Genome-wide analysis of the switchgrass YABBY family and functional characterization of PvYABBY14 in response to ABA and GA stress in Arabidopsis.

BACKGROUND: The small YABBY plant-specific transcription factor has a prominent role in regulating plant growth progress and responding to abiotic stress. RESULTS: Here, a total of 16 PvYABBYs from switchgrass (Panicum virgatum L.) were identified and classified into four distinct subgroups. Proteins within the same subgroup exhibited similar conserved motifs and gene structures. Synteny analyses indicated that segmental duplication contributed to the expansion of the YABBY gene family in switchgrass and that complex duplication events occurred in rice, maize, soybean, and sorghum. Promoter regions of PvYABBY genes contained numerous cis-elements related to stress responsiveness and plant hormones. Expression profile analysis indicated higher expression levels of many PvYABBY genes during inflorescence development and seed maturation, with lower expression levels during root growth. Real-time quantitative PCR analysis demonstrated the sensitivity of multiple YABBY genes to PEG, NaCl, ABA, and GA treatments. The overexpression of PvYABBY14 in Arabidopsis resulted in increased root length after treatment with GA and ABA compared to wild-type plants. CONCLUSIONS: Taken together, our study provides the first genome-wide overview of the YABBY transcription factor family, laying the groundwork for understanding the molecular basis and regulatory mechanisms of PvYABBY14 in response to ABA and GA responses in switchgrass.

A high-precision jujube disease spot detection based on SSD during the sorting process.

The development of automated grading equipment requires achieving high throughput and precise detection of disease spots on jujubes. However, the current algorithms are inadequate in accomplishing these objectives due to their high density, varying sizes and shapes, and limited location information regarding disease spots on jujubes. This paper proposes a method called JujubeSSD, to boost the precision of identifying disease spots in jujubes based on a single shot multi-box detector (SSD) network. In this study, a diverse dataset comprising disease spots of varied sizes and shapes, varying densities, and multiple location details on jujubes was created through artificial collection and data augmentation. The parameter information obtained from transfer learning into the backbone feature extraction network of the SSD model, which reduced the time of spot detection to 0.14 s. To enhance the learning of target detail features and improve the recognition of weak information, the traditional convolution layer was replaced with deformable convolutional networks (DCNs). Furthermore, to address the challenge of varying sizes and shapes of disease spot regions on jujubes, the path aggregation feature pyramid network (PAFPN) and balanced feature pyramid (BFP) were integrated into the SSD network. Experimental results demonstrate that the mean average precision at the IoU (intersection over union) threshold of 0.5 (mAP@0.5) of JujubeSSD reached 97.1%, representing an improvement of approximately 6.35% compared to the original algorithm. When compared to existing algorithms, such as YOLOv5 and Faster R-CNN, the improvements in mAP@0.5 were 16.84% and 8.61%, respectively. Therefore, the proposed method for detecting jujube disease spot achieves superior performance in jujube surface disease detection and meets the requirements for practical application in agricultural production.

Effect of Mowing on Wheat Growth at Seeding Stage.

Winter wheat is used as forage at the tillering stage in many countries; however, the regrowth pattern of wheat after mowing remains unclear. In this study, the growth patterns of wheat were revealed through cytological and physiological assessments as well as transcriptome sequencing. The results of agronomic traits and paraffin sections showed that the shoot growth rate increased, but root growth was inhibited after mowing. The submicroscopic structure revealed a decrease in heterochromatin in the tillering node cell and a change in mitochondrial shape in the tillering node and secondary root. Analysis of the transcriptome showed the number of differentially expressed genes (DEGs) involved in biological processes, cellular components, and molecular functions; 2492 upregulated DEGs and 1534 downregulated DEGs were identified. The results of the experimental study showed that mowing induced expression of DEGs in the phenylpropanoid biosynthesis pathway and increased the activity of PAL and 4CL. The upregulated DEGs in the starch and sucrose metabolism pathways and related enzyme activity alterations indicated that the sugar degradation rate increased. The DEGs in the nitrogen metabolism pathway biosynthesis of the amino acids, phenylpropanoid biosynthesis metabolism, and in the TCA pathway also changed after mowing. Hormone content and related gene expression was also altered in the tillering and secondary roots after mowing. When jasmonic acid and ethylene were used to treat the wheat after mowing, the regeneration rate increased, whereas abscisic acid inhibited regrowth. This study revealed the wheat growth patterns after mowing, which could lead to a better understanding of the development of dual-purpose wheat.

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.

RING finger E3 ubiquitin ligase gene TaAIRP2-1B controls spike length in wheat.

E3 ubiquitin ligase genes play important roles in the regulation of plant development. They have been well studied in plants, but have not been sufficiently investigated in wheat. Here, we identified a highly expressed RING finger E3 ubiquitin ligase gene TaAIRP2-1B (ABA-insensitive RING protein 2) in wheat spike. Sequence polymorphism and association analysis showed that TaAIRP2-1B is significantly associated with spike length under various conditions. The genotype with haplotype Hap-1B-1 of TaAIRP2-1B has a longer spike than that of Hap-1B-2, and was positively selected in the process of wheat breeding in China. Moreover, the TaAIRP2-1B-overexpressing rice lines have longer panicles compared with wild-type plants. The expression levels of TaAIRP2-1B in Hap-1B-1 accessions were higher than in Hap-1B-2 accessions. Further study revealed that the expression of TaAIRP2-1B was negatively regulated by TaERF3 (ethylene-responsive factor 3) via binding to the Hap-1B-2 promoter, but not via binding of Hap-1B-1. Additionally, several candidate genes interacting with TaAIRP2-1B were obtained by screening the cDNA library of wheat in yeast cells. It was found that TaAIRP2-1B interacted with TaHIPP3 (heavy metal-associated isoprenylated protein 3) and promoted TaHIPP3 degradation. Our study demonstrates that TaAIRP2-1B controls spike length, and the haplotype Hap-1B-1 of TaAIRP2-1B is a favorable natural variation for spike length enhancement in wheat. This work also provides genetic resources and functional markers for wheat molecular breeding.

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.

Comprehensive Transcriptomic and Metabolic Profiling of Agrobacterium-tumefaciens-Infected Immature Wheat Embryos.

The transformation efficiency (TE) was improved by a series of special chemical and physical methods using immature embryos from the cultivar Fielder, with the PureWheat technique. To analyze the reaction of immature embryos infected, which seemed to provide the necessary by Agrobacterium tumefaciens in PureWheat, a combination of scanning electron microscopy (SEM), complete transcriptome analysis, and metabolome analysis was conducted to understand the progress. The results of the SEM analysis revealed that Agrobacterium tumefaciens were deposited under the damaged cortex of immature embryos as a result of pretreatment and contacted the receptor cells to improve the TE. Transcriptome analysis indicated that the differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant-pathogen interaction, plant hormone signal transduction, and the MAPK (Mitogen-activated protein kinase) signaling pathway. By analyzing the correlation between differentially expressed genes and metabolites, the expression of many genes and the accumulation of metabolites were changed in glucose metabolism and the TCA cycle (Citrate cycle), as well as the amino acid metabolism; this suggests that the infection of wheat embryos with Agrobacterium is an energy-demanding process. The shikimate pathway may act as a hub between glucose metabolism and phenylpropanoid metabolism during Agrobacterium infection. The downregulation of the F5H gene and upregulation of the CCR gene led to the accumulation of lignin precursors through phenylpropanoid metabolism. In addition, several metabolic pathways and oxidases were found to be involved in the infection treatment, including melatonin biosynthesis, benzoxazinoid biosynthesis, betaine biosynthesis, superoxide dismutase, and peroxidase, suggesting that wheat embryos may be under the stress of Agrobacterium and, thus, undergo an oxidative stress response. These findings explore the physiological and molecular changes of immature embryos during the co-culture stage of the PureWheat technique and provide insights for Agrobacterium-mediated transgenic wheat experiments.

Rapid and Nondestructive Evaluation of Wheat Chlorophyll under Drought Stress Using Hyperspectral Imaging.

Chlorophyll drives plant photosynthesis. Under stress conditions, leaf chlorophyll content changes dramatically, which could provide insight into plant photosynthesis and drought resistance. Compared to traditional methods of evaluating chlorophyll content, hyperspectral imaging is more efficient and accurate and benefits from being a nondestructive technique. However, the relationships between chlorophyll content and hyperspectral characteristics of wheat leaves with wide genetic diversity and different treatments have rarely been reported. In this study, using 335 wheat varieties, we analyzed the hyperspectral characteristics of flag leaves and the relationships thereof with SPAD values at the grain-filling stage under control and drought stress. The hyperspectral information of wheat flag leaves significantly differed between control and drought stress conditions in the 550-700 nm region. Hyperspectral reflectance at 549 nm (r = -0.64) and the first derivative at 735 nm (r = 0.68) exhibited the strongest correlations with SPAD values. Hyperspectral reflectance at 536, 596, and 674 nm, and the first derivatives bands at 756 and 778 nm, were useful for estimating SPAD values. The combination of spectrum and image characteristics (L*, a*, and b*) can improve the estimation accuracy of SPAD values (optimal performance of RFR, relative error, 7.35%; root mean square error, 4.439; R2, 0.61). The models established in this study are efficient for evaluating chlorophyll content and provide insight into photosynthesis and drought resistance. This study can provide a reference for high-throughput phenotypic analysis and genetic breeding of wheat and other crops.

Genome-Wide Identification of Wheat KNOX Gene Family and Functional Characterization of TaKNOX14-D in Plants.

The KNOX genes play important roles in maintaining SAM and regulating the development of plant leaves. However, the TaKNOX genes in wheat are still not well understood, especially their role in abiotic stress. In this study, a total of 36 KNOX genes were identified, and we demonstrated the function of the TaKNOX14-D gene under mechanical injury and cold stress. Thirty-six TaKNOX genes were divided into two groups, and thirty-four TaKNOX genes were predicted to be located in the nucleus by Cell-PLoc. These genes contained five tandem duplications. Fifteen collinear gene pairs were exhibited in wheat and rice, one collinear gene pair was exhibited in wheat and Arabidopsis. The phylogenetic tree and motif analysis suggested that the TaKNOX gene appeared before C3 and C4 diverged. Gene structure showed that the numbers of exons and introns in TaKNOX gene are different. Wheat TaKNOX genes showed different expression patterns during the wheat growth phase, with seven TaKNOX genes being highly expressed in the whole growth period. These seven genes were also highly expressed in most tissues, and also responded to most abiotic stress. Eleven TaKNOX genes were up-regulated in the tillering node during the leaf regeneration period after mechanical damage. When treating the wheat with different hormones, the expression patterns of TaKNOX were changed, and results showed that ABA promoted TaKNOX expression and seven TaKNOX genes were up-regulated under cytokinin and auxin treatment. Overexpression of the TaKNOX14-D gene in Arabidopsis could increase the leaf size, plant height and seed size. This gene overexpression in Arabidopsis also increased the compensatory growth capacity after mechanical damage. Overexpression lines also showed high resistance to cold stress. This study provides a better understanding of the TaKNOX genes.

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.

Bearing Strength of Concrete-Filled Steel Tube Reinforced with Internal Transverse Stiffened Bars under Axial Compression.

A new type of square concrete-filled steel tubular (SCFST) column is proposed, which is characterized by transverse stiffened bars inside the steel tube to improve the effective constraint performance of the concrete core. The experiment of this kind of composite material under axial compression was carried out. The results showed that the bearing capacity of the SCFST column reinforced by internal transverse stiffened bars increased by 4.5%-15% than that of the ordinary SCFST column. The transverse strain is smaller than the SCFST column. As the diameter of the reinforcement increases and decreases the spacing of bars, the axial load bearing capacity increased. The transverse strain of the member decreased obviously. It is noted that the confinement performance of the concrete core of this type was improved to some extent. At the same time, based on the unified theory, the simplified calculation formula of axial compression bearing capacity is derived.

Anthocyanin Biosynthesis and a Regulatory Network of Different-Colored Wheat Grains Revealed by Multiomics Analysis.

Colored wheat has always been a popular research area because of its high performance in the field and significant medical uses. Progress has been made mapping the genes of purple or blue grains; however, the reason why different grain colors form in wheat is not well understood. We created wheat lines with different grain colors (purple and blue) using the white grain cultivar Xiaoyan22 and located the candidate region related to the purple and blue grains in chromosome 2A, 2B, and 4D, 2A, respectively, by the bulked segregant RNA-seq. The transcriptomic and metabolomic analyses of the three grains at different developmental stages indicated that the upregulation of flavonoid 3'-hydroxylase/flavonoid 3',5'hydroxylase 2 and TaMYC1/TaMYC4 was important for the formation of purple/blue grains. The blue TaMYC4 had 16 nonsynonymous single nucleotide variants verified by Sanger sequencing and possessed a different splicing mode in the bHLH_MYC_N domain compared with the reference database. Targeted high-performance liquid chromatography-mass spectrometry/mass spectrometry analysis of anthocyanins found that the purple and blue grains contained more pelargonidin, cyanidin, and delphinidin, respectively. This study provides a comprehensive understanding of the different color formations of wheat grains and useful information about genetic improvements in wheat and other crops.

Genome-Wide Analysis of DEAD-box RNA Helicase Family in Wheat (Triticum aestivum) and Functional Identification of TaDEAD-box57 in Abiotic Stress Responses.

DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.

RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat (Triticum aestivum L.).

Winter wheat (Triticum aestivum L.) is used as fresh green winter forage worldwide, and its ability to regenerate after mowing determines whether it can be used for forage production; however, the molecular mechanism of regeneration is poorly understood. This study identified long-chain coding and non-coding RNAs in the wheat cultivar "XN9106," which is cultivated for forage and grain production separately in winter and summer, and analyzed their function during post-mowing regeneration. The results showed that the degradation of carbohydrate plays an important role in regeneration, as demonstrated by decreased carbohydrate content. The increased gene expression of enzymes including ß-amylase, ß-fructofuranosidase, sucrose synthase, sucrose-6-phosphate synthase, trehalose-6-phosphate synthase, and trehalose-6-phosphate phosphatase in mowed seedlings suggests regeneration is fueled by degraded carbohydrates that provide energy and carbon skeletons for the Krebs cycle and amino acid synthesis. The decreased auxin content relieved the inhibition of cytokinin synthesis, that controls the transition from cell division to cell expansion and stimulates cell expansion and differentiation during the cell expansion phase, and eventually accelerate post-mowing regeneration of seedlings. Additionally, differentially expressed long-chain non-coding RNAs (lncRNAs) might participate in the regulation of gene expression related to carbohydrate metabolism and hormone signal transduction. This study demonstrated the responses of key mRNAs and lncRNAs during post-mowing regeneration of winter wheat and revealed the importance of carbohydrate and hormone during regeneration, providing valuable information for genetic improvement of forage wheat.

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.

MicroRNA and regulation of auxin and cytokinin signalling during post-mowing regeneration of winter wheat (Triticum aestivum L.).

Winter wheat not only provides adequate fresh forage grass in winter, but also ensures ample grain production in summer. The mechanisms underlying the regeneration of winter wheat after mowing or grazing are not well understood. In this study, the miRNA expression profile of winter wheat was determined using RNA sequencing and the endogenous auxin and cis-zeatin concentrations, as well as the expression of related miRNA-targeted genes, were measured. During the post-mowing regeneration of winter wheat, the concentrations of endogenous indole-3-acetic acid (IAA), methyl indole-3-acetate (ME-IAA), and indole-3-carboxaldehyde (ICA) decreased, while those of cis-zeatin (cZ) increased. Moreover, 15 novel miRNAs and three known miRNAs were found to be involved in the synthesis and signalling transduction of auxins and cytokinins (CKs). Among these miRNAs, miR1153-y, miR5059-x, miR2916-x, novel-miR1532-3p, novel-miR1060-3p, and novel-miR0890-3p, were found to be negatively correlated with the expression of their target genes including auxin response GH3.7, auxin response factor (ARF), type-A two-component response regulator (A-ARR), aldehyde dehydrogenase (ALDH), and O-glucosyltransferase (CISZOG). Furthermore, miR1153-y was identified as mediating the cleavage of GH3.7 by RACE assay. In turn, these genes inhibited the biosynthesis and signalling of IAA and activated CK signal transduction, resulting in the rapid regeneration of mowed winter wheat. This study revealed that some miRNAs exert a positive regulatory effect on the post-mowing regeneration of winter wheat by controlling the synthesis and signal transduction of IAA and CK, and our founding will aid developments in biotechnology aimed at improving the post-mowing regeneration ability of winter wheat.

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.

Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.).

BACKGROUND: Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. RESULTS: Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. CONCLUSIONS: The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops.

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.