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Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C₄ grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Setaria italica and its wild ancestor Setaria viridis are diploid C 4 grasses with small genomes of ∼515 Mb. Both species have attributes that make them attractive as model systems. Setaria italica is a grain crop widely grown in Northern China and India that is closely related to the major food and feed crops maize and sorghum. A large collection of S. italica accessions are available and thus opportunities exist for association mapping and allele mining for novel variants that will have direct application in agriculture. Setaria viridis is the weedy relative of S. italica with many attributes suitable for genetic analyses including a small stature, rapid life cycle, and prolific seed production. Setaria sp. are morphologically similar to most of the Panicoideae grasses, including major biofuel feedstocks, switchgrass (Panicum virgatum) and Miscanthus (Miscanthus giganteus). They are broadly distributed geographically and occupy diverse ecological niches. The cross-compatibility of S. italica and S. viridis also suggests that gene flow is likely between wild and domesticated accessions. In addition to serving as excellent models for C 4 photosynthesis, these grasses provide novel opportunities to study abiotic stress tolerance and as models for bioenergy feedstocks.

This study aims to determine the effects of copper, copper oxide nanoparticles, aluminium, and aluminium oxide nanoparticles on the growth rate and expression of ACT-1, CDPK, LIP, NFC, P5CR, P5CS, GR, and SiZIP1 genes in five days old seedling of Setaria italica ssp. maxima, cultivated in hydroponic culture . Depending on their concentration (ranging from 0.1 to 1.8 mg L −1 ), all tested substances had both stimulating and inhibiting effects on the growth rate of the seedlings. Copper and copper oxide-NPs had generally a stimulating effect whereas aluminium and aluminium oxide-NPs at first had a positive effect but in higher concentrations they inhibited the growth. Treating the seedlings with 0.4 mg L −1 of each tested toxicant was mostly stimulating to the expression of the genes and reduced the differences between the transcript levels of the coleoptiles and roots. Increasing concentrations of the tested substances had both stimulating and inhibiting effects on the expression levels of the genes. The highest expression levels were usually noted at concentrations between 0.4 and 1.0 mg/L of each metal and metal nanoparticle, except for SiZIP1, which had the highest transcript amount at 1.6 mg L −1 of Cu 2+ and at 0.1–0.8 mg L −1 of CuO-NPs, and LIP and GR from the seedling treated with Al 2 O 3 -NPs at concentrations of 0.1 and 1.6 mg L −1 , respectively.

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

Backgrounds Adapter proteins (APs) complex is a class of heterotetrameric complexes comprising of 4-subunits with important regulatory functions in eukaryotic cell membrane vesicle trafficking. Foxtail millet ( Setaria italica L.) is a significant C 4 model plant for monocotyledon studies, and vesicle trafficking may plays a crucial role in various life activities related to growth and development. Despite this importance, studies on AP complexes in foxtail millet have been lacking. Results This research conducted genome-wide identification and systematical analysis of AP complexes in foxtail millet. 33 SiAP complex genes were identified and classified into 7 groups, distributed unevenly across 9 chromosomes in foxtail millet. Among these genes, 11 segmental duplication pairs were found. Out of the 33 SiAP complex genes, 24 exhibited collinear relationships with Setaria viridis , while only one showed relationship with Arabidopsis thaliana . Gene structure and motif composition were investigated to understand the function and evolution of these SiAP complex genes. Furthermore, these promoter region of the SiAP complex genes contains 49 cis -elements that are associated with responses to light, hormones, abiotic stress, growth and development. The interaction network between the SiAP complexes was analyzed, and there were strong interactions among the SiAP complex proteins. Expression patterns of SiAP complex genes in different organs and developmental stages of foxtail millet were investigated. The majority of the SiAP complex genes exhibited expressed in multiple tissues, with some genes being predominantly expressed in specific tissues. Subsequently, we selected SiAP4M and SiAP2M for validation of subcellular localization. The signal of 35 S:: SiAP4M: GFP (Long) and 35 S:: SiAP4M: GFP (Short) fused proteins were primarily observed in the nucleus, while the signal of 35 S:: SiAP2M: GFP fused proteins was widely distributed on the cell membrane and vesicles. Conclusions Overall, this study presents a comprehensive map of the SiAP complexes in foxtail millet. These findings not only administer to understanding the biological functions of AP complexes in foxtail millet growth and development but also offer insights for enhancing genetic breeding in this crop.

Completion of genome sequences for the diploid Setaria italica reveals features of C 4 photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass ( Panicum virgatum ). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted. We generated a high-quality reference genome sequence for foxtail millet ( Setaria italica ). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis , the ancestral wild relative of S. italica , and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass ( Panicum virgatum ).

Our study aimed at examining the phylogenetic position of the newly-found Setaria nematodes obtained from the red deer (Cervus elaphus) based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COX-1). Alignment and phylogenetic analyses, as well as SEM microscopic analysis, revealed the presence of two Setaria species: S. cervi and S. tundra. Setaria tundra was noted in only one individual, a calf of the red deer, while S. cervi was observed in three stages, two hinds and one calf of the red deer. According to our knowledge, it is the first case of S. cervi in the red deer in Poland confirmed in molecular studies and also the first case of S. tundra infection in the red deer.

Salinity stress has become an expanding threat to food security worldwide. Revealing the mechanisms of salinity tolerance in plants has immense significance. Foxtail millet ( Setaria italica L.) has been regarded as a model crop for exploring mechanisms under stress, considering its extreme adaptation abilities to adverse ecologies. In present study, two foxtail millet cultivars of Yugu2 and An04 with contrasting salt tolerance properties were investigated through integrative analyses of transcriptomics and metabolomics. In the transcriptomics results, 8887 and 12,249 DEGs were identified in Yugu2 and An04 in response to salinity, respectively, and 3149 of which were overlapped between two varieties. These salinity-responsive genes indicated that ion transport, redox homeostasis, phytohormone metabolism, signaling and secondary metabolism were enriched in Yugu2 by GO and KEGG analyses. The integrative omics analysis implied that phenylpropanoid, flavonoid and lignin biosynthesis pathways, and lysophospholipids were vital in determining the foxtail millet salinity tolerance. Importantly, the tolerance of Yugu2 attributed to higher efficiencies of ion channel and antioxidant system. All these provide a comprehensive regulatory network of foxtail millet to cope with salinity, and shed some lights on salt tolerance which is relevant for other cereal crops.

Nucleoredoxin (NRX), a member of the thioredoxin (TRX) superfamily, plays a crucial role in regulating plant growth and development, as well as in responses to both abiotic and biotic stresses. However, its contribution to drought resistance in foxtail millet remains unclear. In this study, the SiNRX1 of foxtail millet was knocked out using CRISPR/Cas9 system, and the drought resistance of sinrx1 mutants was identified at both the germination stage and the seedling stage. Moreover, through transcriptome sequencing and data-independent acquisition (DIA) quantitative proteomics determination of sinrx1 mutants and wild types (WT) at the seedling stage under drought and control conditions, the molecular mechanism of SiNRX1 regulating drought resistance was preliminarily analyzed. The results indicated that after 7 days of simulated drought treatment during the germination period, the germination rate, root length and bud length of the sinrx1 mutant decreased significantly in comparison with the WT. During the seedling stage under drought stress, the survival rate, chlorophyll content, proline content, peroxidase (POD) activity and catalase (CAT) activity of the sinrx1 mutant decreased markedly compared to those of the WT plants. However, the malondialdehyde (MDA) content of the sinrx1 mutant was significantly higher than that of the WT. This indicates that, during the germination and seedling stages, the drought resistance of the sinrx1 mutant decreased significantly compared to that of the WT. The transcriptome findings suggested that the 2253 differentially expressed genes (DEGs) (1179 up-regulated DEGs and 1074 down-regulated DEGs) are drought-responsive genes specifically influenced by SiNRX1 . The 2253 DEGs were significantly enriched in pathways including phenylalanine, tyrosine and tryptophan biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction. The proteomic results suggests that the 155 differentially expressed proteins (DEPs) (127 up-regulated DEPs and 28 down-regulated DEPs) are drought-responsive proteins specifically influenced by SiNRX1. The 155 DEPs were significantly enriched in pathways including biosynthesis of secondary metabolites, brassinosteroid biosynthesis, metabolic pathways, and phenylpropanoid biosynthesis. Moreover, 2253 DEGs and 155 DEPs were significantly and jointly enriched in the phenylpropanoid biosynthesis pathway. This study provides theoretical guidance for analyzing the drought resistance mechanisms of foxtail millet plants and for drought-resistance breeding.

Key message An efficient and improved transformation method for functional genetics studies in S. italica , being a boon for the Setaria scientific community and for crop improvement. Foxtail millet ( Setaria italica ) is a short life cycle C4 plant, with sequenced genome, and a potential model plant for C4 species. S. italica is also important on a global food security and healthiness context due to its importance in arid and semi-arid areas. However, despite its importance, there are just few transformation protocols directed to this species. The current protocols reached about 5.5–9% of efficiency, which do not make it a valuable model organism. Different types of explants were used in the above mentioned methods, such as immature and mature inflorescence and shoot apex. However, these techniques have many limitations, such as unavailability of explants throughout the year and a crucial, laborious and considerable time-consuming selection. Aiming a simplified and efficient methodology, we adopted dry mature seeds as explants, which are available in abundance, are constant along the year and well responsive to tissue culture, in addition to a differentiated approach that reaches on an average 19.2% transformation efficiency of S. italica. Thus, we propose a protocol that optimizes the transformation efficiency of this cereal crop allowing a high increase on transformation and regeneration rates. Our transformation protocol provides an interesting tool for Setaria community research as well as enables new strategies for breeding enhanced productivity in the species.