The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis

Abscission is predetermined in specialized cell layers called the abscission zone (AZ) and activated by developmental or environmental signals. In the grass family, most identified AZ genes regulate AZ anatomy, which differs among lineages. A YABBY transcription factor, SHATTERING1 (SH1), is a domestication gene regulating abscission in multiple cereals, including rice and Setaria. In rice, SH1 inhibits lignification specifically in the AZ. However, the AZ of Setaria is nonlignified throughout, raising the question of how SH1 functions in species without lignification. Crispr-Cas9 knockout mutants of SH1 were generated in Setaria viridis and characterized with histology, cell wall and auxin immunofluorescence, transmission electron microscopy, hormonal treatment and RNA-Seq analysis. The sh1 mutant lacks shattering, as expected. No differences in cell anatomy or cell wall components including lignin were observed between sh1 and the wild-type (WT) until abscission occurs. Chloroplasts degenerated in the AZ of WT before abscission, but degeneration was suppressed by auxin treatment. Auxin distribution and expression of auxin-related genes differed between WT and sh1, with the signal of an antibody to auxin detected in the sh1 chloroplast. SH1 in Setaria is required for activation of abscission through auxin signaling, which is not reported in other grass species.

First Report of Bipolaris zeae Causing Leaf Spot on Setaria viridis in China

Green bristlegrass (Setaria viridis) is an annual dominant herb in arid sandy grasslands with strong drought resistance to water stress (Valença et al. 2020). In August 2021, brown or dark tan spots on the leaves of S. viridis were observed on natural grassland in Qingyang city, Gansu Province, China (36.55°N, 107.32°E). Leaf disease incidence was around 13%, and the infected area of each leaf was about 20%. For isolation, 30 tissue pieces (5×5 mm) from 10 symptomatic leaf samples were surface-sterilized with 70% ethanol for 30 seconds and rinsed three times with steriled distilled water. Then these tissues were placed on the potato dextrose agar (PDA) at 25 °C, and incubated in dark from 2 to 5 days. Sixteen single-spored cultures with consistent colony characteristics were obtained by single spore isolation as described in Manamgoda et al. (2012). Colonies on PDA were irregular shapes with black color and white edge; conidia were dark brown with septate, cylindrical, straight or flexuous geniculate at the upper end, 22.7 to 69.38×9.2 to 17.6 µm (n = 50; average size 40.8×13.2 µm) under microscope (40X). The internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GPD) regions of the representative isolate 83HXGWC, 84HXGWC and 85HXGWC were amplified using the primers of ITS1/ITS4 and GPD1/GPD2 (Manamgoda et al. 2012). All the amplified gene sequences were deposited into GenBank with accession numbers ITS (OP703331, OQ978850, and OQ978851) and GPD (OQ559683, OQ992505, and OQ992506). BLAST analysis of both the two segments showed 100% identity with those reported sequences of ex-type isolate BRIP 11512 (KJ415538 and KJ415408) of B. zeae Sivan (Tan et al. 2014; Bhunjun et al. 2020), respectively. In the maximum-likelihood phylogenetic tree, 83-HXGWC, 84HXGWC and 85HXGWC strains were grouped with the reference sequences of B. zeae with a high bootstrap supporting values of 100%. Five healthy green bristlegrass (6 weeks) plants in pots were sprayed with conidial suspensions (1×10⁶ conidia ml^-1). Another five pots were sprayed with sterilized distilled water (controls). Then all pots were individually covered with transparent polyethylene bags for 5 days to maintain high relative humidity and placed in a greenhouse maintained at 18 to 25 °C. After incubation for 14 days, the typical symptoms of leaf spots developed from brown to dark brown on the plants inoculated with conidial suspension, whereas no symptoms were observed on the control plants. The measurement of pathogenicity was carried out three times. The same pathogens were consistently reisolated from inoculated leaves, and was confirmed as B. zeae based on morphological and molecular analyses, fulfilling Koch's postulates. This study provides a new record of B. zeae on green bristlegrass on natural grassland in China, which can potentially impose disease challenges to other crops. Since, B. oryzae has been known to cause disease in cereal crops (Manamgoda et al. 2014), this can be a potential alternate source of survival of this pathogen.

Comprehensive expression analyses of the ABCG subfamily reveal SvABCG17 as a potential transporter of lignin monomers in the model C4 grass Setaria viridis

Although several aspects of lignin metabolism have been extensively characterized, the mechanism(s) by which lignin monomers are transported across the plasma membrane remains largely unknown. Biochemical, proteomic, expression and co-expression analyses from several plant species support the involvement of active transporters, mainly those belonging to the ABC superfamily. Here, we report on the genome-wide characterization of the ABCG gene subfamily in the model C4 grass Setaria viridis and further identification of the members potentially involved in monolignol transport. A total of 48 genes encoding SvABCGs were found in the S. viridis genome, from which 21 SvABCGs were classified as full-size transporters and 27 as half-size transporters. Comprehensive analysis of the ABCG subfamily in S. viridis based on expression and co-expression analyses support a role for SvABCG17 in monolignol transport: (i) SvABCG17 is orthologous to AtABCG29, a monolignol transporter in Arabidopsis thaliana; (ii) SvABCG17 displays a similar expression profile to that of lignin biosynthetic genes in a set of different S. viridis tissues and along the elongating internode; (iii) SvABCG17 is highly co-expressed with lignin-related genes in a public transcriptomic database; (iv) SvABCG17displays particularly high expression in the top of the S. viridis elongating internode, a tissue undergoing active lignification; (v) SvABCG17 mRNA localization coincides with the histochemical pattern of lignin deposition; and (vi) the promoter of SvABCG17 is activated by secondary cell wall-associated transcription factors, especially by lignin-specific activators of the MYB family. Further studies might reveal further aspects of this potential monolignol transporter, including its real substrate specificity and whether it works redundantly with other ABC members during S. viridis lignification.

First Report of Colletotrichum truncatum Causing Anthracnose of Green Foxtail (Setaria viridis) in China

Green foxtail (Setaria viridis (L.) Beauv.), belonging to the family Gramineae, is a monocotyledonous plant that is distributed in tropical and subtropical regions of the world. S. viridis is one of the most abundant weeds in corn, soybean, rice and other major crops in China, which competes with crops for light, moisture and nutrients, leading to yield losses. In September 2021, an unknown leaf spot disease was observed on the leaves of S. viridis in many greenhouses of Xinkou town, Xiqing district, Tianjin, China (116.95729, 39.09088), under cloudy and high humid conditions after a week of rain. Over 60% of the weeds were observed with leaf spots in 28 greenhouses of XinKou town. The characteristics of the disease were observed and investigated. Initial symptoms were brown spots of 1 to 5 mms, longitudinal elliptic, round, or spindle-shaped lesions on leaves of S. viridis. These spots continued to spread shortly after the onset of the symptoms. At the late-stage disease, the spots' edges were dark brown and irregular. Eventually, the center of the spots turned grayish-white and became thinner and drier until fracture. To investigate the disease, symptomatic weed leaves were separated and small patches with infected spots were cut out. Diseased tissues (3×3 mm) were disinfected with 75% alcohol for 30s  35s, rinsed three times with sterile distilled water and then placed on potato dextrose agar (PDA) at 25°C with a 12-h photoperiod for 7 days in incubators (RXZ-280C, Ningbo, China). With the pathogen growing on the PDA, three mycelia with uniform morphology were observed, which were named SVCT-01, SVCT-02, and SVCT-03, respectively. These mycelia were transferred and cultured for daily observation. The color of these mycelia on PDA appeared gray at first, which eventually turned to grayish black with numerous black microsclerotia, setae, and a few aerial mycelia after 7 days. The setae were 75 to 120 ×3.5 to 5 μm, with elliptic to claviform appressoria. Conidia were hyaline, falcate, unicellular, 16 to 25 × 2.6 to 3.8 μm (n=50). All characteristics of isolates were consistent with the description of Colletotrichum truncatum (Sutton, 1992). Pathogenicity testing was conducted on 3-leaves-stage S. viridis seedlings. Conidial suspension (106 conidia/mL) of isolates were sprayed on 20 S. viridis seedlings with the suspension of each isolate was sprayed on 10 seedlings. Ten seedlings sprayed with sterilized distilled water were used as the control. Three replicates were performed on each treatment. The treatment plants were maintained in the incubator (25°C, relative humidity > 80%, 12-h photoperiod). Typical leaf spot symptoms were observed on inoculated leaves after 7 days, the control leaves remained symptomless. The fungus reisolated from the lesions of diseased leaves were morphological and molecularly identical to the inoculated isolates. The results echo with Koch's postulates，suggesting that the obtained isolates SVCT-01, SVCT-02 and SVCT-03 are potential pathogen in Setaria viridis. To confirm the species' identity, total genomic DNA of isolates were extracted using a Fungal DNA Kit (GBCBIO, Guangzhou, China). Sequences of internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), and β-tubulin (TUB2) regions were identified via PCR (Guerber et al, 2003; Weir et al, 2012). The sequences of SVCT-01, SVCT-02 and SVCT-03 showed more than 99% homology with Colletotrichum truncatum strains CBS:151.35 (GenBank Accession No. GU227862, GU228254, GU227960, GU228156) (Damm, 2009). The sequences of SVCT-01 were deposited in GenBank as a representative isolate under the accession numbers OL629177, OL627527, OM040388, OM040389. Maximum likelihood trees based on concatenated sequences of the four genes were constructed using MEGA7.0. The results showed that the strains isolated from Setaria viridis were closely related to Colletotrichum truncatum with 100% bootstrap support. According to morphological, pathological characteristics, and multilocus phylogenetic analysis, the isolated strains (SVCT-01, SVCT-02 and SVCT-03) from S. viridis were identified as Colletotrichum truncatum (Weir et al, 2012). Colletotrichum sp. is a significant plant pathogen that was previously reported causing anthracnose on Setaria sp. Up to now, it has been reported that C. graminicola has infected nine species of Setaria sp. Such as Setaria glauca in New Zealand (Pennycook, 1989) and Setaria pumila in Zimbabwe (Lenne, 1990). In 1979s, C.graminicola was obtained from Setaria lutescens in China (Tai, 1979). To our knowledge, this is a new host record for Colletotrichum truncatum causing anthracnose on S. viridis in China. Colletotrichum truncatum spread rapidly and caused serious disease to Setaria viridis. We hope to discovery a biocontrol method against weed on non-host cultivated plants through the production of secondary metabolites by C. truncatum.

MicroRNAs expression profiles in early responses to different levels of water deficit in Setaria viridis

Water deficit is a major constraint for crops of economic importance in almost all agricultural regions. However, plants have an active defense system to adapt to these adverse conditions, acting in the reprogramming of gene expression responsible for encoding microRNAs (miRNAs). These miRNAs promote the regulation to the target gene expression by the post-transcriptional (PTGS) and transcriptional gene silencing (TGS), modulating several pathways including defense response to water deficit. The broader knowledge of the miRNA expression profile and its regulatory networks in response to water deficit can provide evidence for the development of new biotechnological tools for genetic improvement of several important crops. In this study, we used Setaria viridis accession A10.1 as a C4 model plant to widely investigate the miRNA expression profile in early responses to different levels of water deficit. Ecophysiological studies in Setaria viridis under water deficit and after rewatering demonstrated a drought tolerant accession, capable of a rapid recovery from the stress. Deep small RNA sequencing and degradome studies were performed in plants submitted to drought to identify differentially expressed miRNA genes and their predicted targets, using in silico analysis. Our findings showed that several miRNAs were differentially modulated in response to distinctive levels of water deficit and after rewatering. The predicted mRNA targets mainly corresponded to genes related to cell wall remodeling, antioxidant system and drought-related transcription factors, indicating that these genes are rapidly regulated in early responses to drought stress. The implications of these modulations are extensively discussed, and higher-effect miRNAs are suggested as major players for potential use in genetic engineering to improve drought tolerance in economically important crops, such as sugarcane, maize, and sorghum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01226-z.

Isolation of gametes and zygotes from Setaria viridis

Setaria viridis, the wild ancestor of foxtail millet (Setaria italica), is an effective model plant for larger C₄ crops because S. viridis has several desirable traits, such as short generation time, prolific seed production and a small genome size. These advantages are well suited for investigating molecular mechanisms in angiosperms, especially C₄ crop species. Here, we report a procedure for isolating gametes and zygotes from S. viridis flowers. To isolate egg cells, ovaries were harvested from unpollinated mature flowers and cut transversely, which allowed direct access to the embryo sac. Thereafter, an egg cell was released from the cut end of the basal portion of the dissected ovary. To isolate sperm cells, pollen grains released from anthers were immersed in a mannitol solution, resulting in pollen-grain bursting, which released sperm cells. Additionally, S. viridis zygotes were successfully isolated from freshly pollinated flowers. Isolated zygotes cultured in a liquid medium developed into globular-like embryos and cell masses. Thus, isolated S. viridis gametes, zygotes and embryos are attainable for detailed observations and investigations of fertilization and developmental events in angiosperms.

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.

Plant Growth-promoting Effects of Viable and Dead Spores of Bacillus pumilus TUAT1 on Setaria viridis

Spores are a stress-resistant form of Bacillus spp., which include species that are plant growth-promoting rhizobacteria (PGPR). Previous studies showed that the inoculation of plants with vegetative cells or spores exerted different plant growth-promoting effects. To elucidate the spore-specific mechanism, we compared the effects of viable vegetative cells, autoclaved dead spores, and viable spores of Bacillus pumilus TUAT1 inoculated at 10⁷ CFU plant^–1 on the growth of the C4 model plant, Setaria viridis A10.1. B. pumilus TUAT1 spores exerted stronger growth-promoting effects on Setaria than on control plants 14 days after the inoculation. Viable spores increased shoot weight, root weight, shoot length, root length, and nitrogen uptake efficiency 21 days after the inoculation. These increases involved primary and crown root formation. Additionally, autoclaved dead spores inoculated at 10⁸ or 10⁹ CFU plant^–1 had a positive impact on crown root differentiation, which increased total lateral root length, resulting in a greater biomass and more efficient nitrogen uptake. The present results indicate that an inoculation with viable spores of B. pumilus TUAT1 is more effective at enhancing the growth of Setaria than that with vegetative cells. The plant response to dead spores suggests that the spore-specific plant growth-promoting mechanism is at least partly independent of symbiotic colonization.

Efficiency, Specificity and Temperature Sensitivity of Cas9 and Cas12a RNPs for DNA-free Genome Editing in Plants

Delivery of genome editing reagents using CRISPR-Cas ribonucleoproteins (RNPs) transfection offers several advantages over plasmid DNA-based delivery methods, including reduced off-target editing effects, mitigation of random integration of non-native DNA fragments, independence of vector constructions, and less regulatory restrictions. Compared to the use in animal systems, RNP-mediated genome editing is still at the early development stage in plants. In this study, we established an efficient and simplified protoplast-based genome editing platform for CRISPR-Cas RNP delivery, and then evaluated the efficiency, specificity, and temperature sensitivity of six Cas9 and Cas12a proteins. Our results demonstrated that Cas9 and Cas12a RNP delivery resulted in genome editing frequencies (8.7-41.2%) at various temperature conditions, 22°C, 26°C, and 37°C, with no significant temperature sensitivity. LbCas12a often exhibited the highest activities, while AsCas12a demonstrated higher sequence specificity. The high activities of CRISPR-Cas RNPs at 22° and 26°C, the temperature preferred by plant transformation and tissue culture, led to high mutagenesis efficiencies (34.0-85.2%) in the protoplast-regenerated calli and plants with the heritable mutants recovered in the next generation. This RNP delivery approach was further extended to pennycress (Thlaspi arvense), soybean (Glycine max) and Setaria viridis with up to 70.2% mutagenesis frequency. Together, this study sheds light on the choice of RNP reagents to achieve efficient transgene-free genome editing in plants.

Characterization of Programmable Transcription Activators in the Model Monocot Setaria viridis Via Protoplast Transfection

Recent advances in DNA synthesis and assembly allow for genetic constructs to be designed and constructed in high throughput. Characterizing large numbers of variant genetic designs is not feasible with low-throughput and time-consuming plant transformation workflows. Protoplast transformation offers a rapid, high-throughput compatible alternative for testing genetic constructs in plant-relevant molecular environments. Here, we describe a protocol for protoplast transformation using a recent experiment in genetic optimization of dCas9-based programmable transcription activators as an example.

Evaluation of the molecular and physiological response to dehydration of two accessions of the model plant Setaria viridis

Water deficits are responsible for countless agricultural losses. Among the affected crops, C4 plants are of special interest due to their high water and nitrogen use efficiency. Two accessions of Setaria viridis (Ast-1 and A10.1) with contrasting responses to water deficit were used in the current work to better understand the mechanisms behind drought tolerance in C4 species. Our results showed that although the A10.1 accession exhibited a reduced size and lower Rfd values in comparison to Ast-1, it had overall higher Fv/Fm and lower NPQ values in well-watered conditions. The water deficit induction was performed with PEG-8000 at the grain-filling stage using dehydration cycles. Analysis of physiological measurements showed the A10.1 accession as being more tolerant to multiple water deficit exposures. In addition, PCA identified a clear difference in the pattern of drought response of the accessions. Four drought marker genes previously described in the literature were chosen to evaluate the response at the molecular level: SvP5CS2, SvDHN1, SvNAC6, and SvWRKY1. Besides confirming that Ast-1 is a more sensitive accession, the expression analysis revealed that SvNAC1 might better monitor drought stress, while SvWRKY1 was able to differentiate the two accessions. Distinct evolutionary histories of each accession may be behind their differences in response to water deficits.

Expression of a CO2-permeable aquaporin enhances mesophyll conductance in the C4 species Setaria viridis

A fundamental limitation of photosynthetic carbon fixation is the availability of CO₂. In C₄ plants, primary carboxylation occurs in mesophyll cytosol, and little is known about the role of CO₂ diffusion in facilitating C₄ photosynthesis. We have examined the expression, localization, and functional role of selected plasma membrane intrinsic aquaporins (PIPs) from Setaria italica (foxtail millet) and discovered that SiPIP2;7 is CO₂-permeable. When ectopically expressed in mesophyll cells of Setaria viridis (green foxtail), SiPIP2;7 was localized to the plasma membrane and caused no marked changes in leaf biochemistry. Gas exchange and C¹⁸O¹⁶O discrimination measurements revealed that targeted expression of SiPIP2;7 enhanced the conductance to CO₂ diffusion from the intercellular airspace to the mesophyll cytosol. Our results demonstrate that mesophyll conductance limits C₄ photosynthesis at low pCO₂ and that SiPIP2;7 is a functional CO₂ permeable aquaporin that can improve CO₂ diffusion at the airspace/mesophyll interface and enhance C₄ photosynthesis.

Target site mutations and cytochrome P450s-involved metabolism confer resistance to nicosulfuron in green foxtail (Setaria viridis)

Green foxtail [Setaria viridis (L.) P.Beauv.] is a troublesome grass weed that is widely distributed in maize (Zea mays L.) fields across China. Many populations of S. viridis have evolved resistance to the acetolactate synthase (ALS)-inhibiting herbicide nicosulfuron. The objectives of this research were to confirm nicosulfuron resistance in these populations and to investigate the basis of nicosulfuron resistance. Whole-plant dose-response experiments showed 6 out of 13 S. viridis populations were highly resistance (20-30 times) to nicosulfuron. Sequencing of the ALS gene revealed two amino acid mutations, Asp-376-Glu and Pro-197-Ala, in the nicosulfuron-resistant populations. A malathion pretreatment study revealed that the R376 and R197 subpopulations might have cytochrome P450s-mediated herbicide metabolic resistance. The resistant populations were cross-resistant to imazethapyr but sensitive to topramezone and quizalofop-p-ethyl. This is the first report of resistance to ALS inhibitors conferred by target site mutations (Asp-376-Glu or Pro-197-Ser) and possible cytochrome P450s-involved metabolism in S. viridis.

The Characteristics of Mercury Flux at the Interfaces between Two Typical Plants and the Air in Leymus chinensis Grasslands

Mercury is a global pollutant. The mercury exchanges between vegetation and the atmosphere are important for the global mercury cycle. Grassland ecosystems occupy more than 25% of the global land area and have different succession processes and ecological functions. The current research regarding mercury exchanges between forests and the atmosphere have attracted much attention, but the research regarding grasslands tends to be rare. To reveal the characteristics of mercury exchanges in grasslands, this study conducted field in-situ monitoring experiments in a Leymus meadow grassland regions of the Songnen Plains in northeastern China. The exchange flux values of the GEM (gaseous element mercury) between the plants and the atmosphere were measured using a dynamic flux bag method (DFB). The experiments were conducted for the purpose of assessing the mercury flux levels between the vegetation and the atmosphere in a typical Leymus chinensis meadow. The goal was to further the understanding of the change characteristics and influential factors and to describe the source and sink actions and dynamics between the grassland vegetation and the atmosphere. The diurnal variation characteristics were as follows: High during the day and low at night, with peaks generally appearing at noon. The growing period was characterized by absorption peaks of atmospheric mercury by the plants. The breeding period was characterized by the peak release of atmospheric mercury by the plants. The change characteristics were as follows: During the growing period, the duration of the plants in a mercury absorption state exceeded 96.5%, which was represented as the net sink of the atmospheric mercury. During the breeding period, the time of mercury release ranged between 46.4% and 66.8%, making the breeding period the net source of atmospheric mercury. The results of this study's analysis indicated that each environmental factor was correlated with the mercury flux, and the environmental factors had different effects on the mercury flux during the different stages of plant growth. The atmospheric mercury concentration levels were the main factor during the growing period. Atmospheric humidity was the main factor during the breeding period. Solar radiation was the decisive factor during the entire experimental period.

Efficient genome editing and gene knockout in Setaria viridis with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway

The CRISPR/Cas9 system has been used for genome editing in several organisms, including higher plants. This system induces site-specific mutations in the genome based on the nucleotide sequence of engineered guide RNAs. The complex genomes of C4 grasses makes genome editing a challenge in key grass crops like maize (Zea mays), sorghum (Sorghum bicolor), Brachiaria spp., switchgrass (Panicum virgatum), and sugarcane (Saccharum spp.). Setaria viridis is a diploid C4 grass widely used as a model for these C4 crop plants. Here, an optimized CRISPR/Cas9 binary vector that exploits the non-homologous end joining (NHEJ) system was used to knockout a green fluorescent protein (gfp) transgene in S. viridis accession A10.1. Transformation of embryogenic callus by A. tumefaciens generated ten glufosinate-ammonium resistant transgenic events. In the T0 generation, 60% of the events were biallelic mutants in the gfp transgene with no detectable accumulation of GFP protein and without insertions or deletions in predicted off-target sites. The gfp mutations generated by CRISPR/Cas9 were stable and displayed Mendelian segregation in the T1 generation. Altogether, the system described here is a highly efficient genome editing system for S. viridis, an important model plant for functional genomics studies in C4 grasses. Also, this system is a potential tool for improvement of agronomic traits in C4 crop plants with complex genomes.

Agrobacterium-Mediated Transformation of Setaria viridis, a Model System for Cereals and Bioenergy Crops

Setaria viridis is an emerging model system for the genetic and molecular characterization of cereals and bioenergy crops. Here, we describe a detailed procedure for genetic transformation of the S. viridis accession line ME034V-1. This method utilizes callus generated from mature seeds for infection with Agrobacterium tumefaciens strain AGL1 to regenerate hygromycin-resistant stable transgenic plants. It takes approximately 7 weeks to generate callus from mature seeds, 11-17 weeks from infection to the regeneration of transgenic lines, and an additional 3-4 weeks for plant growth in the greenhouse for seed collection. The protocol as presented consistently results in transformation frequency of approximately 25% for the generation of transgenic plants, with fewer escapes and higher survivability in soil for optimal seed collection. © 2021 Donald Danforth Plant Science Center. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of S. viridis (Accession ME034V-1) callus from mature seeds Basic Protocol 2: Agrobacterium-mediated transformation of callus to generate transgenic plants Basic Protocol 3: Plantlet transplantation in soil, plant growth in greenhouse, and seed collection Support Protocol: Preparation of Agrobacterium culture for infection.

Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals

Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Heterologous Overexpression of Arabidopsis cel1 Enhances Grain Yield, Biomass and Early Maturity in Setaria viridis

Heterologous overexpression of Arabidopsis cellulase 1 (Atcel1) results in enhanced yield, early maturity, and increased biomass in dicotyledonous species like poplar and eucalyptus but has not been demonstrated in monocots. We produced transgenic Setaria viridis accession A10.1 plants overexpressing a monocotyledonous codon optimized (MCO) Atcel1. Agronomic characterization of the transgenic events showed that heterologous overexpression of MCOAtcel1 caused enhanced grain yield, shoot biomass, and accelerated maturation rate in the model grass species S. viridis under growth chamber conditions. The agronomic trait differences observed were consistent with previous reports in dicots but are here described in a monocot species and associated with increased seed yield. Overexpression of Atcel1 in S. viridis was shown to increase the number of panicles and seeds by 24-30%, enhance overall grain yield by up to 26%, and lead to a shoot dry biomass increase of 16-19%. Overexpression also reduced time to plant maturation and senescence by 12.5%. Our findings in S. viridis suggest that manipulation of Atcel1 has potential for developing early-maturing and higher-yielding monocotyledonous biomass crops suitable for climate-smart agriculture.

Molecular Manipulation of MicroRNA397 Abundance Influences the Development and Salt Stress Response of Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) has been used extensively as a heterologous system for molecular manipulation to genetically characterize both dicotyledonous and monocotyledonous plant species. Here, we report on Arabidopsis transformant lines molecularly manipulated to over-accumulate the small regulatory RNA microRNA397 (miR397) from the emerging C4 monocotyledonous grass model species Setaria viridis (S. viridis). The generated transformant lines, termed SvMIR397 plants, displayed a range of developmental phenotypes that ranged from a mild, wild-type-like phenotype, to a severe, full dwarfism phenotype. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR)-based profiling of the SvMIR397 transformant population revealed a strong correlation between the degree of miR397 over-accumulation, repressed LACCASE (LAC) target gene expression, reduced lignin content, and the severity of the developmental phenotype displayed by SvMIR397 transformants. Further, exposure of SvMIR397 transformants to a 7-day regime of salt stress revealed the SvMIR397 transformant lines to be more sensitive to the imposed stress than were wild-type Arabidopsis plants. Taken together, the findings reported here via the use of Arabidopsis as a heterologous system show that the S. viridis miR397 small regulatory RNA is able to repress the expression of three Arabidopsis LAC genes which led to reduced lignin content and increased salt stress sensitivity.

QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants

Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as the training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. The average precision was 0.027 for Arabidopsis and 0.029 for rice. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validated Sorghum bicolor and Setaria viridis models. The S. bicolor model was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. In addition, we applied the S. viridis model and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.

Paspalum urvillei and Setaria parviflora, two grasses naturally adapted to extreme iron-rich environments

Paspalum urvillei and Setaria parviflora are two plant species naturally adapted to iron-rich environments such as around iron mines wastes. The aim of our work was to characterize how these two species cope with these extreme conditions by comparing them with related model species, Oryza sativa and Setaria viridis, that appeared to be much less tolerant to Fe excess. Both Paspalum urvillei and Setaria parviflora were able to limit the amount of Fe accumulated within roots and shoots, compared to the less tolerant species. Perls/DAB staining of Fe in root cross sections indicated that Paspalum urvillei and Setaria parviflora responded through the build-up of the iron plaque (IP), suggesting a role of this structure in the limitation of Fe uptake. Synchrotron μXRF analyses showed the presence of phosphorus, calcium, silicon and sulfur on IP of Paspalum urvillei roots and μXANES analyses identified Fe oxyhydroxide (ferrihydrite) as the main Fe form. Once within roots, high concentrations of Fe were localized in the cell walls and vacuoles of Paspalum urvillei, Setaria parviflora and O. sativa whereas Setaria viridis accumulated Fe in ferritins. The Fe forms translocated to the shoots of Setaria parviflora were identified as tri-iron complexes with citrate and malate. In leaves, all species accumulated Fe in the vacuoles of bundle sheath cells and as ferritin complexes in plastids. Taken together, our results strongly suggest that Paspalum urvillei and Setaria parviflora set up mechanisms of Fe exclusion in roots and shoots to limit the toxicity induced by Fe excess.

Pilot study on the uptake and modification of harmaline in acceptor plants: An innovative approach to visualize the interspecific transfer of natural products

Substances which have been leached out from decomposing plant parts or exuded from vital plants (donor plants), are taken up by acceptor plants and subsequently modified. This phenomenon was likewise established for harmala alkaloids. Employing hydroponically grown barley seedlings, it becomes evident that harmaline and harmine are taken up by the roots of the acceptor plants. Furthermore, based on HPLC and GC-MS analyses, it was demonstrated that these alkaloids also are present in Setaria viridis plants, which grew in the direct vicinity of the alkaloid containing Peganum harmala plants. Since harmaline exhibits a bright green fluorescence, this alkaloid was employed to visualize the uptake into the acceptor plants by feeding it to roots of barley seedlings. In the further course, the imported harmaline was converted in the leaves to yield harmine, which exhibits a dark blue fluorescence. This conversion was also verified by HPLC and GC-MS analyses. Based on the massive differences in the fluorescence properties, both processes, uptake and modification in the acceptor plants, could be monitored by macroscopical studies as well as by confocal laser scanning microscopical analyses. As result, for the first time, the phenomenon of "Horizontal Natural Product Transfer" is visualized vividly.

Measuring the Hydraulic Conductivity of Grass Root Systems

Root-system hydraulic conductivity (RSHC) is an important physiological characteristic that describes the inherent ability of roots to conduct water across a water-potential gradient between the root and the stem xylem. RSHC is commonly used as an indicator of plant functioning and adaptability to a given environment. A simple, fast, and easy-to-use protocol is described for the quantification of RSHC at the seedling stage in two important monocot species grown in hydroponic solution: Setaria viridis, a C4 model plant, and wheat, a C3 crop plant. This protocol can also be easily modified for use with almost any grass species and environmental treatments, such as salinity or hormone treatments. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Setaria hydrostatic root-system hydraulic conductivity Alternate Protocol: Measuring the root conductivity of young plants with soft stems.

Robust and Reproducible Agrobacterium-Mediated Transformation System of the C4 Genetic Model Species Setaria viridis

Setaria viridis (green foxtail) has been identified as a potential experimental model system to genetically and molecularly characterise the C4 monocotyledonous grasses due to its small physical size, short generation time and prolific seed production, together with a sequenced and annotated genome. Setaria viridis is the wild ancestor of the cropping species, foxtail millet (Setaria italica), with both Setaria species sharing a close evolutionary relationship with the agronomically important species, maize, sorghum, and sugarcane, as well as the bioenergy feedstocks, switchgrass, and Miscanthus. However, an efficient and reproducible transformation protocol is required to further advance the use of S. viridis to study the molecular genetics of C4 monocotyledonous grasses. An efficient and reproducible protocol was established for Agrobacterium tumefaciens-mediated transformation of S. viridis (Accession A10) regenerable callus material derived from mature seeds, a protocol that returned an average transformation efficiency of 6.3%. The efficiency of this protocol was the result of the: (i) use of mature embryo derived callus material; (ii) age of the seed used to induce callus formation; (iii) composition of the callus induction media, including the addition of the ethylene inhibitor, silver nitrate; (iv) use of a co-cultivation approach, and; (v) concentration of the selective agent. Our protocol furthers the use of S. viridis as an experimental model system to study the molecular genetics of C4 monocotyledonous grasses for the potential future development of improved C4 cropping species.

Contrasting Responses of Plastid Terminal Oxidase Activity Under Salt Stress in Two C4 Species With Different Salt Tolerance

The present study reveals contrasting responses of photosynthesis to salt stress in two C₄ species: a glycophyte Setaria viridis (SV) and a halophyte Spartina alterniflora (SA). Specifically, the effect of short-term salt stress treatment on the photosynthetic CO₂ uptake and electron transport were investigated in SV and its salt-tolerant close relative SA. In this experiment, at the beginning, plants were grown in soil then were exposed to salt stress under hydroponic conditions for two weeks. SV demonstrated a much higher susceptibility to salt stress than SA; while, SV was incapable to survive subjected to about 100 mM, SA can tolerate salt concentrations up to 550 mM with slight effect on photosynthetic CO₂ uptake rates and electrons transport chain conductance (g_ETC ). Regardless the oxygen concentration used, our results show an enhancement in the P₇₀₀ oxidation with increasing O₂ concentration for SV following NaCl treatment and almost no change for SA. We also observed an activation of the cyclic NDH-dependent pathway in SV by about 2.36 times upon exposure to 50 mM NaCl for 12 days (d); however, its activity in SA drops by about 25% compared to the control without salt treatment. Using PTOX inhibitor (n-PG) and that of the Q_o-binding site of Cytb₆/f (DBMIB), at two O₂ levels (2 and 21%), to restrict electrons flow towards PSI, we successfully revealed the presence of a possible PTOX activity under salt stress for SA but not for SV. However, by q-PCR and western-blot analysis, we showed an increase in PTOX amount by about 3-4 times for SA under salt stress but not or very less for SV. Overall, this study provides strong proof for the existence of PTOX as an alternative electron pathway in C₄ species (SA), which might play more than a photoprotective role under salt stress.

The lignin toolbox of the model grass Setaria viridis

The core set of biosynthetic genes potentially involved in developmental lignification was identified in the model C4 grass Setaria viridis. Lignin has been recognized as a major recalcitrant factor negatively affecting the processing of plant biomass into bioproducts. However, the efficient manipulation of lignin deposition in order to generate optimized crops for the biorefinery requires a fundamental knowledge of several aspects of lignin metabolism, including regulation, biosynthesis and polymerization. The current availability of an annotated genome for the model grass Setaria viridis allows the genome-wide characterization of genes involved in the metabolic pathway leading to the production of monolignols, the main building blocks of lignin. Here we performed a comprehensive study of monolignol biosynthetic genes as an initial step into the characterization of lignin metabolism in S. viridis. A total of 56 genes encoding bona fide enzymes catalyzing the consecutive ten steps of the monolignol biosynthetic pathway were identified in the S. viridis genome. A combination of comparative phylogenetic studies, high-throughput expression analysis and quantitative RT-PCR analysis was further employed to identify the family members potentially involved in developmental lignification. Accordingly, 14 genes clustered with genes from closely related species with a known function in lignification and showed an expression pattern that correlates with lignin deposition. These genes were considered the "core lignin toolbox" responsible for the constitutive, developmental lignification in S. viridis. These results provide the basis for further understanding lignin deposition in C4 grasses and will ultimately allow the validation of biotechnological strategies to produce crops with enhanced processing properties.

Response of plasmodesmata formation in leaves of C4 grasses to growth irradiance

Rapid metabolite diffusion across the mesophyll (M) and bundle sheath (BS) cell interface in C₄ leaves is a key requirement for C₄ photosynthesis and occurs via plasmodesmata (PD). Here, we investigated how growth irradiance affects PD density between M and BS cells and between M cells in two C₄ species using our PD quantification method, which combines three-dimensional laser confocal fluorescence microscopy and scanning electron microscopy. The response of leaf anatomy and physiology of NADP-ME species, Setaria viridis and Zea mays to growth under different irradiances, low light (100 μmol m^-2  s^-1 ), and high light (1,000 μmol m^-2  s^-1 ), was observed both at seedling and established growth stages. We found that the effect of growth irradiance on C₄ leaf PD density depended on plant age and species. The high light treatment resulted in two to four-fold greater PD density per unit leaf area than at low light, due to greater area of PD clusters and greater PD size in high light plants. These results along with our finding that the effect of light on M-BS PD density was not tightly linked to photosynthetic capacity suggest a complex mechanism underlying the dynamic response of C₄ leaf PD formation to growth irradiance.

Uncovering the Host Range for Maize Pathogen Magnaporthiopsis maydis

The fungus Magnaporthiopsis maydis is a soil-borne, seed-borne vascular wilt pathogen that causes severe damage to sensitive Zea mays L. (maize) hybrids throughout Egypt, Israel, India, Spain, and other countries. It can undergo virulence variations and survive as spores, sclerotia, or mycelia on plant residues. Maize, Lupinus termis L. (lupine) and Gossypium hirsutum L. (cotton) are the only known hosts of M. maydis. Identification of new plant hosts that can assist in the survival of the pathogen is an essential step in restricting disease outbreak and spread. Here, by field survey and growth chamber pathogenicity test, accompanied by real-time PCR analysis, the presence of the fungal DNA inside the roots of cotton (Pima cv.) plants was confirmed in infested soil. Moreover, we identified M. maydis in Setaria viridis (green foxtail) and Citrullus lanatus (watermelon, Malali cv.). Infected watermelon sprouts had delayed emergence and development, were shorter, and had reduced root and shoot biomass. M. maydis infection also affected root biomass and phenological development of cotton plants but caused only mild symptoms in green foxtail. No M. maydis DNA was detected in Hordeum vulgare (barley, Noga cv.) and the plants showed no disease symptoms except for reduced shoot weight. These findings are an important step towards uncovering the host range and endophytic behavior of M. maydis, encouraging expanding this evaluation to other plant species.

A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants

Background

C4 photosynthesis is a key domain of plant research with outcomes ranging from crop quality improvement, biofuel production and efficient use of water and nutrients. A metabolic network model of C4 “lab organism” Setaria viridis with extensive gene-reaction associations can accelerate target identification for desired metabolic manipulations and thereafter in vivo validation. Moreover, metabolic reconstructions have also been shown to be a significant tool to investigate fundamental metabolic traits.

Results

A mass and charge balance genome-scale metabolic model of Setaria viridis was constructed, which was tested to be able to produce all major biomass components in phototrophic and heterotrophic conditions. Our model predicted an important role of the utilization of NH\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$_{4}^{+}$\end{document}4+ and NO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$_{3}^{-}$\end{document}3− ratio in balancing charges in plants. A multi-tissue extension of the model representing C4 photosynthesis was able to utilize NADP-ME subtype of C4 carbon fixation for the production of lignocellulosic biomass in stem, providing a tool for identifying gene associations for cellulose, hemi-cellulose and lignin biosynthesis that could be potential target for improved lignocellulosic biomass production. Besides metabolic engineering, our modeling results uncovered a previously unrecognized role of the 3-PGA/triosephosphate shuttle in proton balancing.

Conclusions

A mass and charge balance model of Setaria viridis, a model C4 plant, provides the possibility of system-level investigation to identify metabolic characteristics based on stoichiometric constraints. This study demonstrated the use of metabolic modeling in identifying genes associated with the synthesis of particular biomass components, and elucidating new role of previously known metabolic processes.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2941-z) contains supplementary material, which is available to authorized users.

The effect of vanadium on essential element uptake of Setaria viridis' seedlings

High concentrations of vanadium, a ubiquitous element in the environment, in growing media leads to deformation of root structure and leaf chlorosis and necrosis, consequently affecting the translocations of nutrients and essential elements. However, the effects of vanadium on essential element uptake, and the interactions of essential elements in the presence of vanadium, remain incompletely understood. To elucidate the effects of different concentrations of vanadium on major and trace essential elements and plant growth, a native plant species growing in a vanadium mining area, Setaria viridis (dog tail's grass), was incubated in solutions containing 0-55.8 mg/L vanadium. The shoot accumulation of four major essential elements and five trace essential elements was detected, and the root length and stem height were measured. The results showed that vanadium in soil solution enhanced the accumulation of all major essential elements in shoot. Vanadium concentrations lower than 47.4 mg/L showed an obvious positive (p < 0.05) effect on P accumulation and translocation. In the case of trace essential elements, there were threshold values for solution vanadium stimulation of element uptake. The threshold values for Cu and Zn, Fe, and Mo uptake were 4.3, 16.3, and 40.6 mg/L, respectively. When vanadium levels surpassed these values, accumulation was suppressed and the solution vanadium concentrations attenuated the solution-to-shoot translocation of most of the essential elements. Among the trace essential elements, translocation of Fe was obviously enhanced (p < 0.05) by vanadium. Solution vanadium also enhanced plant growth at lower concentrations and inhibited it at higher levels. The threshold values for stem height and root length were 36.8 and 16.3 mg/L, respectively. Concentrations of 40 and 55.8 mg/L vanadium in soil solution caused a 50% decrease in root length and stem height, respectively, showing that root length of Setaria viridis is more susceptible to vanadium toxicity than stem growth.

Importance of Poly-3-Hydroxybutyrate Metabolism to the Ability of Herbaspirillum seropedicae To Promote Plant Growth

The application of bacteria as plant growth promoters is a sustainable alternative to mitigate the use of chemical fertilization in agriculture, reducing negative economic and environmental impacts. Several plant growth-promoting bacteria synthesize and accumulate the intracellular polymer polyhydroxybutyrate (PHB). However, the role of PHB in plant-bacterium interactions is poorly understood. In this study, applying the C4 model grass Setaria viridis and several mutants in the PHB metabolism of the endophyte Herbaspirillum seropedicae yielded new findings on the importance of PHB for bacterial colonization of S. viridis roots. Taken together, the results show that deletion of genes involved in the synthesis and degradation of PHB reduced the ability of the bacteria to enhance plant growth but with little effect on overall root colonization. The data suggest that PHB metabolism likely plays an important role in supporting specific metabolic routes utilized by the bacteria to stimulate plant growth.

Herbaspirillum seropedicae is an endophytic bacterium that establishes an association with a variety of plants, such as rice, corn, and sugarcane, and can significantly increase plant growth. H. seropedicae produces polyhydroxybutyrate (PHB), stored in the form of insoluble granules. Little information is available on the possible role of PHB in bacterial root colonization or in plant growth promotion. To investigate whether PHB is important for the association of H. seropedicae with plants, we inoculated roots of Setaria viridis with H. seropedicae strain SmR1 and mutants defective in PHB production (ΔphaP1, ΔphaP1 ΔphaP2, ΔphaC1, and ΔphaR) or mobilization (ΔphaZ1 ΔphaZ2). The strains producing large amounts of PHB colonized roots, significantly increasing root area and the number of lateral roots compared to those of PHB-negative strains. H. seropedicae grows under microaerobic conditions, which can be found in the rhizosphere. When grown under low-oxygen conditions, only the parental strain and ΔphaP2 mutant exhibited normal growth. The lack of normal growth under low oxygen correlated with the inability to stimulate plant growth, although there was no effect on the level of root colonization. The data suggest that PHB is produced in the root rhizosphere and plays a role in maintaining normal metabolism under microaerobic conditions. To confirm this, we screened for green fluorescent protein (GFP) expression under the control of the H. seropedicae promoters of the PHA synthase and PHA depolymerase genes in the rhizosphere. PHB synthesis is active on the root surface and later PHB depolymerase expression is activated.

IMPORTANCE The application of bacteria as plant growth promoters is a sustainable alternative to mitigate the use of chemical fertilization in agriculture, reducing negative economic and environmental impacts. Several plant growth-promoting bacteria synthesize and accumulate the intracellular polymer polyhydroxybutyrate (PHB). However, the role of PHB in plant-bacterium interactions is poorly understood. In this study, applying the C4 model grass Setaria viridis and several mutants in the PHB metabolism of the endophyte Herbaspirillum seropedicae yielded new findings on the importance of PHB for bacterial colonization of S. viridis roots. Taken together, the results show that deletion of genes involved in the synthesis and degradation of PHB reduced the ability of the bacteria to enhance plant growth but with little effect on overall root colonization. The data suggest that PHB metabolism likely plays an important role in supporting specific metabolic routes utilized by the bacteria to stimulate plant growth.

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5'UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.

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

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.

Reference gene identification for reliable normalisation of quantitative RT-PCR data in Setaria viridis

BACKGROUND

Quantitative real-time polymerase chain reaction (RT-qPCR) is the key platform for the quantitative analysis of gene expression in a wide range of experimental systems and conditions. However, the accuracy and reproducibility of gene expression quantification via RT-qPCR is entirely dependent on the identification of reliable reference genes for data normalisation. Green foxtail (Setaria viridis) has recently been proposed as a potential experimental model for the study of C₄ photosynthesis and is closely related to many economically important crop species of the Panicoideae subfamily of grasses, including Zea mays (maize), Sorghum bicolor (sorghum) and Sacchurum officinarum (sugarcane). Setaria viridis (Accession 10) possesses a number of key traits as an experimental model, namely; (i) a small sized, sequenced and well annotated genome; (ii) short stature and generation time; (iii) prolific seed production, and; (iv) is amendable to Agrobacterium tumefaciens-mediated transformation. There is currently however, a lack of reference gene expression information for Setaria viridis (S. viridis). We therefore aimed to identify a cohort of suitable S. viridis reference genes for accurate and reliable normalisation of S. viridis RT-qPCR expression data.

RESULTS

Eleven putative candidate reference genes were identified and examined across thirteen different S. viridis tissues. Of these, the geNorm and NormFinder analysis software identified SERINE/THERONINE-PROTEIN PHOSPHATASE 2A (PP2A), 5'-ADENYLYLSULFATE REDUCTASE 6 (ASPR6) and DUAL SPECIFICITY PHOSPHATASE (DUSP) as the most suitable combination of reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. To demonstrate the suitability of the three selected reference genes, PP2A, ASPR6 and DUSP, were used to normalise the expression of CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes across the same tissues.

CONCLUSIONS

This approach readily demonstrated the suitably of the three selected reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. Further, the work reported here forms a highly useful platform for future gene expression quantification in S. viridis and can also be potentially directly translatable to other closely related and agronomically important C₄ crop species.

Exchange pattern of gaseous elemental mercury in landfill: mercury deposition under vegetation coverage and interactive effects of multiple meteorological conditions

Landfill is known as a potential source of atmospheric Hg and an important component of the local or regional atmospheric Hg budget. This study investigated the gaseous elemental Hg surface-air fluxes under differing conditions at a typical municipal solid waste landfill site, highlighting the interactive effects of plant coverage and meteorological conditions. The results indicated that Hg fluxes exhibited a feature represented by diel variation. In particular, Hg deposition was observed under a condition of Kochia sieversiana coverage, whereas emission that occurred after K. sieversiana was removed. Hg emission was the dominant mode under conditions of Setaria viridis coverage and its removal; however, the average Hg emission flux with the S. viridis coverage was nearly four times lower than after its removal. These findings verified that the plant coverage should be a key factor influencing the Hg emission from landfills. In addition, Hg fluxes were correlated positively with solar radiation and air/soil temperature and correlated inversely with relative humidity under all conditions, except K. sieversiana coverage. This suggested that the interactive effects of meteorological conditions and plant coverage played a jointly significant role in the Hg emission from landfills. It was established that K. sieversiana can inhibit Hg emission efficiently, and therefore, it could potentially be suitable for use as a plant-based method to control Hg pollution from landfills.

Light Quality Affects Chloroplast Electron Transport Rates Estimated from Chl Fluorescence Measurements

Chl fluorescence has been used widely to calculate photosynthetic electron transport rates. Portable photosynthesis instruments allow for combined measurements of gas exchange and Chl fluorescence. We analyzed the influence of spectral quality of actinic light on Chl fluorescence and the calculated electron transport rate, and compared this with photosynthetic rates measured by gas exchange in the absence of photorespiration. In blue actinic light, the electron transport rate calculated from Chl fluorescence overestimated the true rate by nearly a factor of two, whereas there was closer agreement under red light. This was consistent with the prediction made with a multilayer leaf model using profiles of light absorption and photosynthetic capacity. Caution is needed when interpreting combined measurements of Chl fluorescence and gas exchange, such as the calculation of CO2 partial pressure in leaf chloroplasts.

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.

Relationship of leaf oxygen and carbon isotopic composition with transpiration efficiency in the C4 grasses Setaria viridis and Setaria italica

Leaf carbon and oxygen isotope ratios can potentially provide a time-integrated proxy for stomatal conductance (gs) and transpiration rate (E), and can be used to estimate transpiration efficiency (TE). In this study, we found significant relationships of bulk leaf carbon isotopic signature (δ13CBL) and bulk leaf oxygen enrichment above source water (Δ18OBL) with gas exchange and TE in the model C4 grasses Setaria viridis and S. italica. Leaf δ13C had strong relationships with E, gs, water use, biomass, and TE. Additionally, the consistent difference in δ13CBL between well-watered and water-limited plants suggests that δ13CBL is effective in separating C4 plants with different availability of water. Alternatively, the use of Δ18OBL as a proxy for E and TE in S. viridis and S. italica was problematic. First, the oxygen isotopic composition of source water, used to calculate leaf water enrichment (Δ18OLW), was variable with time and differed across water treatments. Second, water limitations changed leaf size and masked the relationship of Δ18OLW and Δ18OBL with E. Therefore, the data collected here suggest that δ13CBL but not Δ18OBL may be an effective proxy for TE in C4 grasses.

Overexpression of BdMATE Gene Improves Aluminum Tolerance in Setaria viridis

Acidic soils are distributed worldwide, predominantly in tropical and subtropical areas, reaching around 50% of the arable soil. This type of soil strongly reduces crop production, mainly because of the presence of aluminum, which has its solubility increased at low pH levels. A well-known physiological mechanism used by plants to cope with Al stress involves activation of membrane transporters responsible for organic acid anions secretion from the root apex to the rhizosphere, which chelate Al, preventing its absorption by roots. In sorghum, a membrane transporter gene belonging to multidrug and toxic compound extrusion (MATE) family was identified and characterized as an aluminum-activated citrate transporter gene responsible for Al tolerance in this crop. Setaria viridis is an emerging model for C4 species and it is an important model to validate some genes for further C4 crops transformation, such as sugarcane, maize, and wheat. In the present work, Setaria viridis was used as a model plant to overexpress a newly identified MATE gene from Brachypodium distachyon (BdMATE), closely related to SbMATE, for aluminum tolerance assays. Transgenic S. viridis plants overexpressing a BdMATE presented an improved Al tolerance phenotype, characterized by sustained root growth and exclusion of aluminum from the root apex in transgenic plants, as confirmed by hematoxylin assay. In addition, transgenic plants showed higher root citrate exudation into the rhizosphere, suggesting that Al tolerance improvement in these plants could be related to the chelation of the metal by the organic acid anion. These results suggest that BdMATE gene can be used to transform C4 crops of economic importance with improved aluminum tolerance.

Temperature response of mesophyll conductance in three C4 species calculated with two methods: 18 O discrimination and in vitro Vpmax

Mesophyll conductance (g_m ) is an important factor limiting rates of C₃ photosynthesis. However, its role in C₄ photosynthesis is poorly understood because it has been historically difficult to estimate. We use two methods to derive the temperature responses of g_m in C₄ species. The first (Δ¹⁸ O) combines measurements of gas exchange with models and measurements of ¹⁸ O discrimination. The second method (in vitro V_pmax ) derives g_m by retrofitting models of C₄ photosynthesis and ¹³ C discrimination with gas exchange, kinetic constants and in vitro V_pmax measurements. The two methods produced similar g_m for Setaria viridis and Zea mays. Additionally, we present the first temperature response (10-40°C) of C₄ g_m in S. viridis, Z. mays and Miscanthus × giganteus. Values for g_m at 25°C ranged from 2.90 to 7.85 μmol m^-2  s^-1  Pa^-1 . Our study demonstrated that: the two described methods are suitable to calculate g_m in C₄ species; g_m values in C₄ are similar to high-end values reported for C₃ species; and g_m increases with temperature analogous to reports for C₃ species and the response is species specific. These results improve our mechanistic understanding of C₄ photosynthesis.

Effects of reduced carbonic anhydrase activity on CO2 assimilation rates in Setaria viridis: a transgenic analysis

In C4 species, the major β-carbonic anhydrase (β-CA) localized in the mesophyll cytosol catalyses the hydration of CO2 to HCO3-, which phosphoenolpyruvate carboxylase uses in the first step of C4 photosynthesis. To address the role of CA in C4 photosynthesis, we generated transgenic Setaria viridis depleted in β-CA. Independent lines were identified with as little as 13% of wild-type CA. No photosynthetic defect was observed in the transformed lines at ambient CO2 partial pressure (pCO2). At low pCO2, a strong correlation between CO2 assimilation rates and CA hydration rates was observed. C18O16O isotope discrimination was used to estimate the mesophyll conductance to CO2 diffusion from the intercellular air space to the mesophyll cytosol (gm) in control plants, which allowed us to calculate CA activities in the mesophyll cytosol (Cm). This revealed a strong relationship between the initial slope of the response of the CO2 assimilation rate to cytosolic pCO2 (ACm) and cytosolic CA activity. However, the relationship between the initial slope of the response of CO2 assimilation to intercellular pCO2 (ACi) and cytosolic CA activity was curvilinear. This indicated that in S. viridis, mesophyll conductance may be a contributing limiting factor alongside CA activity to CO2 assimilation rates at low pCO2.

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.

Reduced plant water status under sub-ambient pCO2 limits plant productivity in the wild progenitors of C3 and C4 cereals

BACKGROUND AND AIMS

The reduction of plant productivity by low atmospheric CO₂ partial pressure (pCO₂) during the last glacial period is proposed as a limiting factor for the establishment of agriculture. Supporting this hypothesis, previous work has shown that glacial pCO₂ limits biomass in the wild progenitors of C₃ and C₄ founder crops, in part due to the direct effects of glacial pCO₂ on photosynthesis. Here, we investigate the indirect role of pCO₂ mediated via water status, hypothesizing that faster soil water depletion at glacial (18 Pa) compared to post-glacial (27 Pa) pCO₂, due to greater stomatal conductance, feeds back to limit photosynthesis during drying cycles.

METHODS

We grew four wild progenitors of C₃ and C₄ crops at glacial and post-glacial pCO₂ and investigated physiological changes in gas exchange, canopy transpiration, soil water content and water potential between regular watering events. Growth parameters including leaf area were measured.

KEY RESULTS

Initial transpiration rates were higher at glacial pCO₂ due to greater stomatal conductance. However, stomatal conductance declined more rapidly over the soil drying cycle in glacial pCO₂ and was associated with decreased intercellular pCO₂ and lower photosynthesis. Soil water content was similar between pCO₂ levels as larger leaf areas at post-glacial pCO₂ offset the slower depletion of water. Instead the feedback could be linked to reduced plant water status. Particularly in the C₄ plants, soil-leaf water potential gradients were greater at 18 Pa compared with 27 Pa pCO₂, suggesting an increased ratio of leaf evaporative demand to supply.

CONCLUSIONS

Reduced plant water status appeared to cause a negative feedback on stomatal aperture in plants at glacial pCO₂, thereby reducing photosynthesis. The effects were stronger in C₄ species, providing a mechanism for reduced biomass at 18 Pa. These results have added significance when set against the drier climate of the glacial period.

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.

Online CO2 and H2 O oxygen isotope fractionation allows estimation of mesophyll conductance in C4 plants, and reveals that mesophyll conductance decreases as leaves age in both C4 and C3 plants

Mesophyll conductance significantly, and variably, limits photosynthesis but we currently have no reliable method of measurement for C4 plants. An online oxygen isotope technique was developed to allow quantification of mesophyll conductance in C4 plants and to provide an alternative estimate in C3 plants. The technique is compared to an established carbon isotope method in three C3 species. Mesophyll conductance of C4 species was similar to that in the C3 species measured, and declined in both C4 and C3 species as leaves aged from fully expanded to senescing. In cotton leaves, simultaneous measurement of carbon and oxygen isotope discrimination allowed the partitioning of total conductance to the chloroplasts into cell wall and plasma membrane versus chloroplast membrane components, if CO2 was assumed to be isotopically equilibrated with cytosolic water, and the partitioning remained stable with leaf age. The oxygen isotope technique allowed estimation of mesophyll conductance in C4 plants and, when combined with well-established carbon isotope techniques, may provide additional information on mesophyll conductance in C3 plants.

Spike-dip transformation of Setaria viridis

Traditional method of Agrobacterium-mediated transformation through the generation of tissue culture had limited success for Setaria viridis, an emerging C4 monocot model. Here we present an efficient in planta method for Agrobacterium-mediated genetic transformation of S. viridis using spike dip. Pre-anthesis developing spikes were dipped into a solution of Agrobacterium tumefaciens strain AGL1 harboring the β-glucuronidase (GUS) reporter gene driven by the cauliflower mosaic virus 35S (CaMV35S) promoter to standardize and optimize conditions for transient as well as stable transformations. A transformation efficiency of 0.8 ± 0.1% was obtained after dipping of 5-day-old S3 spikes for 20 min in Agrobacterium cultures containing S. viridis spike-dip medium supplemented with 0.025% Silwet L-77 and 200 μm acetosyringone. Reproducibility of this method was demonstrated by generating stable transgenic lines expressing β-glucuronidase plus (GUSplus), green fluorescent protein (GFP) and Discosoma sp. red fluorescent protein (DsRed) reporter genes driven by either CaMV35S or intron-interrupted maize ubiquitin (Ubi) promoters from three S. viridis genotypes. Expression of these reporter genes in transient assays as well as in T1 stable transformed plants was monitored using histochemical, fluorometric GUS activity and fluorescence microscopy. Molecular analysis of transgenic lines revealed stable integration of transgenes into the genome, and inherited transgenes expressed in the subsequent generations. This approach provides opportunities for the high-throughput transformation and potentially facilitates translational research in a monocot model plant.

The solute specificity profiles of nucleobase cation symporter 1 (NCS1) from Zea mays and Setaria viridis illustrate functional flexibility

The solute specificity profiles (transport and binding) for the nucleobase cation symporter 1 (NCS1) proteins, from the closely related C4 grasses Zea mays and Setaria viridis, differ from that of Arabidopsis thaliana and Chlamydomonas reinhardtii NCS1. Solute specificity profiles for NCS1 from Z. mays (ZmNCS1) and S. viridis (SvNCS1) were determined through heterologous complementation studies in NCS1-deficient Saccharomyces cerevisiae strains. The four Viridiplantae NCS1 proteins transport the purines adenine and guanine, but unlike the dicot and algal NCS1, grass NCS1 proteins fail to transport the pyrimidine uracil. Despite the high level of amino acid sequence similarity, ZmNCS1 and SvNCS1 display distinct solute transport and recognition profiles. SvNCS1 transports adenine, guanine, hypoxanthine, cytosine, and allantoin and competitively binds xanthine and uric acid. ZmNCS1 transports adenine, guanine, and cytosine and competitively binds, 5-fluorocytosine, hypoxanthine, xanthine, and uric acid. The differences in grass NCS1 profiles are due to a limited number of amino acid alterations. These amino acid residues do not correspond to amino acids essential for overall solute and cation binding or solute transport, as previously identified in bacterial and fungal NCS1, but rather may represent residues involved in subtle solute discrimination. The data presented here reveal that within Viridiplantae, NCS1 proteins transport a broad range of nucleobase compounds and that the solute specificity profile varies with species.

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.

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.

Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling

Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4model plants, Setaria italica (SiWRKY) and S. viridis (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling.