Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives

Characterizing serotonin biosynthesis in Setaria viridis leaves and its effect on aphids

A combined transcriptomic and metabolic analysis of Setaria viridis leaves responding to aphid infestation was used to identify genes related to serotonin biosynthesis. Setaria viridis (green foxtail), a short life-cycle C4 plant in the Poaceae family, is the wild ancestor of Setaria italica (foxtail millet), a resilient crop that provides good yields in dry and marginal land. Although S. viridis has been studied extensively in the last decade, the molecular mechanisms of insect resistance in this species remain under-investigated. To address this issue, we performed a metabolic analysis of S. viridis and discovered that these plants accumulate the tryptophan-derived compounds tryptamine and serotonin. To elucidate the defensive functions of serotonin, Rhophalosiphum padi (bird cherry-oat aphids) were exposed to this compound, either by exogenous application to the plant medium or with artificial diet bioassays. In both cases, exposure to serotonin increased aphid mortality. To identify genes that are involved in serotonin biosynthesis, we conducted a transcriptome analysis and identified several predicted S. viridis tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) genes. Two candidate genes were ectopically expressed in Nicotiana tabacum, where SvTDC1 (Sevir.6G066200) had tryptophan decarboxylase activity, and SvT5H1 (Sevir.8G219600) had tryptamine hydroxylase activity. Moreover, the function of the SvTDC1 gene was validated using virus-induced gene silencing in S. italica, which caused a reduction in serotonin levels. This study provides the first evidence of serotonin biosynthesis in Setaria leaves. The biosynthesis of serotonin may play an important role in defense responses and could prove to be useful for developing more pest-tolerant Setaria italica cultivars.

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a 'loss of shattering' trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.

Divergent gene expression networks underlie morphological diversity of abscission zones in grasses

Abscission is a process in which plants shed their parts, and is mediated by a particular set of cells, the abscission zone (AZ). In grasses (Poaceae), the position of the AZ differs among species, raising the question of whether its anatomical structure and genetic control are conserved. The ancestral position of the AZ was reconstructed. A combination of light microscopy, transmission electron microscopy, RNA-Seq analyses and RNA in situ hybridisation were used to compare three species, two (weedy rice and Brachypodium distachyon) with the AZ in the ancestral position and one (Setaria viridis) with the AZ in a derived position below a cluster of flowers (spikelet). Rice and Brachypodium are more similar anatomically than Setaria. However, the cell wall properties and the transcriptome of rice and Brachypodium are no more similar to each other than either is to Setaria. The set of genes expressed in the studied tissues is generally conserved across species, but the precise developmental and positional patterns of expression and gene networks are almost entirely different. Transcriptional regulation of AZ development appears to be extensively rewired among the three species, leading to distinct anatomical and morphological outcomes.

Identification and characterization of core abscisic acid (ABA) signaling components and their gene expression profile in response to abiotic stresses in Setaria viridis

Abscisic acid (ABA) is an essential phytohormone that regulates growth, development and adaptation of plants to environmental stresses. In Arabidopsis and other higher plants, ABA signal transduction involves three core components namely PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs) and class III SNF-1-related protein kinase 2 (SnRK2s). In the present study, we reported the identification and characterization of the core ABA signaling components in Setaria viridis, an emerging model plant for cereals and feedstock crops presenting C4 metabolism, leading to the identification of eight PYL (SvPYL1 to 8), twelve PP2C (SvPP2C1 to 12) and eleven SnRK2 (SvSnRK2.1 through SvSnRK2.11) genes. In order to study the expression profiles of these genes, two different S. viridis accessions (A10.1 and Ast-1) were submitted to drought, salinity and cold stresses, in addition to application of exogenous ABA. Differential gene expression profiles were observed in each treatment and plant genotype, demonstrating variations of ABA stress responses within the same species. These differential responses to stresses were also assessed by physiological measurements such as photosynthesis, stomatal conductance and transpiration rate. This study allows a detailed analysis of gene expression of the core ABA signaling components in Setaria viridis submitted to different treatments and provides suitable targets for genetic engineering of C4 plants aiming tolerance to abiotic stresses.

Taxonomic Demarcation of Setaria pumila (Poir.) Roem. & Schult., S. verticillata (L.) P. Beauv., and S. viridis (L.) P. Beauv. (Cenchrinae, Paniceae, Panicoideae, Poaceae) From Phytolith Signatures

Background and Aims: The role and significance of phytoliths in taxonomic diagnosis of grass species has been well documented with a focus on the types found in foliar epidermis and the synflorescence. The present paper is an attempt to broaden the scope of phytoliths in species diagnosis of grasses by developing phytolith signatures of some species of the foxtail genus Setaria P. Beauv. through in situ location and physico-chemical analysis of various phytolith morphotypes in different parts of the plant body. Methods: Clearing solution and dry ashing extraction methods were employed for in situ location and isolation of phytolith morphotypes respectively. Ultrastructural details were worked out by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy. Morphometric and frequency data of phytolith morphotypes were also recorded. Biochemical architecture of various phytolith types was worked out through SEM-EDX, XRD, and FTIR analysis. Data were analyzed through Principal Component Analysis and Cluster Analysis. Key Results:In situ location of phytoliths revealed species specific epidermal patterns. The presence of cystoliths (calcium oxalate crystals) in the costal regions of adaxial leaf surface of S. verticillata (L.) P. Beauv. is the first report for the genus Setaria. Our results revealed marked variations in epidermal ornamentation and undulation patterns with a novel "Λ" (Lamda) type of undulated ornamentation reported in S. verticillata. Dry ashing method revealed species specific clusters of phytolith morphotypes. Conclusions: The study revealed that phytoliths can play a significant role in resolution of taxonomic identity of three species of Setaria. Each species was marked out by a unique assemblage of phytolith morphotypes from various parts of the plant body. Apart from in situ location and epidermal patterning, diagnostic shapes, frequency distribution, size dimensions, and biochemical architecture emerged as complementary traits that help in developing robust phytolith signatures for plant species.

Domestication and Improvement in the Model C4 Grass, Setaria

Setaria viridis (green foxtail) and its domesticated relative S. italica (foxtail millet) are diploid C4 panicoid grasses that are being developed as model systems for studying grass genomics, genetics, development, and evolution. According to archeological evidence, foxtail millet was domesticated from green foxtail approximately 9,000 to 6,000 YBP in China. Under long-term human selection, domesticated foxtail millet developed many traits adapted to human cultivation and agricultural production. In comparison with its wild ancestor, foxtail millet has fewer vegetative branches, reduced grain shattering, delayed flowering time and less photoperiod sensitivity. Foxtail millet is the only present-day crop in the genus Setaria, although archeological records suggest that other species were domesticated and later abandoned in the last 10,000 years. We present an overview of domestication in foxtail millet, by reviewing recent studies on the genetic regulation of several domesticated traits in foxtail millet and discuss how the foxtail millet and green foxtail system could be further developed to both better understand its domestication history, and to provide more tools for future breeding efforts.

Understanding the Differential Response of Setaria viridis L. (green foxtail) and Setaria pumila Poir. (yellow foxtail) to Pyroxsulam

Green foxtail [Setaria viridis (L) Beauv.] and yellow foxtail [Setaria pumila (Poir.) Roem. & Schult.] are among the most abundant and troublesome annual grass weeds in cereal crops in the Northern Plains of the United States and the Prairie Provinces of Canada. Greenhouse and laboratory experiments were conducted to examine the differential responses of both weed species to foliar applications of the new triazolopyrimidine sulfonamide acetolactate synthase-inhibiting herbicide, pyroxsulam, and to determine the mechanism(s) of differential weed control. Foliar applications of pyroxsulam resulted in >90% control of yellow foxtail at rates between 7.5 and 15 g ai ha^-1, whereas the same rates resulted in a reduced efficacy on green foxtail (≤81%). The absorption and translocation of [¹⁴C]pyroxsulam in green and yellow foxtail were similar and could not explain the differential whole-plant efficacy. Studies with [¹⁴C]pyroxsulam revealed a higher percentage of absorbed pyroxsulam was metabolized into an inactive metabolite in the treated leaf of green foxtail than in the treated leaf of yellow foxtail. Metabolism studies demonstrated that, 48 h after application, 50 and 35% of pyroxsulam in the treated leaf was converted to 5-hydroxy-pyroxsulam in green and yellow foxtail, respectively. The acetolactate synthase (ALS) inhibition assay showed that ALS extracted from green foxtail was more tolerant to pyroxsulam than the enzyme extracted from yellow foxtail was. The in vitro ALS assay showed IC₅₀ values of 8.39 and 0.26 μM pyroxsulam for green and yellow foxtail, respectively. The ALS genes from both green and yellow foxtail were sequenced and revealed amino acid differences; however, the changes are not associated with known resistance-inducing mutations. The differential control of green and yellow foxtail following foliar applications of pyroxsulam was attributed to differences in both metabolism and ALS sensitivity.

The C4 Model Grass Setaria Is a Short Day Plant with Secondary Long Day Genetic Regulation

The effect of photoperiod (day:night ratio) on flowering time was investigated in the wild species, Setaria viridis, and in a set of recombinant inbred lines (RILs) derived from a cross between foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis). Photoperiods totaled 24 h, with three trials of 8:16, 12:12 and 16:8 light:dark hour regimes for the RIL population, and these plus 10:14 and 14:10 for the experiments with S. viridis alone. The response of S. viridis to light intensity as well as photoperiod was assessed by duplicating photoperiods at two light intensities (300 and 600 μmol.m^-2.s^-1). In general, day lengths longer than 12 h delayed flowering time, although flowering time was also delayed in shorter day-lengths relative to the 12 h trial, even when daily flux in high intensity conditions exceeded that of the low intensity 12 h trial. Cluster analysis showed that the effect of photoperiod on flowering time differed between sets of RILs, with some being almost photoperiod insensitive and others being delayed with respect to the population as a whole in either short (8 or 12 h light) or long (16 h light) photoperiods. QTL results reveal a similar picture, with several major QTL colocalizing between the 8 and 12 h light trials, but with a partially different set of QTL identified in the 16 h trial. Major candidate genes for these QTL include several members of the PEBP protein family that includes Flowering Locus T (FT) homologs such as OsHd3a, OsRFT1, and ZCN8/12. Thus, Setaria is a short day plant (flowering quickest in short day conditions) whose flowering is delayed by long day lengths in a manner consistent with the responses of most other members of the grass family. However, the QTL results suggest that flowering time under long day conditions uses additional genetic pathways to those used under short day conditions.

Optimization of Phenotyping Assays for the Model Monocot Setaria viridis

Setaria viridis (green foxtail) is an important model plant for the study of C4 photosynthesis in panicoid grasses, and is fast emerging as a system of choice for the study of plant development, domestication, abiotic stress responses and evolution. Basic research findings in Setaria are expected to advance research not only in this species and its close relative S. italica (foxtail millet), but also in other panicoid grasses, many of which are important food or bioenergy crops. Here we report on the standardization of multiple growth and development assays for S. viridis under controlled conditions, and in response to several phytohormones and abiotic stresses. We optimized these assays at three different stages of the plant's life: seed germination and post-germination growth using agar plate-based assays, early seedling growth and development using germination pouch-based assays, and adult plant growth and development under environmentally controlled growth chambers and greenhouses. These assays will be useful for the community to perform large scale phenotyping analyses, mutant screens, comparative physiological analysis, and functional characterization of novel genes of Setaria or other related agricultural crops. Precise description of various growth conditions, effective treatment conditions and description of the resultant phenotypes will help expand the use of S. viridis as an effective model system.

Effects of abiotic stress on physiological plasticity and water use of Setaria viridis (L.)

The emerging model Setaria viridis with its C4 photosynthesis and adaptation to hot and dry locations is a promising system to investigate water use and abiotic stress tolerance. We investigated the physiological plasticity of six S. viridis natural accessions that originated from different regions of the world under normal conditions and conditions of water-deficit stress and high temperatures. Accessions Zha-1, A10.1 and Ula-1 showed significantly higher leaf water potential (Ψleaf), photosynthesis (A), transpiration (E), and stomatal conductance (gs) rates compared to Ast-1, Aba-1 and Sha-1 when grown under stress conditions. Expression analysis of genes associated with C4 photosynthesis, aquaporins, ABA biosynthesis and signaling including genes involved in stress revealed an increased sensitivity of Ast-1, Aba-1 and Sha-1 to stresses. Correlation analysis of gene expression data with physiological and biochemical changes characterized A10.1 and Ast-1 as two extreme tolerant and sensitive accessions originated from United States and Azerbaijan under water-deficit and heat stress, respectively. Although preliminary, our study demonstrated the plasticity of S. viridis accessions under stress, and allows the identification of tolerant and sensitive accessions that could be use to study the mechanisms associated with stress tolerance and to characterize of the regulatory networks involved in C4 grasses.

A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species

BACKGROUND

Recently, there has been interest in establishing a monocot C4 model species with a small genome, short lifecycle, and capacity for genetic transformation. Setaria viridis has been adopted to fill this role, since reports of Agrobacterium-mediated transformation in 2010, and sequencing of its genome in 2012. To date, S. viridis has primarily been used to further our understanding of C4 photosynthesis, but is also an ideal system for the study of biomass crops, which are almost exclusively C4 panicoid grasses. Biogenesis of stem tissue, its cell wall composition, and soluble sugar content are important determinants of bioenergy crop yields. Here we show that a developing S. viridis internode is a valuable experimental system for gene discovery in relation to these important bioenergy feedstock traits.

RESULTS

The rate of maximal stem biomass accumulation in S. viridis A10 under long day growth was at the half-head emergence developmental stage. At this stage of development, internode 5 (of 7) was found to be rapidly expanding with an active meristem, a zone of cell expansion (primary cell walls), a transitional zone where cell expansion ceased and secondary cell wall deposition was initiated, and a mature zone that was actively accumulating soluble sugars. A simple method for identifying these zones was established allowing rapid dissection and snap-freezing for RNAseq analysis. A transcriptome profile was generated for each zone showing a transition from cell division and nucleic acid synthesis/processing in the meristem, to metabolism, energy synthesis, and primary cell wall synthesis in the cell expansion zone, to secondary cell wall synthesis in the transitional zone, to sugar transport, and photosynthesis in the mature zone.

CONCLUSION

The identification of these zones has provided a valuable experimental system for investigating key bioenergy traits, including meristematic activity, cell wall biosynthesis, and soluble sugar accumulation, in a C4 panicoid grass that has genetic resources, a short life cycle, and small stature allowing controlled experimental conditions in growth cabinets. Here we have presented a comprehensive map of gene expression and metabolites in this experimental system to facilitate gene discovery and controlled hypothesis testing for bioenergy research in S. viridis.