A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system

Genomic characterization and expression analysis of TCP transcription factors in Setaria italica and Setaria viridis

The plant-specific TCP transcription factor plays important roles in plant development and environment adaptation. Setaria italica and Setaria viridis, the C4 model plants, can grow on drought or arid soils. However, there is no systematic information about the genomic dissection and the expression of Setaria TCP genes. A total of 22 TCP genes were both identified from S. italica and S. viridis genomes. They all contained bHLH domain and were grouped into three main clades (PCF, CIN, and CYC/TB1). The TCP genes in the same clades shared similar gene structures. Cis-element in the TCP promoter regions were analyzed and associated with hormones and stress responsiveness. Ten TCP genes were predicted to be targets of miRNA319. Moreover, gene ontology analysis indicated three SiTCP and three SvTCP genes were involved in the regulation of shoot development, and SiTCP16/SvTCP16 were clustered together with tillering controlling gene TB1. The TCP genes were differentially expressed in the organs, but SiTCP/SvTCP orthologs shared similar expression patterns. Ten SiTCP members were downregulated under drought or salinity stresses, indicating they may play regulatory roles in abiotic stresses. The study provides detailed information regarding Setaria TCP genes, providing the theoretical basis for agricultural applications.

Total Protein Content, Amino Acid Composition and Eating-Quality Evaluation of Foxtail Millet (Setaria italica (L.) P. Beauv)

Foxtail millet has attracted substantial attention in recent years because of its excellent properties as a cereal crop with high nutritional value. Although the cultivation area of foxtail millet keeps growing, the fundamental research into the nutritional and eating qualities of foxtail millet germplasm collections is limited. In this study, we performed a survey of protein content, amino acid composition and eating quality among a germplasm collection of foxtail millet accessions grown in different environments. Our results revealed 21 accessions with stable protein content under different environments. The correlation analysis further revealed that the protein content of the grains was affected by environmental and genotypic interactions. The further amino acid composition analyses suggested that higher protein content accessions have a better essential amino acid index, providing more nutritional value for human beings and animal feedstock. Moreover, the flavor-related amino acid content and other eating-quality trait analyses were also performed. The subordinative analysis suggested that B331 could be the best accession with high protein content and superior eating quality. Taken together, this study provides essential nutritional and eating-quality data on our germplasm collection of foxtail millets, and provides a core genetic resource from which to breed elite foxtail millet varieties in the future.

Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria

Introduction

Nitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N.

Methods

Bioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2.

Results

We identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins withNO 3 - were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs-NO 3 - binding energy ranged from -3.8 to -2.7 kcal/mol.

Discussion

Taken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.

First Report of Rhizoctonia solani AG-4 HG-III Causing Sheath Blight on Foxtail Millet in China

Foxtail millet (Setaria italica) is an important grain and forage crop. This crop is widely grown in Northern China (Yang et al.2020). In Aug 2021, foxtail millet variety of Jigu42 showing lodging were found in Baoding China with the incidence of 30% and irregular brown lesions were found in sheaths and leaves of infected plants. The center of the lesions was kraurotic and pale, and the edges were gray-brown or dark brown. Twelve samples with typical lesions were collected from the surveyed field to isolate the pathogen. The infected samples were cut into square pieces of about 3 to 5 mm and were immersed into NaOCl (1%) for 1 min followed by washing with sterile water for three times. Then all sterilized tissues were inoculated on potato dextrose agar (PDA) plates and incubated at 25℃. After 3 days, fresh mycelial tips grown from the tissues were transferred to new plates for purification and incubated in the dark at 25°C for 4-5 days until the hyphae covered the whole plates. The colonies of 15 isolates on PDA medium showed similar colonial characteristics, which were fluffy and white initially, gradually turned light brown, and no sclerotia was observed even at 20 days later. Micro-examination revealed that all isolates showed the identical morphological features as Rhizoctonia sp. (Sneh et al. 1991), which contained the septate and right-angled branching hyphae with slight constriction at the base of mycelial branches, and three to seven nuclei per cell (Yang et al. 2013). Total genomic DNA was extracted from 5-day-old cultures, and the internal transcribed spacer (ITS) region of rDNA was amplified with ITS1 and ITS4 as the primers (Garibaldi et al. 2019). The sequencing results showed that the nucleotide sequences of 15 amplicons were identical and shared 100% identity with the corresponding fragments of R. solani AG-4 HG-III from sugar beet (GenBank accession No. MH172666 and MH172663) in Blastn search. The sequencing size of ITS in this study was 3 bp shorter than that of sugar beet, with a length of 722, because the base 'T' in the beginning and 'GA' in the end of the sequences did not detected in our study. Phylogenetic tree of 16 isolates of different AG4 subgroups was created by the software MEGA 7.0 through the NJ method, and the showed that the isolates were clustered to the clade of AG-4 HG-III group. The sequences of three isolates were deposited in GenBank under the accession No. ON810364, ON810365 and ON810366. For pathogenicity test, 5 mm diameters plate of the 5-day-old fungus which cultured on PDA were inoculated to the sheath of 10 foxtail millet plants grown in pots at 5- or 6-leaf stage. Then, the inoculated plants were placed into a growth chamber, and the inoculated sheaths were covered with wet cotton ball for 2 days to keep humidity, while sterile water was inoculated as the control. All plants were cultivated at 26°C with 14 h light and 10 h dark for 14 days. The experiment was repeated for three times. As the result, the same lesions observed in the field appeared on the inoculated plants at 10-14 days post inoculation, whereas the mock was healthy. The pathogen was re-isolated from the infected samples. The morphological characteristics and the nucleotide sequences of ITSs were same as that of the original isolates. All in above, the pathogen cusing sheath blight on foxtail millet was identified as R. solani AG-4 HG-III. To our knowledge, this is the first report of R. solani AG-4 HG-III causing sheath blight on S. italica in China. This finding expands the host range known for R. solani AG-4 HG-III and will be helpful for developing effective control strategies of foxtail millet sheath blight.

Role of miRNAs in regulation of SA-mediated upregulation of genes involved in folate and methionine metabolism in foxtail millet

The effect of exogenous salicylic acid (SA) on folate metabolism and the related gene regulatory mechanisms is still unclear. In this study, the panicle of foxtail millet treated with different SA concentrations showed that 6 mM SA doubled the 5-methyltetrahydrofolate content compared to that of the control. An untargeted metabolomic analysis revealed that 275 metabolites were enriched in amino acid metabolic pathways. Significantly, the relative content of methionine (Met) after 6 mM SA treatment was 3.14 times higher than the control. Transcriptome analysis revealed that differentially expressed genes were mainly enriched in the folate and amino acid biosynthesis pathways (including Met, Cys, Pro, Ser et al.). The miRNA-mRNA interactions related to the folate and Met metabolic pathways were analyzed and several likely structural gene targets for miRNAs were identified, miRNA-seq analysis revealed that 33 and 51 miRNAs targeted 11 and 15 genes related to the folate and Met pathways, respectively. Eight key genes in the folate metabolism pathway were likely to be up-regulated by 14 new miRNAs and 20 new miRNAs up-regulated the 9 key genes in the Met metabolism pathway. The 6 miRNA-mRNA interactions related to the folate and Met metabolism pathways were verified by qRT-PCR, and consistent with the prediction. The results showed that DHFR1 gene expression level related to folate synthesis was directly up-regulated by Nov-m0139-3p with 3.8 times, but DHFR2 was down-regulated by Nov-m0731-5p with 0.62 times. The expression level of CYSC1 and APIP related to Met synthesis were up-regulated by Nov-m0461-5p and Nov-m0664-3p with 4.27 and 1.32 times, respectively. Our results suggested that exogenous SA could induce the folate and Met accumulated in the panicle of foxtail millet. The higher expression level of DHFR1, FTHFD, CYSC1 and APIP in the folate and Met metabolism pathway and their regulators, including Nov-m0139-3p, Nov-m0717-5p, Nov-m0461-5p and Nov-m0664-3p, could be responsible for these metabolites accumulation. This study lays the theoretical foundation for elucidating the post-transcription regulatory mechanisms of folate and Met metabolism.

Comparative transcriptome profiling of resistant and susceptible foxtail millet responses to Sclerospora graminicola infection

BACKGROUND

Downy mildew of foxtail millet, which is caused by the biotrophic oomycete Sclerospora graminicola (Sacc.) Schroeter, is one of the most disruptive diseases. The foxtail millet-S. graminicola interaction is largely unexplored. Transcriptome sequencing technology can help to reveal the interaction mechanism between foxtail millet and its pathogens.

RESULTS

Transmission electron microscopy observations of leaves infected with S. graminicola showed that the structures of organelles in the host cells gradually became deformed and damaged, or even disappeared from the 3- to 7-leaf stages. However, organelles in the leaves of resistant variety were rarely damaged. Moreover, the activities of seven cell wall degrading enzymes in resistant and susceptible varieties were also quite different after pathogen induction and most of enzymes activities were significantly higher in the susceptible variety JG21 than in the resistant variety G1 at all stages. Subsequently, we compared the transcriptional profiles between the G1 and JG21 in response to S. graminicola infection at 3-, 5-, and 7-leaf stages using RNA-Seq technology. A total of 473 and 1433 differentially expressed genes (DEGs) were identified in the resistant and susceptible varieties, respectively. The pathway analysis of the DEGs showed that the highly enriched categories were related to glutathione metabolism, plant hormone signalling, phenylalanine metabolism, and cutin, suberin and wax biosynthesis. Some defence-related genes were also revealed in the DEGs, including leucine-rich protein kinase, Ser/Thr protein kinase, peroxidase, cell wall degrading enzymes, laccases and auxin response genes. Our results also confirmed the linkage of transcriptomic data with qRT-PCR data. In particular, LRR protein kinase encoded by Seita.8G131800, Ser/Thr protein kinase encoded by Seita.2G024900 and Seita. 2G024800, which have played an essential resistant role during the infection by S. graminicola.

CONCLUSIONS

Transcriptome sequencing revealed that host resistance to S. graminicola was likely due to the activation of defence-related genes, such as leucine-rich protein kinase and Ser/Thr protein kinase. Our study identified pathways and genes that contribute to the understanding of the interaction between foxtail millet and S. graminicola at the transcriptomic level. The results will help us better understand the resistance mechanism of foxtail millet against S. graminicola.

Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant

Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C₄ model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.

Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis

Anthocyanin is a natural pigment that has a functional role in plants to attract pollinating insects and is important in stress response. Foxtail millet (Setaria italica) is known as a nutritional crop with high resistance to drought and barren. However, the molecular mechanism regulating anthocyanin accumulation and the relationship between anthocyanin and the stress resistance of foxtail millet remains obscure. In this study, we screened hundreds of germplasm resources and obtained several varieties with purple plants in foxtail millet. By studying the purple-leaved B100 variety and the control variety, Yugu1 with green leaves, we found that B100 could accumulate a large amount of anthocyanin in the leaf epiderma, and B100 had stronger stress tolerance. Further transcriptome analysis revealed the differences in gene expression patterns between the two varieties. We identified nine genes encoding enzymes related to anthocyanin biosynthesis using quantitative PCR validation that showed significantly higher expression levels in B100 than Yugu1. The results of this study lay the foundation for the analysis of the molecular mechanism of anthocyanin accumulation in foxtail millet, and provided genetic resources for the molecular breeding of crops with high anthocyanin content.

Progress and prospects of C4 trait engineering in plants

Incorporating C₄ photosynthetic traits into C₃ crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C₃ , C₄ , and C₃ -C₄ intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C₄ photosynthetic traits in C₃ crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C₃ crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C₃ crops for sustaining food, fibre and fuel production around the globe.

Identification and exploration of the GRF and GIF families in maize and foxtail millet

Plant growth and development are dependent on complex regulatory networks to adapt various environments. The growth regulatory factor (GRF) and GRF-interacting factor (GIF) families have been shown to control growth in various plant species. There are growing evidences that GRFs and GIFs can improve crop genetic transformation efficiency. In this study, we identified and classified 17 ZmGRFs, 10 SiGRFs, 4 ZmGIFs and 3 SiGIFs in maize (Zea mays L.) and foxtail millet (Setaria italica L.) using updated genome data. Many ABREs (Abscisic Acid-responsive elements) were present in the promoter regions of GRFs by analysis, and the expression levels of ZmGRF4, 9, 12, 14 and ZmGIF2 were associated with the Abscisic Acid (ABA) response. Furthermore, ZmGRF9 showed collinearity with AtGRF5 between Arabidopsis and maize. ZmGRF9 conservatively interacts with ZmGIF 2, 3, and 4. As a result, we systematically identified GRF and GIF family members, analyzed the regulatory network, and found that exogenous ABA inhibited the expression of GRFs, regulating responses to stress in the environment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01234-z.

Integrative genomics analysis of the ever-shrinking pectin methylesterase (PME) gene family in foxtail millet (Setaria italica)

Pectin methylesterase (PME) plays a vital role in the growth and development of plants. Their genes can be classified into two types, with Type-1 having an extra domain, PMEI. PME genes in foxtail millet (Setaria italica L.) have not been identified, and their sequence features and evolution have not been explored. Here, we identified 41 foxtail millet PME genes. Decoding the pro-region, containing the PMEI domain, revealed its more active nature than the DNA encoding PME domain, easier to be lost to produce Type-2 PME genes. We inferred that the active nature of the pro-region could be related to its harbouring more repetitive DNA sequences. Further, we revealed that though whole-genome duplication and tandem duplication contributed to producing new copies of PME genes, phylogenetic analysis provided clear evidence of ever-shrinking gene family size in foxtail millet and the other grasses in the past 100 million years. Phylogenetic analysis also supports the existence of two gene groups, Group I and Group II, with genes in Group II being more conservative. Our research contributes to understanding how DNA sequence structure affects the functional innovation and evolution of PME genes.

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C₄ photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

Carotenoid Cleavage Dioxygenase 1 Catalyzes Lutein Degradation To Influence Carotenoid Accumulation and Color Development in Foxtail Millet Grains

Foxtail millet is a minor but economically important crop in certain regions of the world. Millet color is often used to judge grain quality, yet the molecular determinants of millet coloration remain unclear. Here, we explored the relationship between SiCCD1 and millet coloration in yellow and white millet varieties. Carotenoid levels declined with grain maturation and were negatively correlated with SiCCD1 expression, which was significantly higher in white millet as compared to yellow millet during the color development stage. Cloning of the SiCCD1 promoter and CDS sequences from these different millet varieties revealed the presence of two additional cis-regulatory elements within the SiCCD1 promoter in white millet varieties, including an enhancer-like GC motif element associated with anoxic specific inducibility and a GCN4-motif element associated with endosperm expression. Dual-luciferase reporter assays confirmed that SiCCD1 promoter fragments containing these additional cis-acting elements derived from white millet varieties were significantly more active than those from yellow millet varieties, consistent with the observed SiCCD1 expression patterns. Further in vitro enzyme detection assays confirmed that SiCCD1 primarily targets and degrades lutein. Together, these data suggest that SiCCD1 promoter variation was a key factor associated with the observed differences in SiCCD1 expression, which in turn led to the difference in millet coloration.

Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects

Foxtail millet (Setaria italica), which was domesticated from the wild species green foxtail (Setaria viridis), is a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail millet grains, we generated and analyzed the datasets encompassing the genomes, transcriptomes, metabolomes, and anti-inflammatory indices from 398 foxtail millet accessions. We identified hundreds of common variants that influence numerous secondary metabolites. We observed tremendous differences in natural variations of the metabolites and their underlying genetic architectures between distinct sub-groups of foxtail millet. Furthermore, we found that the selection of the gene alleles associated with yellow grains led to altered profiles of metabolites such as carotenoids and endogenous phytohormones. Using CRISPR-mediated genome editing we validated the function of PHYTOENE SYNTHASE 1 (PSY1) gene in affecting millet grain color and quality. Interestingly, our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects. Taken together, our multi-omics study illustrates how the breeding history of foxtail millet has shaped its metabolite profile. The datasets we generated in this study also provide important resources for further understanding how millet grain quality is affected by different metabolites, laying the foundations for future millet genetic research and metabolome-assisted improvement.

Genome-wide investigation of histone acetyltransferase gene family and its responses to biotic and abiotic stress in foxtail millet (Setaria italica [L.] P. Beauv)

BACKGROUND

Modification of histone acetylation is a ubiquitous and reversible process in eukaryotes and prokaryotes and plays crucial roles in the regulation of gene expression during plant development and stress responses. Histone acetylation is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT plays an essential regulatory role in various growth and development processes by modifying the chromatin structure through interactions with other histone modifications and transcription factors in eukaryotic cells, affecting the transcription of genes. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana and Oryza sativa. However, little information is available on the HAT genes in foxtail millet (Setaria italica [L.] P. Beauv).

RESULTS

In this study, 24 HAT genes (SiHATs) were identified and divided into four groups with conserved gene structures via motif composition analysis. Phylogenetic analysis of the genes was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa, and foxtail millet; 19 and 2 orthologous gene pairs were individually identified. Moreover, all identified HAT gene pairs likely underwent purified selection based on their non-synonymous/synonymous nucleotide substitutions. Using published transcriptome data, we found that SiHAT genes were preferentially expressed in some tissues and organs. Stress responses were also examined, and data showed that SiHAT gene transcription was influenced by drought, salt, low nitrogen, and low phosphorus stress, and that the expression of four SiHATs was altered as a result of infection by Sclerospora graminicola.

CONCLUSIONS

Results indicated that histone acetylation may play an important role in plant growth and development and stress adaptations. These findings suggest that SiHATs play specific roles in the response to abiotic stress and viral infection. This study lays a foundation for further analysis of the biological functions of SiHATs in foxtail millet.

Exploring the SiCCT Gene Family and Its Role in Heading Date in Foxtail Millet

CCT transcription factors are involved in the regulation of photoperiod and abiotic stress in Arabidopsis and rice. It is not clear that how CCT gene family expand and regulate heading date in foxtail millet. In this study, we conducted a systematic analysis of the CCT gene family in foxtail millet. Thirty-nine CCT genes were identified and divided into four subfamilies based on functional motifs. Analysis showed that dispersed duplication played a predominant role in the expansion of CCT genes during evolution. Nucleotide diversity analysis suggested that genes in CONSTANS (COL)-like, CCT MOTIF FAMILY (CMF)-like, and pseudoresponse response regulator (PRR)-like subfamilies were subjected to selection. Fifteen CCT genes were colocalized with previous heading date quantitative trait loci (QTL) and genome-wide association analysis (GWAS) signals. Transgenic plants were then employed to confirm that overexpression of the CCT gene SiPRR37 delayed the heading date and increased plant height. Our study first investigated the characterization and expansion of the CCT family in foxtail millet and demonstrated the role of SiPRR37. These results lay a significant foundation for further research on the function of CCT genes and provide a cue for the regulation of heading date.

Heterologous Expression of SiFBP, a Folate-Binding Protein from Foxtail Millet, Confers Increased Folate Content and Altered Amino Acid Profiles with Nutritional Potential to Arabidopsis

The mechanism underlying folate degradation in foxtail millet grains remains unclear. Here, we identified SiFBP (Setaria italica folate-binding protein) from foxtail millet. A phylogenetic tree revealed that FBPs have close genetic relationships among cereal crop species. Docking analysis and heterologous expression of SiFBP in yeast showed that it could bind folic acid (FA). The SiFBP localized to the plasma membrane in tobacco mesophyll cells by transient expression. In Arabidopsis, it was expressed specifically in the roots and germinating seeds. Overexpressing SiFBP in yeast and Arabidopsis significantly increased folate contents. Untargeted metabolome analysis revealed differentially accumulated metabolites between the transgenic lines (TLs) and wild type (WT); these metabolites were mainly enriched in the amino acid metabolism pathway. The relative contents of lysine and leucine, threonine, and l-methionine were significantly higher in the TLs than in WT. Genes related to the folate and lysine synthesis pathways were upregulated in the TLs. Thus, SiFBP can be used for biofortification of folate and important amino acids in crops via genetic engineering.

The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Setaria italica L.)

MicroRNA (miRNA) is an essential endogenous post-transcriptional regulatory factor, and foxtail millet (Setaria italica L.) is an ideal C4 model cereal that is a highly valuable crop in semiarid and arid areas. The Research on comprehensive and high confidence identification and annotation of foxtail millet miRNAs needs to be strengthened, and to our knowledge, there is no information on the regulatory network of foxtail millet miRNA. In this study, 136 high confidence miRNAs were identified through high-throughput sequencing of the small RNAs in seven tissues at the shooting and grain filling stages of foxtail millet. A total of 2,417 target genes were obtained by combining computational biology software and degradome sequencing methods. Furthermore, an analysis using transcriptome sequencing revealed the relationships between miRNAs and their target genes and simultaneously explored key regulatory modules in panicles during the grain filling stage. An miRNA regulatory network was constructed to explore the functions of miRNA in more detail. This network, centered on miRNAs and combining upstream transcriptional factors and downstream target genes, is primarily composed of feed forward loop motifs, which greatly enhances our knowledge of the potential functions of miRNAs and uncovers numerous previously unknown regulatory links. This study provides a solid foundation for research on the function and regulatory network of miRNAs in foxtail millet.

Time-series transcriptomics reveals a drought-responsive temporal network and crosstalk between drought stress and the circadian clock in foxtail millet

Drought stress is a serious factor affecting crop growth and production worldwide. The circadian clock has been identified as key to improving regional adaptability of plants. However, our understanding of the contribution of the circadian clock to drought response and the impacts of drought stress on the circadian clock in plants is still limited. To explore the interactions between the circadian clock and drought stress, foxtail millet seedlings were treated with simulated drought (20% polyethylene glycol-6000) treatment starting at the day (DD) onset zeitgeber time 0 (ZT0, lights on) and at the night (DN) onset zeitgeber time 16 (ZT16, lights off). A high temporal-resolution transcriptomic investigation was performed using DD and DN samples collected at intervals of 2 or 4 h within a 24-h drought-treatment period. Overall, we identified 13 294 drought-responsive genes (DRGs). Among these DRGs, 7931 were common between DD and DN samples, 2638 were specific to DD, and 2725 were specific to DN. Additionally, we identified 1257 circadian genes, of which 67% were DRGs. Interestingly, with drought treatment starting at the day for 8, 12 or 16 h, the circadian phase shifted to 12 h. We also found that the circadian clock led to different day and night drought-responsive pathways. The identification of DRG_Clock (DRG and circadian clock) and DRG_NonClock (DRG and not circadian clock) genes provides a reference for selecting candidate drought resistance genes. Our work reveals the temporal drought-response process and crosstalk between drought stress and the circadian clock in foxtail millet.

Conjunctive Analyses of Bulk Segregant Analysis Sequencing and Bulk Segregant RNA Sequencing to Identify Candidate Genes Controlling Spikelet Sterility of Foxtail Millet

Foxtail millet has gradually become a model gramineous C4 crop owing to its short growth period and small genome. Research on the development of its spikelets is not only directly related to the yield and economic value of foxtail millet but also can provide a reference for studying the fertility of other C4 crops. In this study, a hybrid population containing 200 offspring was constructed from the Xinong8852 and An15 parental lines, and two extreme trait populations were constructed from the F2 generation for analysis of the spikelet sterility. The F2 population conformed to a 3:1 Mendelian segregation ratio, and it was thus concluded that this trait is likely controlled by a single recessive gene. Bulk segregant analysis sequencing (BSA-Seq) was used to determine the candidate regions and candidate genes related to the development of foxtail millet spikelets. Additionally, the functional analysis of differentially expressed genes in populations with different traits was conducted by bulk segregant RNA sequencing (BSR-Seq). Finally, conjunctive analysis of BSA-Seq and BSR-Seq results, combined with biological information analysis, revealed six genes on chromosome VII that were ultimately identified as candidate genes controlling foxtail millet spikelet development. This study provides a new reference for research on foxtail millet sterility and lays a solid foundation for the examination of fertility in other gramineous crops.

Comparative metabolomic and transcriptomic analysis reveals a coexpression network of the carotenoid metabolism pathway in the panicle of Setaria italica

BACKGROUND

The grains of foxtail millet are enriched in carotenoids, which endow this plant with a yellow color and extremely high nutritional value. However, the underlying molecular regulation mechanism and gene coexpression network remain unclear.

METHODS

The carotenoid species and content were detected by HPLC for two foxtail millet varieties at three panicle development stages. Based on a homologous sequence BLAST analysis, these genes related to carotenoid metabolism were identified from the foxtail millet genome database. The conserved protein domains, chromosome locations, gene structures and phylogenetic trees were analyzed using bioinformatics tools. RNA-seq was performed for these samples to identify differentially expressed genes (DEGs). A Pearson correlation analysis was performed between the expression of genes related to carotenoid metabolism and the content of carotenoid metabolites. Furthermore, the expression levels of the key DEGs were verified by qRT-PCR. The gene coexpression network was constructed by a weighted gene coexpression network analysis (WGCNA).

RESULT

The major carotenoid metabolites in the panicles of DHD and JG21 were lutein and β-carotene. These carotenoid metabolite contents sharply decreased during the panicle development stage. The lutein and β-carotene contents were highest at the S1 stage of DHD, with values of 11.474 μg /100 mg and 12.524 μg /100 mg, respectively. Fifty-four genes related to carotenoid metabolism were identified in the foxtail millet genome. Cis-acting element analysis showed that these gene promoters mainly contain 'plant hormone', 'drought stress resistance', 'MYB binding site', 'endosperm specific' and 'seed specific' cis-acting elements and especially the 'light-responsive' and 'ABA-responsive' elements. In the carotenoid metabolic pathways, SiHDS, SiHMGS3, SiPDS and SiNCED1 were more highly expressed in the panicle of foxtail millet. The expression of SiCMT, SiAACT3, SiPSY1, SiZEP1/2, and SiCCD8c/8d was significantly correlated with the lutein content. The expression of SiCMT, SiHDR, SiIDI2, SiAACT3, SiPSY1, and SiZEP1/2 was significantly correlated with the content of β-carotene. WGCNA showed that the coral module was highly correlated with lutein and β-carotene, and 13 structural genes from the carotenoid biosynthetic pathway were identified. Network visualization revealed 25 intramodular hub genes that putatively control carotenoid metabolism.

CONCLUSION

Based on the integrative analysis of the transcriptomics and carotenoid metabonomics, we found that DEGs related to carotenoid metabolism had a stronger correlation with the key carotenoid metabolite content. The correlation analysis and WGCNA identified and predicted the gene regulation network related to carotenoid metabolism. These results lay the foundation for exploring the key target genes regulating carotenoid metabolism flux in the panicle of foxtail millet. We hope that these target genes could be used to genetically modify millet to enhance the carotenoid content in the future.

Identification, Molecular Characteristics, and Evolution of GRF Gene Family in Foxtail Millet (Setaria italica L.)

Growth-regulating factor (GRF) is a multigene family that plays a vital role in the growth and development of plants. In the past, the GRF family of many plants has been studied. However, there is not a report about identification and evolution of GRF in foxtail millet (Setaria italia). Here, we identified 10 GRF genes in foxtail millet. Seven (70.00%) were regulated by Sit-miR396, and there were 19 optimal codons in GRFs of foxtail millet. Additionally, we found that WGD or segmental duplication have affected GRFs in foxtail millet between 15.07 and 45.97 million years ago. Regarding the GRF gene family of land plants, we identified a total of 157 GRF genes in 15 representative land plants. We found that GRF gene family originated from Group E, and the GRF gene family in monocots was gradually shrinking. Also, more loss resulted from the small number of GRF genes in lower plants. Exploring the evolution of GRF and functional analysis in the foxtail millet help us to understand GRF better and make a further study about the mechanism of GRF. These results provide a basis for the genetic improvement of foxtail millet and indicate an improvement of the yield.

Efficient Genome Editing in Setaria italica Using CRISPR/Cas9 and Base Editors

The genome editing toolbox based on CRISPR/Cas9 has brought revolutionary changes to agricultural and plant scientific research. With the development of stable genetic transformation protocols, a highly efficient genome editing system for foxtail millet (Setaria italica) is required. In the present study, we use the CRISPR/Cas9 single- and multi-gene knockout system to target the SiFMBP, SiDof4, SiBADH2, SiGBSS1, and SiIPK1 genes in the foxtail millet protoplasts to screen out highly efficient targeted sgRNAs. Then, we recovered homozygous mutant plants with most of the targeted genes through an Agrobacterium-mediated genetic transformation of foxtail millet. The mutagenesis frequency in the T₀ generation was as high as 100%, and it was passed stably on to the next generation. After screening these targeted edited events, we did not detect off-target mutations at potential sites. Based on this system, we have achieved base editing successfully using two base editors (CBE and ABE) to target the SiALS and SiACC genes of foxtail millet. By utilizing CBE to target the SiALS gene, we created a homozygous herbicide-tolerant mutant plant. The current system could enhance the analysis of functional genomics and genetic improvement of foxtail millet.

Response of Multiple Tissues to Drought Revealed by a Weighted Gene Co-Expression Network Analysis in Foxtail Millet [Setaria italica (L.) P. Beauv.]

Characterization of drought-tolerance mechanisms during the jointing stage in foxtail millet under water-limited conditions is essential for improving the grain yield of this C₄ crop species. In this trial, two drought-tolerant and two drought-sensitive cultivars were examined using transcriptomic dissections of three tissues (root, stem, and leaf) under naturally occurring water-limited conditions. We detected a total of 32,170 expressed genes and characterized 13,552 differentially expressed genes (DEGs) correlated with drought treatment. The majority of DEGs were identified in the root tissue, followed by leaf and stem tissues, and the number of DEGs identified in the stems of drought-sensitive cultivars was about two times higher than the drought-tolerant ones. A total of 127 differentially expressed transcription factors (DETFs) with different drought-responsive patterns were identified between drought-tolerant and drought-sensitive genotypes (including MYB, b-ZIP, ERF, and WRKY). Furthermore, a total of 34 modules were constructed for all expressed genes using a weighted gene co-expression network analysis (WGCNA), and seven modules were closely related to the drought treatment. A total of 1,343 hub genes (including RAB18, LEA14, and RD22) were detected in the drought-related module, and cell cycle and DNA replication-related transcriptional pathways were identified as vital regulators of drought tolerance in foxtail millet. The results of this study provide a comprehensive overview of how Setaria italica copes with drought-inflicted environments during the jointing stage through transcriptional regulating strategies in different organs and lays a foundation for the improvement of drought-tolerant cereal cultivars through genomic editing approaches in the future.

Cloning and functional identification of setaria italica somatic embryogenesis receptor-like kinase1 gene (SiSERK1)

Plant somatic embryogenesis receptor-like kinases (SERK), members of leucine-rich repeat receptor-like kinases (LRR-RLKs) subfamily, are widely involved in plant growth, development and innate immunity. In this study, the setaria italica somatic embryogenesis receptor-like kinase1 gene (SiSERK1) was cloned by gateway technology, and transferred into a brasssinosteroid (BR) receptor mutant of Arabidopsis thaliana WS2 (bri1-5). After BL treatment, the transgenic plants could partially restore the phenotype of bri1-5. After Pst DC3000 treatment, the CFU value of SiSERK1 overexpression plant pathogen was between WS2 and bri1-5. Stomatal opening and plant height were also between them. Therefore, it is speculated that SiSERK1 gene is involved in BR signaling pathway and can improve the resistance of bri1-5 to Pst DC3000 through SA and NHP mediated systemic acquired resistance (SAR).

Genome-editing in millets: current knowledge and future perspectives

Millets are small seeded cereal crops predominantly cultivated and consumed by resource-poor farmers in the semi-arid tropics of Asia and Africa. Millets possess rich nutrients and a climate resilience property when compared to the other cereals such as rice and wheat. Millet improvement using modern genetic and genomic tools is falling behind other cereal crops due to their cultivation being restricted to less developed countries. Genome editing tools have been successfully applied to major cereal crops and, as a result, many key traits have been introduced into rice, wheat and maize. However, genome editing tools have not yet been used for most millets although they possess rich nutrients. The foxtail millet is the only millet utilised up to now for genome editing works. Limited genomic resources and lack of efficient transformation systems may slow down genome editing in millets. As millets possess many important traits of agricultural importance, high resolution studies with genome editing tools will help to understand the specific mechanism and transfer such traits to major cereals in the future. This review covers the current status of genome editing studies in millets and discusses the future prospects of genome editing in millets to understand key traits of nutrient fortification and develop climate resilient crops in the future.

Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1

Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.

The Responses of the Lipoxygenase Gene Family to Salt and Drought Stress in Foxtail Millet (Setaria italica)

Plant lipoxygenases (LOXs), a kind of non-heme iron-containing dioxygenases, participate plant physiological activities (especially in response to biotic and abiotic stresses) through oxidizing various lipids. However, there was few investigations on LOXs in foxtail millet (Setaria italica). In this study, we identified the LOX gene family in foxtail millet, and divided the total 12 members into three sub-families on the basis of their phylogenetic relationships. Under salt and drought stress, LOX genes showed different expression patterns. Among them, only SiLOX7 showed up-regulated expression in Yugu1 (YG1) and Qinhuang2 (QH2), two stress-tolerant varieties, indicating that SiLOX7 may play an important role in responses to abiotic stress. Our research provides a basis for further investigation of the role of LOX genes in the adaptation to abiotic stresses and other possible biological functions in foxtail millet.

SiCEP3, a C-terminally encoded peptide from Setaria italica, promotes ABA import and signaling

C-terminally encoded peptides (CEPs) are small peptides, typically post-translationally modified, and highly conserved in many species. CEPs are known to inhibit plant growth and development, but the mechanisms are not well understood. In this study, 14 CEPs were identified in Setaria italica and divided into two groups. The transcripts of most SiCEPs were more abundant in roots than in other detected tissues. SiCEP3, SiCEP4, and SiCEP5 were also highly expressed in panicles. Moreover, expression of all SiCEPs was induced by abiotic stresses and phytohormones. SiCEP3 overexpression and application of synthetic SiCEP3 both inhibited seedling growth. In the presence of abscisic acid (ABA), growth inhibition and ABA content in seedlings increased with the concentration of SiCEP3. Transcripts encoding eight ABA transporters and six ABA receptors were induced or repressed by synthetic SiCEP3, ABA, and their combination. Further analysis using loss-of-function mutants of Arabidopsis genes functioning as ABA transporters, receptors, and in the biosynthesis and degradation of ABA revealed that SiCEP3 promoted ABA import at least via NRT1.2 (NITRATE TRANSPORTER 1.2) and ABCG40 (ATP-BINDING CASSETTE G40). In addition, SiCEP3, ABA, or their combination inhibited the kinase activities of CEP receptors AtCEPR1/2. Taken together, our results indicated that the CEP-CEPR module mediates ABA signaling by regulating ABA transporters and ABA receptors in planta.

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

Background

Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C₄ grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet.

Results

Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F₆ and F₇ recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively.

Conclusions

This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07882-x.

Comparative Analysis of Flavonoid Metabolites in Foxtail Millet (Setaria italica) with Different Eating Quality

Foxtail millet (Setaria italica) is an important minor cereal crop in China. The yellow color of the de-husked grain is the most direct aspect for evaluating the foxtail millet quality. The yellow pigment mainly includes carotenoids (lutein and zeaxanthin) and flavonoids. To reveal the diversity and specificity of flavonoids in foxtail millet, we chose three high eating quality and two poor eating quality varieties as research materials. A total of 116 flavonoid metabolites were identified based on Ultra Performance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (UPLC-ESI-MS/MS) system. The tested varieties contained similar levels of flavonoid metabolites, but with each variety accumulating its unique flavonoid metabolites. A total of 33 flavonoid metabolites were identified as significantly discrepant between high eating quality and poor eating quality varieties, which were mainly in the flavonoid biosynthesis pathway and one of its branches, the flavone and flavonol biosynthesis pathway. These results showed the diversified components of flavonoids accumulated in foxtail millets and laid the foundation for further research on flavonoids and the breeding for high-quality foxtail millet varieties.

Alternative Strategies for Multi-Stress Tolerance and Yield Improvement in Millets

Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops by more than 50%. Although millets are tolerant to most abiotic stresses including drought and high temperatures, further improvement is needed to make them more resilient to unprecedented effects of climate change and associated environmental stresses. Incorporation of stress tolerance traits in millets will improve their productivity in marginal environments and will help in overcoming future food shortage due to climate change. Recently, approaches such as application of plant growth-promoting rhizobacteria (PGPRs) have been used to improve growth and development, as well as stress tolerance of crops. Moreover, with the advance of next-generation sequencing technology, genome editing, using the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system are increasingly used to develop stress tolerant varieties in different crops. In this paper, the innate ability of millets to tolerate abiotic stresses and alternative approaches to boost stress resistance were thoroughly reviewed. Moreover, several stress-resistant genes were identified in related monocots such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), and other related species for which orthologs in millets could be manipulated by CRISPR/Cas9 and related genome-editing techniques to improve stress resilience and productivity. These cutting-edge alternative strategies are expected to bring this group of orphan crops at the forefront of scientific research for their potential contribution to global food security.

Making Sense of the Way Plants Sense Herbivores

Plants are constantly threatened by herbivore attacks and must devise survival strategies. Some plants sense and respond to elicitors including specific molecules secreted by herbivores and molecules that are innate to plants. Elicitors activate diverse arrays of plant defense mechanisms that confer resistance to the predator. Recent new insights into the cellular pathways by which plants sense elicitors and elicit defense responses against herbivores are opening doors to a myriad of agricultural applications. This review focuses on the machinery of herbivory-sensing and on cellular and systemic/airborne signaling via elicitors, exemplified by the model case of interactions between Arabidopsis hosts and moths of the genus Spodoptera.

Foxtail Millet: A New Model for C4 Plants

Arabidopsis and rice are major models for C3 plants, but we still lack a model for C4 plants. Recently, Yang and coworkers developed foxtail millet as a C4 plant model; with the rapid development of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas technology, this will open a new era for plant functional studies and crop improvement.

Orphan Crops and their Wild Relatives in the Genomic Era

More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.