; Estelle, Aiden B; Vijayakumar, Anitha; Zhu, Chuanmei; Hovis, Laryssa; Pandey, Sona

doi:10.3389/fpls.2017.02172

Cited by 25 publications

(25 citation statements)

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“…Sterilized Setaria seeds were plated on 0.5 X MS media (Caisson labs, Smithfield, UT, United States) with 0.4% phytagel. Seeds were stratified at 4°C in the darkness for 2 days followed by transfer to the growth chamber maintained at a 12 h (31°C)/ 12 h (22°C) light/dark cycle ( Acharya et al, 2017 ). Germination was defined as protrusion of the radicle from seeds and quantified as the percentage of total seeds at 5 days after plating.…”

Section: Methodsmentioning

confidence: 99%

“…To examine early seedling growth, Setaria seeds sown on 0.5 X MS media plates were stratified at 4°C in the dark for 2 days followed by transfer to the growth chamber with 12 h (31°C)/ 12 h (22°C) light/dark cycle for another 2 days. To evaluate the effect of ABA, glucose or salt (NaCl) on post-germination growth, germinated seeds were transferred on plates containing 2 μM ABA, 3% glucose or 100 mM NaCl ( Acharya et al, 2017 ). Seedlings (20–24 seedlings per genotype per treatment) were grown vertically in the 12 h dark/12 h light cycle and coleoptile and root lengths were measured after 3 days of growth.…”

Section: Methodsmentioning

confidence: 99%

“…To gain a better understanding of the role of type III Gγ proteins, we have overexpressed a monocot codon optimized AGG3 gene in Setaria viridis (green foxtail), a member of the Panicoideae subfamily of grasses which also include food crops like maize and sorghum. The availability of a sequenced genome, efficient transformation system and rapid life cycle with ample seed production makes it an ideal model system for the study of physiological, developmental and yield traits of important grain crops ( Acharya et al, 2017 ). The data presented in this manuscript confirm that the AGG3 gene is functional in Setaria and while some of the traits are indeed positively regulated by constitutive overexpression of AGG3 gene, others might have a more complex regulation, dependent on the presence of specific alleles, genetic background or environmental conditions.…”

Section: Introductionmentioning

confidence: 99%

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Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis

et al. 2018

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Heterotrimeric G-proteins are key regulators of a multitude of growth and development pathways in eukaryotes. Along with the conserved G-protein components found in all organisms, plants have certain novel variants with unique architecture, which may be involved in the regulation of plant-specific traits. The higher plant-specific type III (or Class C) Gγ protein, which possesses a large C terminal extension, represented by AGG3 in Arabidopsis, is one such variant of canonical Gγ proteins. The type III Gγ proteins are involved in regulation of many agronomically important traits in plants, including seed yield, organ size regulation, abscisic acid (ABA)-dependent signaling and stress responses, and nitrogen use efficiency. However, the extant data, especially in the monocots, present a relatively complex and sometimes contradictory picture of the regulatory role of these proteins. It remains unclear if the positive traits observed in certain naturally occurring populations are due to the presence of specific allelic variants of the proteins or due to the altered expression of the gene itself. To address these possibilities, we have overexpressed the Arabidopsis AGG3 gene in the model monocot Setaria viridis and systematically evaluated its role in conferring agriculturally relevant phenotypes. Our data show that AtAGG3 is indeed functional in Setaria and suggest that a subset of the traits affected by the type III Gγ proteins are indeed positively correlated with the gene expression level, while others might have more complex, allele specific regulation.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis

et al. 2018

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“…A CRISPR/Cas9 construct was designed containing two guide (g)RNAs that specifically targeted the first exon of SvFul2 in the highly transformable S. viridis accession, ME034 ( Fig. 4A; (Acharya et al, 2017;Van Eck, 2018). In the T1 generation, individual plants carrying a homozygous 540 bp deletion in the 1st exon of SvFul2 were selected ( Fig.…”

Section: Gene Editing Of Svful2 Validates the Mutant Phenotype In S mentioning

confidence: 99%

SvFUL2, an A-class MADS-box transcription factor, is necessary for inflorescence determinacy in model panicoid cereal,Setaria viridis

Yang

Bertolini

Braud

et al. 2020

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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, yet little is known about the intersecting pathways and how they are rewired during development. 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. Previous reports of A-class genes in cereals have revealed extensive functional redundancy, and in panicoid grasses, no associated inflorescence phenotypes have been described. In S. viridis, perturbation of SvFul2, both through chemical mutagenesis and CRISPR/Cas9-based gene editing, converted a normally determinate inflorescence habit to an indeterminate one, and also repressed determinacy in axillary branch and floral meristems. Our analysis of gene networks connected to disruption of SvFul2 identified regulatory hubs at the intersect of floral transition and inflorescence determinacy, providing insights into the optimization of cereal crop architecture.

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“…Historically, much of the Setaria 65 literature referred to A10 for phenotypic evaluation, which made selecting it for whole 66genome sequencing a logical choice. However, many laboratories have opted to use 67 the S. viridis cultivar ME034V (hereafter referred to as ME034V) due to its exceptionally 68 high transformation efficiency, informally described at greater than 80% infected calli 69 4 giving rise to at least one independent transgenic line (Acharya et al 2017; Zhu et al 70 2017). Given its high transformability and phenotypic similarity to A10, transition to 71 ME034V as the cultivar of choice for research involving genetic modification offers 72 significant advantages by reducing the resources required for time consuming and 73 highly technical transformation protocols.…”

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confidence: 99%

Reference genome for the highly transformableSetaria viridiscultivar ME034V

Thielen

Pendleton²,

Player

et al. 2020

Preprint

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24Setaria viridis (green foxtail) is an important model system for improving cereal crops 25 due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. 26 viridis cultivar ME034V is exceptionally transformable, but the lack of a sequenced 27 genome for this cultivar has limited its utility. We present a 397 Mb highly contiguous de 28 novo assembly of ME034V using ultra-long nanopore sequencing technology (read 29 N50=41kb). We estimate that this genome is largely complete based on our updated k-30 mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 31 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the 32 genome. We compared the ME034V assembly with two other previously sequenced 33Setaria genomes as well as to a diversity panel of 235 S. viridis cultivars. We found the 34 genome assemblies to be largely syntenic, but numerous unique polymorphic structural 35 variants were discovered. Several ME034V deletions may be associated with recent 36 retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low 37 genotype frequencies in the sampled population. Lastly, we performed a phylogenomic 38 analysis to identify gene families that have expanded in Setaria, including those 39 involved in specialized metabolism and plant defense response. The high continuity of 40 the ME034V genome assembly validates the utility of ultra-long DNA sequencing to 41 improve genetic resources for emerging model organisms. Structural variation present 42 in Setaria illustrates the importance of obtaining the proper genome reference for 43 genetic experiments. Thus, we anticipate that the ME034V genome will be of significant 44 utility for the Setaria research community. 45 47 Grasses of the genus Setaria represent diverse species, with phenotypes ranging from 48 the domesticated food crop foxtail millet, S. italica, to its weedy ancestral progenitor, 49 green foxtail, S. viridis (Li and Brutnell 2011). Simple growth requirements, small 50 stature, and short lifecycle make Setaria a tractable monocot model system for studying 51 C4 photosynthesis (Brutnell et al. 2010; Li and Brutnell 2011; Van Eck and Swartwood 52 2015). Furthermore, close phylogenetic relationships with agriculturally important crops 53 such as maize and sorghum promise to inform genetic and cell biology knowledge of 54 other food crops of global importance. Current genome resources for Setaria include a 55 reference genome for S. italica (Bennetzen et al. 2012; Zhang et al. 2012) based on the 56 cultivar Yugu1, a variety of foxtail millet widely grown as a food crop in China. 57 Additionally, a de novo assembly of S. viridis cultivar A10.1 (hereafter referred to as 58 A10) was recently made available alongside low coverage resequencing of more than 59 600 Setaria ecotypes (Huang et al. 2019). 60 61 Efficient genetic modification is a primary requirement for development of any model 62 organism. Approaches for Setaria protoplasting, particle bombardment, and 63...

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Optimization of Phenotyping Assays for the Model Monocot Setaria viridis

Cited by 25 publications

References 83 publications

Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis

Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis

SvFUL2, an A-class MADS-box transcription factor, is necessary for inflorescence determinacy in model panicoid cereal,Setaria viridis

Reference genome for the highly transformableSetaria viridiscultivar ME034V

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