Genome-wide identification, classification, and expression analysis of heat shock transcription factor family in switchgrass (Panicum virgatum L.).

Switchgrass is one of the most promising bioenergy crops and is generally cultivated in arid climates and poor soils. Heat shock transcription factors (Hsfs) are key regulators of plant responses to abiotic and biotic stressors. However, their role and mechanism of action in switchgrass have not been elucidated. Hence, this study aimed to identify the Hsf family in switchgrass and understand its functional role in heat stress signal transduction and heat tolerance by using bioinformatics and RT-PCR analysis. Forty-eight PvHsfs were identified and divided into three main classes based on their gene structure and phylogenetic relationships: HsfA, HsfB, and HsfC. The results of the bioinformatics analysis showed a DNA-binding domain (DBD) at the N-terminal in PvHsfs, and they were not evenly distributed on all chromosomes except for chromosomes 8 N and 8 K. Many cis-elements related to plant development, stress responses, and plant hormones were identified in the promoter sequence of each PvHsf. Segmental duplication is the primary force underlying Hsf family expansion in switchgrass. The results of the expression pattern of PvHsfs in response to heat stress showed that PvHsf03 and PvHsf25 might play critical roles in the early and late stages of switchgrass response to heat stress, respectively, and HsfB mainly showed a negative response to heat stress. Ectopic expression of PvHsf03 in Arabidopsis significantly increased the heat resistance of seedlings. Overall, our research lays a notable foundation for studying the regulatory network in response to deleterious environments and for further excavating tolerance genes in switchgrass.

Analysis of morphological traits and regulatory mechanism of a semi-dwarf, albino, and blue grain wheat line.

The plant height and leaf color are important traits in crops since they contribute to the production of grains and biomass. Progress has been made in mapping the genes that regulate plant height and leaf color in wheat (Triticum aestivum L.) and other crops. Wheat line DW-B (dwarfing, white leaves, and blue grains) with semi-dwarfing and albinism at the tillering stage and re-greening at the jointing stage was created using Lango and Indian Blue Grain. Transcriptomic analyses of the three wheat lines at the early jointing stages indicated that the genes of gibberellin (GA) signaling pathway and chlorophyll (Chl) biosynthesis were expressed differently in DW-B and its parents. Furthermore, the response to GA and Chl contents differed between DW-B and its parents. The dwarfing and albinism in DW-B were owing to defects in the GA signaling pathway and abnormal chloroplast development. This study can improve understanding of the regulation of plant height and leaf color. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01379-z.

Overexpression of PvSTK1 gene from Switchgrass (Panicum virgatum L.) affects flowering time and development of floral organ in transgenic Arabidopsis thaliana.

Flowering means that the plant enters the reproductive growth stage, which is a crucial stage in the plant life cycle. Delaying flowering time to prolong vegetative growth is an important method to increase biomass yield and saccharification efficiency in switchgrass, It is of great significance to study the molecular mechanism of plant flowering and regulate the process of plant flowering in the process of biomass production. In this study, we identified 55 serine/threonine-protein kinase genes related to flower development from the switchgrass transcriptome database. Simultaneously, we cloned one of them, PvSTK1, whose expression level and differential fold were significantly higher than other members. PvSTK1 is located on chromosome 8N and its protein was in the cell membrane, cytoplasm, and nucleus. The spatio-temporal expression analysis of the PvSTK1 in switchgrass displayed that the PvSTK1 is crucial in vegetative period, however, not in the transition to reproductive period. Overexpression of PvSTK1 in Arabidopsis resulted in down-regulation of flower-promoting genes and up-regulation of flower-suppressing genes, thereby delaying flowering. In addition, PvSTK1 caused atrophy of the ovules of the florets at the base of the inflorescence, leading to sterility of the florets. The function of PvSTK1 is to inhibit the development of floral organs, and its overexpression can prolong its vegetative period. In the future, overexpression of the PvSTK1 gene in switchgrass will change the flowering time and increase yield and utilization efficiency of biomass.

Regulatory Network of Preharvest Sprouting Resistance Revealed by Integrative Analysis of mRNA, Noncoding RNA, and DNA Methylation in Wheat.

Preharvest sprouting (PHS) of grain occurs universally and sharply decreases grain quality and yield, but the mechanism remains unclear. MingXian169, a breeding inducer wheat for stripe rust, is widely used in the Huanghuai wheat-producing region, China. In this study, we found that MingXian169 could be considered an ideal material for PHS research because of its high PHS resistance. To further analyze the network of PHS, transcriptome sequencing of mRNA, noncoding RNA (ncRNA), and DNA methylome data were used to comparison germination seeds (GS) and dormant seeds (DS); 3027, 1516, and 22 genes and 95 103 methylation regions were identified as differentially expressed mRNA, DE-microRNAs (DE-miRNA), DE-long noncoding RNAs (DE-lncRNA), and differentially methylated regions (DMRs). Pathway enrichment tests highlighted plant hormone biosynthesis and signal transduction, glutathione-ascorbate metabolism, and starch and sucrose metabolism processes related to PHS mechanisms. Further analysis demonstrated that long noncoding RNA, miRNA, and DNA methylation played critical roles in transcriptional regulation of critical pathways during PHS by modifying and interacting with target genes. Quantitative real-time polymerase chain reaction (PCR) analyses of mRNA and miRNA confirmed the sequencing results. In the phytohormone content assay, abscisic acid (ABA) and jasmonic acid (JA) increased significantly in DS, and GA19 increased in GS. The ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), and ß-d-glucosidase (BGLU) enzyme activities and the substance content of glutathione and sucrose were significantly higher in GS than in DS, implying that they were responsible for increasing PHS in MingXian169. Our results provide new insights into wheat PHS resistance at mRNA, ncRNA, and DNA methylation levels, with suggestions for crop breeding and production.

Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass.

The large basic leucine zipper (bZIP) transcription factor family is conserved in plants. These proteins regulate growth, development, and stress response. Here, we conducted a genome-wide analysis to identify the bZIP genes associated with stress resistance in switchgrass (Panicum virgatum L.). We identified 178 PvbZIPs unevenly distributed on 18 switchgrass chromosomes. An evolutionary analysis segregated them into 10 subfamilies. Gene structure and conserved motif analyses indicated that the same subfamily members shared similar intron-exon modes and motif compositions. This finding corroborated the proposed PvbZIP family grouping. A promoter analysis showed that PvbZIP genes participate in various stress responses. Phylogenetic and synteny analyses characterized 111 switchgrass bZIPs as orthologs of 70 rice bZIPs. A protein interaction network analysis revealed that 22 proteins are involved in salt and drought tolerance. An expression atlas disclosed that the expression patterns of several PvbZIPs differ among various tissues and developmental stages. Online data demonstrated that 16 PvbZIPs were significantly downregulated and five were significantly upregulated in response to heat stress. Other PvbZIPs participated in responses to abiotic stress such as salt, drought, cold, and heat. Our genome-wide analysis and identification of the switchgrass bZIP family characterized multiple candidate PvbZIPs that regulate growth and stress response. This study lays theoretical and empirical foundations for future functional investigations into other transcription factors.

Proteomic analysis of the similarities and differences of soil drought and polyethylene glycol stress responses in wheat (Triticum aestivum L.).

KEY MESSAGE: Our results reveal both soil drought and PEG can enhance malate, glutathione and ascorbate metabolism, and proline biosynthesis, whereas soil drought induced these metabolic pathways to a greater degree than PEG. Polyethylene glycol (PEG) is widely used to simulate osmotic stress, but little is known about the different responses of wheat to PEG stress and soil drought. In this study, isobaric tags for relative quantification (iTRAQ)-based proteomic techniques were used to determine both the proteomic and physiological responses of wheat seedlings to soil drought and PEG. The results showed that photosynthetic rate, stomatal conductance, intercellular CO2 concentration, transpiration rate, maximum potential efficiency of PS II, leaf water content, relative electrolyte leakage, MDA content, and free proline content exhibited similar responses to soil drought and PEG. Approximately 15.8% of differential proteins were induced both by soil drought and PEG. Moreover, both soil drought and PEG inhibited carbon metabolism and the biosynthesis of some amino acids by altering the accumulation of glyceraldehyde-3-phosphate dehydrogenase, ribulose-bisphosphate carboxylase, and phosphoglycerate kinase, but they both enhanced the metabolism of malate, proline, glutathione, and ascorbate by increasing the accumulation of key enzymes including malate dehydrogenase, monodehydroascorbate reductase, pyrroline-5-carboxylate dehydrogenase, pyrroline-5-carboxylate synthetase, ascorbate peroxidase, glutathione peroxidase, and glutathione S-transferase. Notably, the latter five of these enzymes were found to be more sensitive to soil drought. In addition, polyamine biosynthesis was specifically induced by increased gene expression and protein accumulation of polyamine oxidase and spermidine synthase under PEG stress, whereas fructose-bisphosphate aldolase and arginase were induced by soil drought. Therefore, present results suggest that PEG is an effective method to simulate drought stress, but the key proteins related to the metabolism of malate, glutathione, ascorbate, proline, and polyamine need to be confirmed under soil drought.

Genome-wide identification of members of the TCP gene family in switchgrass (Panicum virgatum L.) and analysis of their expression.

Teosinte branched 1/Cycloidea/Proliferating cell factor 1 (TCP) proteins belongs to a plant-specific transcription factor family that plays important roles in plant development. TCP gene-regulated plant branching occurs downstream in the strigolactone pathway. In this study, 41 TCP genes were identified in the genome of Panicum virgatum L. (switchgrass). These genes all contained the TCP conserved domain, and they belonged to two subfamilies distributed across 18 chromosomes. Analysis of gene expression using RNA-Seq data showed that 16 TCP genes were highly expressed in the inflorescence and shoot. The expression patterns of 13 selected PvTCP genes were analyzed in different tissues, and their responses to strigolactones (SLs) were examined. The selected genes were expressed differentially in a range of tissues and to application of SLs, indicating that PvTCPs were involved in a range of developmental and physiological processes. This genome-wide analysis and determination of PvTCP gene-expression patterns yielded valuable information on switchgrass development that will inform studies into improving switchgrass and other species for crop production.

Proteomic analysis of melatonin-mediated osmotic tolerance by improving energy metabolism and autophagy in wheat (Triticum aestivum L.).

MAIN CONCLUSION: Melatonin-mediated osmotic tolerance was attributed to increased antioxidant capacity, energy metabolism, osmoregulation and autophagy in wheat (Triticum aestivum L.). Melatonin is known to play multiple roles in plant abiotic stress tolerance. However, its role in wheat has been rarely investigated. In this study, 25% polyethylene glycol 6000 (PEG 6000) was used to simulate osmotic stress, and wheat seeds and seedlings were treated with different concentrations of melatonin under PEG stress. Isobaric tag for relative and absolute quantification (iTRAQ)-based proteomic techniques were used to identify the differentially accumulated proteins from melatonin-treated and non-treated seedlings. Seeding priming with melatonin significantly increased the germination rate, coleoptile length, and primary root number of wheat under PEG stress, as well as the fresh weight, dry weight, and water content of wheat seedlings. Under PEG stress, melatonin significantly improved reactive oxygen species homeostasis, as revealed by lower H2O2 and O 2· content; and the expression of antioxidant enzymes at the transcription and translation levels was increased. Melatonin maintained seedling growth by improving photosynthetic rates and instantaneous and intrinsic water use efficiencies, as well as carbon fixation and starch synthesis at the protein level. Melatonin treatment significantly affected the expression of glycolytic proteins, including fructose-1,6-bisphosphate aldolase, hexokinase, glyceraldehyde-3-phosphate dehydrogenase, and enolase, and remarkably increased the expression of the nicotinamide adenine dinucleotide transporter and nicotinamide adenine dinucleotide binding protein, thereby indirectly modulating electron transport in the respiratory chain. This indicated that melatonin improved energy production in PEG-stressed seedlings. Further, melatonin played a regulatory role in autophagy, protease expression, and ubiquitin-mediated protein degradation by significantly upregulating rab-related protein, fused signal recognition particle receptor, aspartyl protease, serine protease, ubiquitin-fold modifier 1, and ubiquitin at the mRNA or protein level. These findings suggested that melatonin might activate a metabolic cascade related to autophagy under PEG stress in wheat seedlings.