Search Results (44)

Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to comprehensively identify SiLEA genes in foxtail millet and elucidate their functional roles and tissue-specific expression patterns. Methods: Genome-wide identification of SiLEA genes was conducted, followed by phylogenetic reconstruction, cis-acting element analysis of promoters, synteny analysis, and expression profiling. Results: Ninety-four SiLEA genes were identified and classified into nine structurally distinct subfamilies, which are unevenly distributed across all nine chromosomes. Phylogenetic analysis showed closer clustering of SiLEA genes with sorghum and rice orthologs than with Arabidopsis thaliana AtLEA genes. Synteny analysis indicated the LEA gene family expansion through tandem and segmental duplication. Promoter cis-element analysis linked SiLEA genes to plant growth regulation, stress responses, and hormone signaling. Transcriptome analysis revealed tissue-specific expression patterns among SiLEA members, while RT-qPCR verified ABA-induced transcriptional regulation of SiLEA genes. Conclusions: This study identified 94 SiLEA genes grouped into nine subfamilies with distinct spatial expression profiles. ABA treatment notably upregulated SiASR-2, SiASR-5, and SiASR-6 in both shoots and roots. Full article

Soil salinization and alkalization are becoming increasingly severe in recent decades, which poses serious threats to crop production and food security in the world. Foxtail millet (Setaria italica L.) is an important cereal crop in China, and it is important to elucidate its saline-alkali tolerance mechanisms for the breeding of new saline-alkali tolerant varieties. In this study, we used 75% seawater to treat two foxtail millet varieties with different saline-alkali tolerances (JK3, saline-alkali tolerant; B175, saline-alkali sensitive) during the seedling stage, and conducted morphological, cellular ultrastructure, physiological, and transcriptomic analyses on the two varieties. The morphological analysis of the saline-alkali response indicated that JK3 exhibited stronger saline-alkali tolerance than B175. The results of the cellular ultrastructure showed that under saline-alkali stress, JK3 had a more intact leaf cell structure than B175, indicating that saline-alkali stress causes less damage to its cells. The physiological analysis of saline-alkali response indicated that JK3 had consistently higher activities of catalase and polyphenol oxidase, as well as higher contents of soluble sugars and soluble proteins at 48–120 h than B175. Transcriptomic analysis revealed that JK3 enhanced its saline-alkali tolerance by positively regulating pathways such as tryptophan/fatty acid metabolism, the MAPK signaling pathway, and peroxisome pathways. Further, WGCNA combining morphological and physiological indicators identified four key modules and five functional pathways (MAPK signaling, glycerolipid metabolism, phosphate and phosphonate metabolism, galactose metabolism, and endoplasmic reticulum protein processing) in response to saline-alkali stress, and identified a total of 24 core genes. Functional annotation indicated that these genes may be involved in the response to saline-alkali stress. These findings lay a foundation for in-depth studies of the molecular mechanisms for saline-alkali tolerance in foxtail millet. Full article

Foxtail millet (Setaria italica L.), a representative C4 species, is recognized for its efficient nutrient utilization and robust abiotic stress responses. However, the molecular mechanisms mediating its tolerance to biotic stresses are poorly understood. In this study, we investigated the root transcriptomic response of foxtail millet to the damage-associated molecular pattern (DAMP), the plant elicitor peptide 1 (Pep1). Transcriptome analysis of Pep1-treated roots identified 401 differentially expressed genes (DEGs), comprising 144 up-regulated and 257 down-regulated genes. Gene Ontology (GO) enrichment analysis revealed a significant enrichment of ‘peroxidase activity’. This finding was corroborated by DAB staining, which confirmed H₂O₂ accumulation, along with elevated malondialdehyde (MDA) levels, collectively indicating oxidative stress. Notably, Pep1 treatment also resulted in a marked up-regulation of the pathogenesis-related protein 1 (PR1) gene in leaves, suggesting the activation of systemic acquired resistance. Together, these results demonstrate that Pep1 triggers substantial transcriptional reprogramming in roots, induces oxidative stress, and activates systemic defense signaling in foxtail millet. Full article

Global agricultural systems are predominantly concentrated in regions characterized by fertile soils, abundant precipitation, and gentle slopes. However, a significant proportion of farmland is situated in areas with poor soil quality, arid conditions, and steep slopes. In such challenging environments, particularly sandy-arid sloping farmlands, selecting native crops that are well-adapted to local conditions is critical for sustainable agricultural practices. This study categorizes local crops in arid regions into four distinct types: tall-stem monocotyledonous plants (represented by maize, Zea mays L.), short-stem monocotyledonous plants (represented by millet, Setaria italica), tap-rooted dicotyledonous plants (represented by soybean, Glycine max (L.) Merr.), and tuberous dicotyledonous plants (represented by potato, Solanum tuberosum L.). A quantitative evaluation framework was developed using five key indices: nitrogen fixation, anti-wind erosion, roots reinforcement, anti-water erosion, and water conservation. These indices were used to calculate the suitability index values for each crop type. The findings revealed that in sandy-arid sloping farmland regions, maize and millet emerged as the most suitable crops for cultivation, followed by soybean, while potato was identified as the least suitable. Maize exhibited high values across all five indices, particularly demonstrating exceptional performance in nitrogen fixation. Additionally, the study demonstrated that traditional farming practices are highly effective in sloping farmlands, since they not only promote crop growth but also mitigate soil erosion. This research offers insights into agricultural management in regions affected by drought, soil erosion, and steep terrain. The results highlight the feasibility of employing traditional farming methods to cultivate maize in such challenging environments, providing practical guidance for sustainable agricultural development. Full article

Background: Weed herbicide resistance is a serious problem in crop protection globally. Giant foxtail (Setaria faberi R.A.N. Herrm.) populations cannot be controlled by acetolactate synthase (ALS)-inhibiting herbicides in a few corn (Zea mays L.) monoculture fields. Methods: Five putative resistant giant foxtail populations, originating from corn monoculture fields in northeastern Greece, were evaluated for possible evolution of ALS-inhibitor resistance (nicosulfuron, rimsulfuron). The resistance ratio, the underlying resistance mechanism, and its impact on competitive ability against corn were studied. Results: The whole-plant rate-response assays showed that these populations were resistant (R) to the sulfonylureas nicosulfuron and rimsulfuron, but susceptible (S) to imidazolinone imazamox, triketone 4-hydroxyphenylpyruvate dioxygenase inhibitor tembotrione, and acetyl-CoA carboxylase inhibitor cycloxydim. The sequencing of the ALS gene did not reveal the presence of resistance-associated point mutations, indicating that the resistance was probably not target-site mediated. This was confirmed by the application of piperonyl butoxide two hours before nicosulfuron application, which reversed the resistance in all R giant foxtail populations, supporting the evidence of enhanced metabolism-mediated resistance. The competition study between corn and R or S giant foxtail populations indicated no stable trend reduction in corn traits, suggesting that the resistance mechanism was not associated with the competitive ability of the R populations. The novel ALS genotype in S. faberi, characterized for the first time and submitted to the GenBank database with accession number PV016837, indicated a closer genetic relationship with the S. viridis ALS gene than with S. italica. Conclusions: Five giant foxtail populations have evolved metabolism-based resistance to the ALS-inhibiting herbicides nicosulfuron and rimsulfuron. Full article

Nitrogen crucially impacts foxtail millet (Setaria italica) growth and development. Uncovering low nitrogen (LN) tolerance genes and mechanisms is vital for breeding high nitrogen use efficiency varieties. In this study, the LN tolerance of 50 foxtail millet genotypes was assessed through field trials and seedling hydroponic experiments. Subsequently, transcriptome analysis was performed on one highly sensitive genotype, named Maotigu, and on one highly tolerant genotype, named Dahuanggu, under LN (0.1 mmol/L) and control (5 mmol/L) conditions in seedling hydroponic experiments. Compared to the control treatment, 823 differentially expressed genes (DEGs) (350 upregulated, 473 downregulated) were identified in the roots of Dahuanggu, while 2427 DEGs (1703 upregulated, 724 downregulated) were detected in Maotigu under LN treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that a total of 3134 DEGs were associated with pathways including plant–pathogen interaction, amino sugar and nucleotide sugar metabolism, nitrogen metabolism, and others. A total of 116 DEGs were commonly identified between Dahuanggu and Maotigu, involving pathways like plant–pathogen interaction, galactose metabolism, and flavone and flavonol biosynthesis. The 28 of 116 DEGs showed opposite expression patterns between Dahuanggu and Maotigu; the expression of 18 genes was further validated using qRT-PCR. These offer valuable insights into the molecular mechanisms underlying LN stress responses in foxtail millet. Full article

The flavour of foxtail millet (Setaria italica (L.) P. Beauv.) is an important indicator for evaluating the quality of the millet. The volatile components in steamed millet porridge samples were analysed using electronic nose (E-Nose) and gas chromatography–ion mobility spectrometry (GC-IMS) techniques, and characteristic volatile fingerprints were constructed to clarify the differences in the main flavour substances in different foxtail millet varieties (two hybrids and two conventional foxtail millets). After sensory evaluation by judges, Jingu 21 (JG) scored significantly higher than the other varieties, and the others were, in order, Jinmiao K1 (JM), Changzagu 466 (CZ) and Zhangzagu 3 (ZZ). E-Nose analysis showed differences in sulphides and terpenoids, nitrogen oxides, organosulphides and aromatic compounds in different varieties of millet porridge. A total of 59 volatile components were determined by GC-IMS in the four varieties of millet porridge, including 23 aldehydes, 17 alcohols, 9 ketones, 4 esters, 2 acids, 3 furans and 1 pyrazine. Comparative analyses of the volatile components in JG, JM, ZZ and CZ revealed that the contents of octanal, nonanal and 3-methyl-2-butenal were higher in JG; the contents of trans-2-butenal, 2-methyl-1-propanol, trans-2-heptenal and trans-2-pentenal were higher in JM; and the contents of 2-octanone, hexanol, 1-octen-3-ol, 2-pentanone and butyraldehyde were higher in ZZ. The contents of 2-butanol, propionic acid and acetic acid were higher in CZ. A prediction model with good stability was established by orthogonal partial least squares discriminant analysis (OPLS-DA), and 25 potential characteristic markers (VIP > 1) were screened out from 59 volatile organic compounds (VOCs). These volatile components can be used to distinguish the different varieties of millet porridge samples. Moreover, we found conventional foxtail millet contained more aldehydes than the hybridised foxtail millet; especially decanal, 1-nonanal-D, heptanal-D, 1-octanal-M, 1-octanal-D and 1-nonanal-M were significantly higher in JG than in the other varieties. These results indicate that the E-Nose combined with GC-IMS can be used to characterise the flavour volatiles of different foxtail millet, and the results of this study may provide some information for future understanding of the aroma characteristics of foxtail millet and the genetic improvement of hybrid grains. Full article

Hexokinases (HXKs) in plants are multifunctional enzymes that not only phosphorylate hexose but also function as glucose sensors, integrating nutrient, light, and hormone signaling networks to regulate cell metabolism and signaling pathways, thereby controlling growth and development in response to environmental changes. To date, limited information is available regarding the HXKs of foxtail millet (Setaria italica L.). In this study, six HXK genes were identified and characterized in foxtail millet. Phylogenetic analysis revealed that the foxtail millet hexokinases were classified into three subfamilies, corresponding to the two types (B-type and C-type) of hexokinases in plants. Gene structure and conserved motif analysis showed that the SiHXKs exhibited varying numbers of introns and exons, with proteins in each subfamily showing similar motif organization. Evolutionary divergence analysis indicated that the foxtail millet HXK and green foxtail HXK genes families underwent both positive and negative selection and experienced a large-scale duplication event approximately 1.18–154.84 million years ago. Expression analysis revealed that these genes are widely expressed in roots, stems, leaves, panicles, anthers, and seeds, with most genes showing significantly increased expression in roots under abiotic stress conditions, including 20% PEG 6000 (drought stress), 200 μmol/L NaCl (salt stress), and 1 μmol/L BR (brassinosteroid-mediated stress response). These results suggest that these genes may play a pivotal role in enhancing stress tolerance. Subcellular localization assay showed that SiHXK5 and SiHXK6 were predominantly localized in mitochondria. Haplotype analysis revealed that SiHXK3-H1 was associated with higher plant height and grain yield. These findings provide valuable insights into the functional characteristics of HXK genes, especially in the context of marker-assisted selection and the pyramiding of advantageous haplotypes in foxtail millet breeding programs. Full article

The foxtail millet exhibits a diverse range of hull colors, which are crucial indicators for assessing its nutritional and economic value. However, the molecular regulatory mechanisms that govern the hull color of foxtail millet are largely unknown at present. This gap in knowledge significantly impedes efforts to enhance the quality traits of foxtail millet. This study utilized a population of 250 F₆ recombinant inbred lines (RILs) generated from a cross between two foxtail millet varieties: Yugu18 (with light yellow seeds) and Hongjiugu19 (with red seeds). Four methods, the visual grouping method (I), the visual colorimetric method (II), the Lab determination method (III), and the RGB determination method (IV), were employed to determine the hull color of each line across four environments and QTL identification were conducted subsequently. It showed that there were 10, 12, 69 and 56 QTLs were detected for hull color through four methods, and these QTLs were integrated into 4, 6, 27 and 25 unique QTLs, respectively. There were three, four, four and four major QTLs. Of which, three major QTLs (qHC1.1, qHC1.2 and qHC9.3) on chromosomes 1 and 9 could be detected by all 4 methods. qHC9.1 was detected by all four methods except for method I. There were also one, one, seven and four minor identity QTLs identified across the 4 methods. Four minor QTLs (qHC3.1, qHC3.3, qHC4.1 and qHC5.1) can be stably detected only in method III, and two minor QTLs (qHC8.2 and qHC9.2) can be stably detected only in method IV. Generally, method I is fast, efficient and cost-effective, which is suitable for the rapid detection of hull color. Method II is also low-cost; however, it can detect more QTL for hull color, making it suitable for identifying major QTL loci in large populations. Methods III and IV can map more minor QTL and are more accurate in hull color characterization. This study identified four important hull color QTL for foxtail millet, which largely align with those reported in previous research. These findings establish a foundation for characterizing hull color indices and further advancing QTL mapping for grain color. Full article

The grain filling rate (GFR) plays a crucial role in determining grain yield. However, the regulatory and molecular mechanisms of the grain filling rate (GFR) in foxtail millet remains unclear. In this study, we found that the GFR of ′Changnong No.47′ (CN47) was significantly higher at 14 DAF (days after flowering) and 21 DAF in comparison to ‘Changsheng 13’ (CS13). Furthermore, CN47 also exhibited higher a thousand-grain weight and yield than CS13. Therefore, RNA-seq and UHPLC-MS/MS were used to conduct transcriptome and metabolome analyses during two stages of grain filling in both cultivars. Conjoint analysis of transcriptomics and metabolomics was adopted in order to analyze the biological processes and functional genes associated with GFR. The results identified a total of 765 differentially expressed genes (DEGs) and 246 differentially accumulated metabolites (DAMs) at the 14 DAF stage, while at the 21 DAF stage, a total of 908 DEGs and 268 DAMs were identified. The integrated analysis of co-mapped DAMs and DEGs revealed enriched pathways, including flavonoid biosynthesis, plant hormone signal transduction, tyrosine metabolism, ATP-binding cassette (ABC) transporters, and beta-Alanine metabolism, as well as stilbenoid, diarylheptanoid, and gingerol biosynthesis. In order to elucidate their potential functions in the context of GFR, we developed a gene–metabolite regulatory network for these metabolic pathways. Notably, we found that some genes associated with ABC transporters and the plant hormone signal transduction pathway were implicated in auxin transport and signal transduction, highlighting the crucial role of auxin during grain filling. These findings provide initial insights into the regulatory and molecular mechanisms underlying GFR in foxtail millet, as well as offering valuable genetic resources for further elucidation of GFR in future studies. The findings have also established a theoretical basis for improving the efficiency of yield breeding in foxtail millet. Full article

DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. DNA demethylase (DNA-deMTase) genes have been identified in some plant species; however, there are no reports on the identification and analysis of DNA-deMTase genes in Foxtail millet (Setaria italica L.). In this study, seven DNA-deMTases were identified in S. italica. These DNA-deMTase genes were divided into four subfamilies (DML5, DML4, DML3, and ROS1) by phylogenetic and gene structure analysis. Further analysis shows that the physical and chemical properties of these DNA-deMTases proteins are similar, contain the typical conserved domains of ENCO3c and are located in the nucleus. Furthermore, multiple cis-acting elements were observed in DNA-deMTases, including light responsiveness, phytohormone responsiveness, stress responsiveness, and elements related to plant growth and development. The DNA-deMTase genes are expressed in all tissues detected with certain tissue specificity. Then, we investigated the abundance of DNA-deMTase transcripts under abiotic stresses (cold, drought, salt, ABA, and MeJA). The results showed that different genes of DNA-deMTases were involved in the regulation of different abiotic stresses. In total, our findings will provide a basis for the roles of DNA-deMTase in response to abiotic stress. Full article

WUSCHEL-related homeobox (WOX) transcription factors are unique to plants and play pivotal roles in plant development and stress responses. In this investigation, we acquired protein sequences of foxtail millet WOX gene family members through homologous sequence alignment and a hidden Markov model (HMM) search. Utilizing conserved domain prediction, we identified 13 foxtail millet WOX genes, which were classified into ancient, intermediate, and modern clades. Multiple sequence alignment results revealed that all WOX proteins possess a homeodomain (HD). The SiWOX genes, clustered together in the phylogenetic tree, exhibited analogous protein spatial structures, gene structures, and conserved motifs. The foxtail millet WOX genes are distributed across 7 chromosomes, featuring 3 pairs of tandem repeats: SiWOX1 and SiWOX13, SiWOX4 and SiWOX5, and SiWOX11 and SiWOX12. Collinearity analysis demonstrated that WOX genes in foxtail millet exhibit the highest collinearity with green foxtail, followed by maize. The SiWOX genes primarily harbor two categories of cis-acting regulatory elements: Stress response and plant hormone response. Notably, prominent hormones triggering responses include methyl jasmonate, abscisic acid, gibberellin, auxin, and salicylic acid. Analysis of SiWOX expression patterns and hormone responses unveiled potential functional diversity among different SiWOX genes in foxtail millet. These findings lay a solid foundation for further elucidating the functions and evolution of SiWOX genes. Full article

Foxtail millet (Setaria italica [L.] P. Beauv.) is a climate-change-ready crop, and it is crucial for predicting the impact of ecological factors on grain quality. In this study, multivariate statistical analysis was used to explore the relationship between ecological factors and the key nutritional quality of Jingu 21 from twelve production areas. The results showed that the crude fat and amylopectin content of foxtail millets showed a downward trend from south to north. The nutritional quality was significantly affected by geographical, climatic, and soil factors, and the foxtail millet produced in geographically close areas was extremely similar in nutritional quality. Most nutritional quality indicators of Jingu 21 had a strong correlation with the latitude and climatic factors such as average temperature, diurnal temperature range, and average precipitation, while the content of mineral elements was greatly affected by soil factors. Moreover, higher average precipitation in the jointing, booting–heading, and heading stages, a higher average temperature, and a lower diurnal temperature range in the heading and grain-filling stages are conducive to the establishment of nutritional quality. The findings could facilitate the rational distribution of high-quality foxtail millets under global climate change. Full article

The development of modern genomic tools has helped accelerate genetic gains in the breeding program of food crops. More recently, genomic resources have been developed for tropical forages, providing key resources for developing new climate-resilient high-yielding forage varieties. In this study, we present a genome-wide association study for biomass yield and feed quality traits in buffel grass (Cenchrus ciliaris L. aka Pennisetum ciliare L.). Genome-wide markers, generated using the DArTSeq platform and mapped onto the Setaria italica reference genome, were used for the genome-wide association study. The results revealed several markers associated with biomass yield and feed quality traits. A total of 78 marker–trait associations were identified with R² values ranging from 0.138 to 0.236. The marker–trait associations were distributed across different chromosomes. Of these associations, the most marker–trait associations (23) were observed on Chr9, followed by Chr5 with 12. The fewest number of marker–trait associations were observed on Chr4 with 2. In terms of traits, 17 markers were associated with biomass yield, 24 with crude protein, 26 with TDN, 14 with ADF, 10 with NDF and 6 with DMI. A total of 20 of the identified markers were associated with at least two traits. The identified marker–trait associations provide a useful genomic resource for the future improvement and breeding of buffel grass. Full article

Innovative measures of nitrogen (N) fertilization to increase season-long N availability is essential for gaining the optimal foxtail millet (Setaria italica L. Beauv.) productivity and N use efficiency. A split plot field experiment was conducted using the foxtail millet variety Huayougu 9 in 2020 and 2021 in Northeast China to clarify the physiological mechanism of a novel polyaspartic acid–chitosan (PAC)-coated urea on N assimilation and utilization from foxtail millet. Conventional N fertilizer (CN) and the urea-coated -PAC treatments were tested under six nitrogen fertilizer application levels of 0, 75, 112.5, 150, 225, and 337.5 kg N ha⁻¹. The results showed that compared to CN, PN increased the foxtail millet yield by 5.53–15.75% and 10.43–16.17% in 2020 and 2021, respectively. PN increased the leaf area index and dry matter accumulation by 7.81–18.15% and 12.91–41.92%, respectively. PN also enhanced the activities of nitrate reductase, glutamine synthetase, glutamic oxaloacetic transaminase, and glutamic–pyruvic transaminase, thereby increasing the soluble protein in the leaf, plant, and grain N content at harvest compared to CN. Consequently, partial factor productivity from applied N, the agronomic efficiency of applied N, recovery efficiency of applied N, and physiological efficiency of applied N of foxtail millet under PN treatments compared to CN were increased. The improvement effect of the items above was more noticeable under the low–middle N application levels (75, 112.5, and 150 kg N ha⁻¹). In conclusion, the PAC could achieve the goal of high yield and high N use efficiency in foxtail millet under the background of a one-time basic fertilizer application. Full article