Panicoid Grasses Research Articles

Time-specific lipid and gene expression responses to chilling stress in panicoid grass.

This article comments on: Kenchanmane Raju SK, Zhang Y, Mahboub S, Ngu DW, Qiu Y, Harmon FG, Schnable JC, Roston RL. 2024. Rhythmic lipid and gene expression responses to chilling in panicoid grasses. Journal of Experimental Botany 75, https://doi.org/10.1093/jxb/erae247

Rhythmic lipid and gene expression responses to chilling in panicoid grasses.

Chilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species. Here, we investigated changes in gene expression and membrane lipids in response to chilling stress during one 24h cycle in chilling-tolerant foxtail millet (Setaria italica), and chilling-sensitive sorghum (Sorghum bicolor) and Urochloa (browntop signal grass, Urochloa fusca, lipids only), leveraging their evolutionary relatedness and differing levels of chilling stress tolerance. We show that most chilling-induced lipid changes are conserved across the three species, while we observed distinct, time-specific responses in chilling-tolerant foxtail millet, indicating the presence of a finely orchestrated adaptive mechanism. We detected rhythmicity in lipid responses to chilling stress in the three grasses, which were also present in Arabidopsis thaliana, suggesting the conservation of rhythmic patterns across species and highlighting the importance of accounting for time of day. When integrating lipid datasets with gene expression profiles, we identified potential candidate genes that showed corresponding transcriptional changes in response to chilling stress, providing insights into the differences in regulatory mechanisms between chilling-sensitive sorghum and chilling-tolerant foxtail millet.

Environmental DNA analysis of airborne poaceae (grass) pollen reveals taxonomic diversity across seasons and climate zones

BackgroundGrasses populate most biogeographical zones, and their diversity influences allergic sensitisation to pollen. Previously, the contribution of different Poaceae subfamilies to airborne pollen has mostly been inferred from historical herbarium records. We recently applied environmental (e)DNA metabarcoding at one subtropical site revealing that successive airborne grass pollen peaks were derived from repeated flowering of Chloridoid and Panicoid grasses over a season. This study aimed to compare spatiotemporal patterns in grass pollen exposure across seasons and climate zones. MethodsAirborne pollen concentrations across two austral pollen seasons spanning 2017–2019 at subtropical (Mutdapilly and Rocklea, Queensland) and temperate (Macquarie Park and Richmond, New South Wales) sites, were determined with a routine volumetric impaction sampler and counting by light microscopy. Poaceae rbcL metabarcode sequences amplified from daily pollen samples collected once per week were assigned to subfamily and genus using a ribosomal classifier and compared with Atlas of Living Australia sighting records. ResultseDNA analysis revealed distinct dominance patterns of grass pollen at various sites: Panicoid grasses prevailed in both subtropical Mutdapilly and temperate Macquarie Park, whilst Chloridoid grasses dominated the subtropical Rocklea site. Overall, subtropical sites showed significantly higher proportion of pollen from Chloridoid grasses than temperate sites, whereas the temperate sites showed a significantly higher proportion of pollen from Pooideae grasses than subtropical sites. Timing of airborne Pooid (spring), Panicoid and Chloridoid (late spring to autumn), and Arundinoid (autumn) pollen were significantly related to number of days from mid-winter. Proportions of eDNA for subfamilies correlated with distributions grass sighting records between climate zones. ConclusionseDNA analysis enabled finer taxonomic discernment of Poaceae pollen records across seasons and climate zones with implications for understanding adaptation of grasslands to climate change, and the complexity of pollen exposure for patients with allergic respiratory diseases.

Plasma membrane aquaporins regulate root hydraulic conductivity in the model plant Setaria viridis.

The high rate of productivity observed in panicoid crops is in part due to their extensive root system. Recently, green foxtail (Setaria viridis) has emerged as a genetic model system for panicoid grasses. Natural accessions of S. viridis originating from different parts of the world, with differential leaf physiological behavior, have been identified. This work focused on understanding the physiological and molecular mechanisms controlling root hydraulic conductivity and root-to-shoot gas exchange signaling in S. viridis. We identified 2 accessions, SHA and ZHA, with contrasting behavior at the leaf, root, and whole-plant levels. Our results indicated a role for root aquaporin (AQP) plasma membrane (PM) intrinsic proteins in the differential behavior of SHA and ZHA. Moreover, a different root hydraulic response to low levels of abscisic acid between SHA and ZHA was observed, which was associated with root AQPs. Using cell imaging, biochemical, and reverse genetic approaches, we identified PM intrinsic protein 1;6 (PIP1;6) as a possible PIP1 candidate that regulates radial root hydraulics and root-to-shoot signaling of gas exchange in S. viridis. In heterologous systems, PIP1;6 localized in the endoplasmic reticulum, and upon interaction with PIP2s, relocalization to the PM was observed. PIP1;6 was predominantly expressed at the root endodermis. Generation of knockout PIP1;6 plants (KO-PIP1;6) in S. viridis showed altered root hydraulic conductivity, altered gas exchange, and alteration of root transcriptional patterns. Our results indicate that PIPs are essential in regulating whole-plant water homeostasis in S. viridis. We conclude that root hydraulic conductivity and gas exchange are positively associated and are regulated by AQPs.

Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize and Setaria viridis.

The Heat Shock Factor (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess and compare the composition, heat responsiveness, and chromatin profiles of the HSF families in maize and Setaria viridis (Setaria), two model C4 panicoid grasses. Both species encode a similar number of HSFs, and examples of both conserved and variable expression responses to a heat stress event were observed between the two species. Chromatin accessibility and genome-wide DNA-binding profiles were generated to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both chromatin accessibility and promoter occupancy within similarly regulated sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. Additionally, we observed the widespread presence of TF binding at HSF promoters in control conditions, even at HSFs that are only expressed in response to heat stress. TF-binding peaks were typically near putative HSF-binding sites in HSFs upregulated in response to heat stress, but not in stable or not expressed HSFs. These observations collectively support a complex scenario of expansion and subfunctionalization within this transcription factor family and suggest that within-family HSF transcriptional regulation is a conserved, defining feature of the family.

An Update of the Cenchrinae (Poaceae, Panicoideae, Paniceae) and a New Genus for the Subtribe to Clarify the Dubious Position of a Species of Panicum L.

Subtribe Cenchrinae, so-called as the "bristle clade", is a monophyletic group of panicoid grasses characterized by having sterile branches or bristles on the inflorescences in most of its species. Within this subtribe is also placed Panicum antidotale Retz., an "incertae sedis" species of Panicum L. which lacks bristles along the inflorescence. In this study, we present an update of the subtribe Cenchrinae based on molecular, morphological, and anatomical evidence to clarify the systematic position of P. antidotale in the Cenchrinae, excluding it from Panicum and establishing it in a new genus (i.e., Janochloa Zuloaga & Delfini); the morphological features distinguishing the new genus from other closely related taxa are properly discussed and an identification key to the 24 genera recognized within Cenchrinae is presented. We also add American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus as well as defining placements in the tree of Setaria species that were imprecisely located in previous analyses. A comparison with the results from other studies, comments on Stenotaphrum Trin. and a brief discussion on conflicting placements in Cenchrus and related taxa, and of Acritochaete Pilg. are also included.

A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species.

Leveraging existing resources in studied species to predict gene functions has the potential to rapidly expand understanding of annotated genes in other, less well-studied, species with assembled genomes. However, orthology is not a reliable predictor for the transcriptional responses of genes to stress. Machine learning methods can quantitatively estimate expression patterns and gene functions using known annotations and collections of features describing each gene. In this chapter, we describe a supervised machine learning framework to predict stress-responsive genes across species using only features derived from nucleotide sequences, using the example of cold stress-responsive genes in different Panicoid grass species.

谷子近缘野生种的亲缘关系及其利用研究

<p id="C3">Foxtail millet (<italic>Setaria italica</italic>) was domesticated from the wild ancestor, green foxtail (<italic>S. viridis</italic>), about ten thousand years ago in China. Foxtail millet belongs to <italic>Setaria</italic> genus, which includes about 125 species of panicoid grasses worldwide, and 15 species of them in China varied from diploid to octoploid. Currently, six genomes in the <italic>Setaria</italic> genus have been identified by GISH (genomic in situ hybridization). Molecular phylogenetic analyses show that the <italic>Setaria</italic> genus is polyphyletic, in line with the characteristic of diversified genomes. Phylogeny of <italic>Setaria</italic> genus reveal that foxtail millet is most closely related with green foxtail, and then <italic>S. fabrei</italic> and <italic>S. verticillata</italic>, and that A genome of <italic>S. italica</italic>/<italic>S. viridis</italic> appears to be closer to B genome of <italic>S. adhaeran</italic> and C genome of <italic>S. grisebachii </italic>than the other known genomes. For utilization of wild species resources, foxtail millet breeders have successfully introduced the naturally mutated herbicide-resistant genes from green foxtail into cultivars, resulting in the herbicide-resistant foxtail millet variety. Here, we review the recent advances of wild species of foxtail millet in species classification, genome constitution and phylogenetic relationships, and highlight the utility of the wild species resources for breeding and domestication of foxtail millet. We also discuss the potentials of the wild <italic>Setaria</italic> species in discovery of domestication genes and breeding in foxtail millet in the future.

Plant bedding construction between 60,000 and 40,000 years ago at Border Cave, South Africa

Extraordinary preservation of plant remains provides an insight into the construction and materials of bedding at Border Cave, South Africa. Towards the back of the cave there are particularly thick layers of desiccated and charred grass and our botanical study is from bulk samples of these approximately 60,000 to 40,000 year-old layers (Members 3 BS, 2 WA, 2 BS and 1 BS Lower C). More than one type of panicoid grass was identified, sedge nutlets were present in the older layers and in Member 2 WA particularly, eudicotyledon leaves were preserved. Plant bedding construction may have altered slightly over time with the use of sedges decreasing in favour of grass. A small item that appears to be woven monocotyledon leaf blades was recovered from Member 1 BS Lower C (42,600 years old), potentially making it the oldest evidence of simple weaving. The bedding is generally desiccated rather than burned, and often lies on an ash base. It is possible that the site's occupants burned old bedding to provide an ash base for fresh bedding. The unique preservation of desiccated plant material from as early as 60,000 years ago may in part be due to these ashy surfaces.

Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses.

Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.

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

Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture, yet little is known about the intersecting pathways and how they are rewired during development. Here, we show that a single mutation in a gene encoding an AP1/FUL-like MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis. Previous reports of AP1/FUL-like genes in cereals have revealed extensive functional redundancy, and in panicoid grasses, no associated inflorescence phenotypes have been described. In S. viridis, perturbation of SvFul2, both through chemical mutagenesis and gene editing, converted a normally determinate inflorescence habit to an indeterminate one, and also repressed determinacy in axillary branch and floral meristems. Our analysis of gene networks connected to disruption of SvFul2 identified regulatory hubs at the intersection of floral transition and inflorescence determinacy, providing insights into the optimization of cereal crop architecture.

The CLV3 Homolog in Setaria viridis Selectively Controls Inflorescence Meristem Size

The CLAVATA pathway controls meristem size during inflorescence development in both eudicots and grasses, and is initiated by peptide ligands encoded by CLV3/ESR-related (CLE) genes. While CLV3 controls all shoot meristems in Arabidopsis, evidence from cereal grasses indicates that different meristem types are regulated by different CLE peptides. The rice peptide FON2 primarily controls the size of the floral meristem, whereas the orthologous peptides CLE7 and CLE14 in maize have their most dramatic effects on inflorescence and branch meristems, hinting at diversification among CLE responses in the grasses. Setaria viridis is more closely related to maize than to rice, so can be used to test whether the maize CLE network can be generalized to all members of subfamily Panicoideae. We used CRISPR-Cas9 in S. viridis to knock out the SvFON2 gene, the closest homolog to CLV3 and FON2. Svfon2 mutants developed larger inflorescence meristems, as in maize, but had normal floral meristems, unlike Osfon2, suggesting a panicoid-specific CLE network. Vegetative traits such as plant height, tiller number and leaf number were not significantly different between mutant and wild type plants, but time to heading was shorter in the mutants. In situ hybridization showed strong expression of Svfon2 in the inflorescence and branch meristems, consistent with the mutant phenotype. Using bioinformatic analysis, we predicted the co-expression network of SvFON2 and its signaling components, which included genes known to control inflorescence architecture in maize as well as genes of unknown function. The similarity between SvFON2 function in Setaria and maize suggests that its developmental specialization in inflorescence meristem control may be shared among panicoid grasses.

Corythaica bellula Torre-Bueno (Hemiptera: Tingidae): Scribner's Panicgrass, Dichanthelium oligosanthes subsp. Scribnerianum, as a Host Plant in the Nebraska Sandhills

The lace bug Corythaica bellula Torre-Bueno is one of four North American species in this mainly Neotropical genus. All species known from Canada and the United States are seldom collected and their bionomics little known. Adults and nymphs of C. bellula were collected from Scribner's panicgrass (Dichanthelium oligosanthes subsp. scribnerianum [Nash] Freckmann and Lelong; Poaceae) in 12 counties of the Nebraska Sandhills. Its collection in South Dakota from this host represents a new state record. The panicoid grass is the tingid's second host plant identified to species level. All adult males (n = 51) were brachypterous, as were 90 of 91 females; the single macropter was collected in mid-July. The collection of nymphs in May and July suggests bivoltinism. Nymphs and adults of a congener, C. venusta (Champion), were syntopic with C. bellula at a site in Grant County, Nebraska, which is the first specific locale recorded for C. venusta in the state. Corythaica bellula, whose adults are only 1.98 (brachypters) to 2.20 mm long (macropters), is part of the hidden biodiversity of the vast Nebraska Sandhills.

New species in Aciculosporium, Shimizuomyces and a new genus Morakotia associated with plants in Clavicipitaceae from Thailand.

Three new fungal species in the Clavicipitaceae (Hypocreales, Ascomycota) associated with plants were collected in Thailand. Morphological characterisation and phylogenetic analyses based on multi-locus sequences of LSU, RPB1 and TEF1 showed that two species belong to Aciculosporium and Shimizuomyces. Morakotia occupies a unique clade and is proposed as a novel genus in Clavicipitaceae. Shimizuomyces cinereus and Morakotia fusca share the morphological characteristic of having cylindrical to clavate stromata arising from seeds. Aciculosporium siamense produces perithecial plates and occurs on a leaf sheath of an unknown panicoid grass.

Could the grasses have played a role in the earliest salt exploitation? Phytoliths analysis of prehistoric salt spring from H\u0103l\u0103butoaia - \u0162olici (Romania)

The salt spring exploitation from Hălăbutoaia - Ţolici (Neamț County, Romania) dates back to the Early Neolithic and lasted throughout Chalcolithic. The deposit stratigraphy is estimated at 8 m and covers 2500 years of history (c. 6000–3500 BCE). In order to document the possible use of plants, particularly of the grasses, in the salt production process, we realized a detailed study of phytoliths preserved in several archaeological levels of Hălăbutoaia site. The most identified morphotypes come from grass family. Analysis revealed an important representation of inflorescence bracts phytoliths (especially Elongate dendritic) showing the anthropogenic origin of the assemblages. Bilobate are also well represented. These forms attest the presence of wild panicoid grasses (e.g. wild millet) and/or cultivated millets in the area. In some very punctual assemblages, forms produced by dicots are well represented. Considering the low phytoliths production by dicots plants, it involves a special accumulation of these types of plants that could be related to woody plants used as fuel for salt production. It is very possible that grasses had a very important role in pyrotechnology used to produce salt, either as the main fuel or as a mean for controlling the temperature or even as a firelighter.

The Halophyte Seashore Paspalum Uses Adaxial Leaf Papillae for Sodium Sequestration.

Salinity is a growing issue worldwide, with nearly 30% of arable land predicted to be lost due to soil salinity in the next 30 years. Many grass crops that are vital to sustain the world's caloric intake are salt sensitive. Studying mechanisms of salt tolerance in halophytic grasses, plants that thrive in salt conditions, may be an effective approach to ultimately improve salt-sensitive grass crops. Seashore paspalum (Paspalum vaginatum) is a halophytic Panicoid grass able to grow in salt concentrations near that of seawater. Despite its widespread cultivation as a sustainable turfgrass, the mechanism underlying its ability to retain high Na+ concentrations in photosynthetic tissue while maintaining growth remains unknown. We examined the leaf structure and ion content in P. vaginatum 'HI10', which shows increased growth under saline conditions, and Paspalum distichum 'Spence', which shows reduced growth under salt, to better understand the superior salt tolerance of cv HI10. A striking difference between cv HI10 and cv Spence was the high steady-state level of K+ in cv HI10. Imaging further showed that the adaxial surface of both cv HI10 and cv Spence contained dense costal ridges of papillae. However, these unicellular extensions of the epidermis were significantly larger in cv HI10 than in cv Spence. The cv HI10 papillae were shown to act as Na+ sinks when plants were grown under saline conditions. We provide evidence that leaf papillae function as specialized structures for Na+ sequestration in P. vaginatum, illustrating a possible path for biotechnological improvement of salt-sensitive Panicoid crops with analogous leaf structures.

Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs

BackgroundThe circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.ResultsComparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities.ConclusionsThis study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.

New insights on Neolithic food and mobility patterns in Mediterranean coastal populations.

The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE. The samples used in this study were excavated from the Les Bréguières site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30). Stable isotope ratios for human bones range from -20.3 to -18.1‰ for C, from 8.9 to 11.1‰ for N and from 6.4 to 15‰ for S. Domestic animal data range from -22.0 to -20.2‰ for C, from 4.1 to 6.9‰ for N, and from 10.2 to 12.5‰ for S. Human enamel 87 Sr/86 Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization. Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Bréguières consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available.

IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae.

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long‐read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co‐opted into C4 were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript‐based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long‐read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses—wild species and species utilizing C3 photosynthesis—will aid in future studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.

Setaria viridis as a model for translational genetic studies of jasmonic acid-related insect defenses in Zea mays

Little is known regarding insect defense pathways in Setaria viridis (setaria), a model system for panicoid grasses, including Zea mays (maize). It is thus of interest to compare insect herbivory responses of setaria and maize. Here we use metabolic, phylogenetic, and gene expression analyses to measure a subset of jasmonic acid (JA)-related defense responses to leaf-chewing caterpillars. Phylogenetic comparisons of known defense-related maize genes were used to identify putative orthologs in setaria, and candidates were tested by quantitative PCR to determine transcriptional responses to insect challenge. Our findings show that while much of the core JA-related metabolic and genetic responses appear conserved between setaria and maize, production of downstream secondary metabolites such as benzoxazinoids and herbivore-induced plant volatiles are dissimilar. This diversity of chemical defenses and gene families involved in secondary metabolism among grasses presents new opportunities for cross species engineering. The high degree of genetic similarity and ease of orthologous gene identification between setaria and maize make setaria an excellent species for translational genetic studies, but the species specificity of downstream insect defense chemistry makes some pathways unamenable to cross-species comparisons.