PsSOC1 is involved in the gibberellin pathway to trigger cell proliferation and budburst during endodormancy release in tree peony.

Tree peony (Paeonia suffruticosa) undergoes bud endodormancy, and gibberellin (GA) pathway plays a crucial role in dormancy regulation. Recently, a key DELLA protein PsRGL1 has been identified as a negative regulator of bud dormancy release. However, the mechanism of GA signal to break bud dormancy remains unknown. In this study, yeast two-hybrid screened PsSOC1 interacting with PsRGL1 through its MADS domain, and interaction was identified using pull-down and luciferase complementation imaging assays Transformation in tree peony and hybrid poplar confirmed that PsSOC1 facilitated bud dormancy release. Transcriptome analysis of PsSOC1-overexpressed buds indicated PsCYCD3.3 and PsEBB3 were its potential downstream targets combining with promoter survey, and they also accelerated bud dormancy release verified by genetic analysis. Yeast one-hybrid, electrophoretic mobility shifts assays, chromatin immunoprecipitation quantitative PCR, and dual luciferase assays confirmed that PsSOC1 could directly bind to the CArG motif of PsCYCD3.3 and PsEBB3 promoters via its MADS domain. PsRGL1-PsSOC1 interaction inhibited the DNA-binding activity of PsSOC1. Additionally, PsCYCD3.3 promoted bud dormancy release by rebooting cell proliferation. These findings elucidated a novel GA pathway, GA-PsRGL1-PsSOC1-PsCYCDs, which expanded our understanding of the GA pathway in bud dormancy release.

Auxin efflux carrier PsPIN4 identified through genome-wide analysis as vital factor of petal abscission.

PIN-FORMED (PIN) proteins, which function as efflux transporters, play many crucial roles in the polar transportation of auxin within plants. In this study, the exogenous applications of auxin IAA and TIBA were found to significantly prolong and shorten the florescence of tree peony (Paeonia suffruticosa Andr.) flowers. This finding suggests that auxin has some regulatory influence in petal senescence and abscission. Further analysis revealed a total of 8 PsPINs distributed across three chromosomes, which could be categorized into two classes based on phylogenetic and structural analysis. PsPIN1, PsPIN2a-b, and PsPIN4 were separated into the "long" PIN category, while PsPIN5, PsPIN6a-b, and PsPIN8 belonged to the "short" one. Additionally, the cis-regulatory elements of PsPIN promoters were associated with plant development, phytohormones, and environmental stress. These genes displayed tissue-specific expression, and phosphorylation sites were abundant throughout the protein family. Notably, PsPIN4 displayed distinct and elevated expression levels in roots, leaves, and flower organs. Expression patterns among the abscission zone (AZ) and adjacent areas during various flowering stages and IAA treatment indicate that PsPIN4 likely influences the initiation of peony petal abscission. The PsPIN4 protein was observed to be co-localized on both the plasma membrane and the cell nucleus. The ectopic expression of PsPIN4 reversed the premature flower organs abscission in the Atpin4 and significantly protracted florescence when introduced to Col Arabidopsis. Our findings established a strong basis for further investigation of PIN gene biological functions, particularly concerning intrinsic relationship between PIN-mediated auxin polar.

Physiological response and molecular mechanism of Quercus variabilis under cadmium stress.

Heavy metal pollution is a global environmental problem, and Quercus variabilis has a stronger tolerance to Cd stress than do other species. We aimed to explore the physiological response and molecular mechanisms of Q. variabilis to Cd stress. In this study, the antioxidant enzyme activities of leaves were determined, while the photosynthetic parameters of leaves were measured using Handy PEA, and ion fluxes and DEGs in the roots were investigated using noninvasive microtest technology (NMT) and RNA sequencing techniques, respectively. Cd stress at different concentrations and for different durations affected the uptake patterns of Cd2+ and H+ by Q. variabilis and affected the photosynthetic efficiency of leaves. Moreover, there was a positive relationship between antioxidant enzyme (CAT and POD) activity and Cd concentration. Transcriptome analysis revealed that many genes, including genes related to the cell wall, glutathione metabolism, ion uptake and transport, were significantly upregulated in response to cadmium stress in Q. variabilis roots. WGCNA showed that these DEGs could be divided into eight modules. The turquoise and blue modules exhibited the strongest correlations, and the most significantly enriched pathways were the phytohormone signaling pathway and the phenylpropanoid biosynthesis pathway, respectively. These findings suggest that Q. variabilis can bolster plant tolerance by modulating signal transduction and increasing the synthesis of compounds, such as lignin, under Cd stress. In summary, Q. variabilis can adapt to Cd stress by increasing the activity of antioxidant enzymes, and regulating the fluxes of Cd2+ and H+ ions and the expression of Cd stress-related genes.

PsmiR159b-PsMYB65 module functions in the resumption of bud growth after endodormancy by affecting the cell cycle in tree peony.

Bud endodormancy in perennial plants is a sophisticated system that adapts to seasonal climatic changes. Growth-promoting signals such as low temperature and gibberellins (GAs) are crucial for facilitating budbreak following endodormancy release (EDR). However, the regulatory mechanisms underlying GA-mediated budbreak in tree peony (Paeonia suffruticosa) remain unclear. In tree peony, the expression of PsmiR159b among three differentially expressed miR159 members was inhibited with the prolonged chilling, and overexpression of PsMIR159b delayed budbreak, whereas silencing PsmiR159b promoted budbreak after dormancy. PsMYB65, a downstream transcription factor in the GA pathway, was induced by prolonged chilling and exogenous GA3 treatments. PsMYB65 was identified as a target of PsmiR159b, and promoted budbreak in tree peony. RNA-seq of PsMYB65-slienced buds revealed significant enrichment in the GO terms regulation of 'cell cycle' and 'DNA replication' among differentially expressed genes. Yeast one-hybrid and electrophoretic mobility shift assays demonstrated that PsMYB65 directly bound to the promoter of the type-D cyclin gene PsCYCD3;1. Dual-luciferase reporter assay indicated that PsMYB65 positively regulate PsCYCD3;1 expression, suggesting that miR159b-PsMYB65 module contributes to budbreak by influencing the cell cycle. Our findings revealed that the PsmiR159b-PsMYB65 module functioned in budbreak after dormancy by regulating cell proliferation, providing valuable insights into the endodormancy release regulation mechanism.

PsRGL1 negatively regulates chilling- and gibberellin-induced dormancy release by PsF-box1-mediated targeting for proteolytic degradation in tree peony.

Tree peony bud endodormancy is a common survival strategy similar to many perennial woody plants in winter, and the activation of the GA signaling pathway is the key to breaking endodormancy. GA signal transduction is involved in many physiological processes. Although the GA-GID1-DELLA regulatory module is conserved in many plants, it has a set of specific components that add complexity to the GA response mechanism. DELLA proteins are key switches in GA signaling. Therefore, there is an urgent need to identify the key DELLA proteins involved in tree peony bud dormancy release. In this study, the prolonged chilling increased the content of endogenously active gibberellins. PsRGL1 among three DELLA proteins was significantly downregulated during chilling- and exogenous GA3-induced bud dormancy release by cell-free degradation assay, and a high level of polyubiquitination was detected. Silencing PsRGL1 accelerated bud dormancy release by increasing the expression of the genes associated with dormancy release, including PsCYCD, PsEBB1, PsEBB3, PsBG6, and PsBG9. Three F-box protein family members responded to chilling and GA3 treatments, resulting in PsF-box1 induction. Yeast two-hybrid and BiFC assays indicated that only PsF-box1 could bind to PsRGL1, and the binding site was in the C-terminal domain. PsF-box1 overexpression promoted dormancy release and upregulated the expression of the dormancy-related genes. In addition, yeast two-hybrid and pull-down assays showed that PsF-box1 also interacted with PsSKP1 to form an E3 ubiquitin ligase. These findings enriched the molecular mechanism of the GA signaling pathway during dormancy release, and enhanced the understanding of tree peony bud endodormancy.

Climatic responses and variability in bark anatomical traits of 23 Picea species.

In woody plants, bark is an important protective tissue which can participate in photosynthesis, manage water loss, and transport assimilates. Studying the bark anatomical traits can provide insight into plant environmental adaptation strategies. However, a systematic understanding of the variability in bark anatomical traits and their drivers is lacking in woody plants. In this study, the bark anatomical traits of 23 Picea species were determined in a common garden experiment. We analyzed interspecific differences and interpreted the patterns in bark anatomical traits in relation to phylogenetic relationships and climatic factors of each species according to its global distribution. The results showed that there were interspecific differences in bark anatomical traits of Picea species. Phloem thickness was positively correlated with parenchyma cell size, possibly related to the roles of parenchyma cells in the radial transport of assimilates. Sieve cell size was negatively correlated with the radial diameter of resin ducts, and differences in sieve cells were possibly related to the formation and expansion of resin ducts. There were no significant phylogenetic signals for any bark anatomical trait, except the tangential diameter of resin ducts. Phloem thickness and parenchyma cell size were affected by temperature-related factors of their native range, while sieve cell size was influenced by precipitation-related factors. Bark anatomical traits were not significantly different under wet and dry climates. This study makes an important contribution to our understanding of variability in bark anatomical traits among Picea species and their ecological adaptations.

Dual functions of PsmiR172b-PsTOE3 module in dormancy release and flowering in tree peony (Paeonia suffruticosa).

MicroRNAs (miRNAs) are non-coding RNAs that interact with target genes and are involved in many physiological processes in plants. miR172-AP2 mainly plays a role in the regulation of flowering time and floral organ differentiation. Bud dormancy release is necessary for forcing culture of tree peony in winter, but the mechanism of dormancy regulation is unclear. In this study, we found that a miR172 family member, PsmiR172b, was downregulated during chilling-induced bud dormancy release in tree peony, exhibiting a trend opposite to that of PsTOE3. RNA ligase-mediated (RLM) 5'-RACE (rapid amplification of cDNA ends) confirmed that miR172b targeted PsTOE3, and the cleavage site was between bases 12 (T) and 13 (C) within the complementary site to miR172b. The functions of miR172b and PsTOE3 were detected by virus-induced gene silencing (VIGS) and their overexpression in tree peony buds. PsmiR172b negatively regulated bud dormancy release, but PsTOE3 promoted bud dormancy release, and the genes associated with bud dormancy release, including PsEBB1, PsEBB3, PsCYCD, and PsBG6, were upregulated. Further analysis indicated that PsTOE3 directly regulated PsEBB1 by binding to its promoter, and the specific binding site was a C-repeat (ACCGAC). Ectopic expression in Arabidopsis revealed that the PsmiR172b-PsTOE3 module displayed conservative function in regulating flowering. In conclusion, our results provided a novel insight into the functions of PsmiR172-PsTOE3 and possible molecular mechanism underlying bud dormancy release in tree peony.

Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis.

Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.

Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance.

The HVA22 family of genes, induced by abscisic acid and stress, encodes a class of stress response proteins with a conserved TB2/DP1/HVA22 domain that are unique among eukaryotes. Previous studies have shown that HVA22s play an important role in plant responses to abiotic stresses. In the present study, 34, 32, 16, and 17 HVA22s were identified in G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively. These HVA22 genes were classified into nine subgroups, randomly distributed on the chromosomes. Synteny analysis showed that the amplification of the HVA22s were mainly due to segmental duplication or whole genome replication (WGD). Most HVA22s promoter sequences contain a large number of drought response elements (MYB), defense and stress response elements (TC-rich repeats), and hormone response elements (ABRE, ERE, SARE, etc.), suggesting that HVA22s may respond to adversity stresses. Expression profiling demonstrated that most GhHVA22s showed a constitutive expression pattern in G. hirsutum and could respond to abiotic stresses such as salt, drought, and low temperature. Overexpression of GhHVA22E1D (GH_D07G0564) in Arabidopsis thaliana enhances salt and drought tolerance in Arabidopsis. Virus-induced gene silencing of GhHVA22E1D reduced salt and drought tolerance in cotton. This indicates that GhHVA22E1D plays an active role in the plant response to salt stress and drought stress. GhHVA22E1D may act in plant response to adversity by altering the antioxidant capacity of plants. This study provides valuable information for the functional genomic study of the HVA22 gene family in cotton. It also provides a reference for further elucidation of the functional studies of HVA22 in plant resistance to abiotic stress response.

HRU-Net: A Transfer Learning Method for Carotid Artery Plaque Segmentation in Ultrasound Images.

Carotid artery stenotic plaque segmentation in ultrasound images is a crucial means for the analysis of plaque components and vulnerability. However, segmentation of severe stenotic plaques remains a challenging task because of the heterogeneities of inter-plaques and intra-plaques, and obscure boundaries of plaques. In this paper, we propose an automated HRU-Net transfer learning method for segmenting carotid plaques, using the limited images. The HRU-Net is based on the U-Net encoder−decoder paradigm, and cross-domain knowledge is transferred for plaque segmentation by fine-tuning the pretrained ResNet-50. Moreover, a cropped-blood-vessel image augmentation is customized for the plaque position constraint during training only. Moreover, hybrid atrous convolutions (HACs) are designed to derive diverse long-range dependences for refined plaque segmentation that are used on high-level semantic layers to exploit the implicit discrimination features. The experiments are performed on 115 images; Firstly, the 10-fold cross-validation, using 40 images with severe stenosis plaques, shows that the proposed method outperforms some of the state-of-the-art CNN-based methods on Dice, IoU, Acc, and modified Hausdorff distance (MHD) metrics; the improvements on metrics of Dice and MHD are statistically significant (p < 0.05). Furthermore, our HRU-Net transfer learning method shows fine generalization performance on 75 new images with varying degrees of plaque stenosis, and it may be used as an alternative for automatic noisy plaque segmentation in carotid ultrasound images clinically.

Genome-Wide Identification of Membrane-Bound Fatty Acid Desaturase Genes in Three Peanut Species and Their Expression in Arachis hypogaea during Drought Stress.

As a crop irrigated primarily by rain, the quality and yield of peanuts are significantly limited by drought. To date, many studies have indicated that fatty acid desaturase (FAD) genes enhance plant tolerance to drought stresses. In this study, 16, 15, and 31 FADs were identified in Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. All the FADs were divided into four subfamilies, which had relatively conserved gene structures, motifs, and domains. The synteny relationships and chromosomal position analysis showed that the FADs in subgenome pairs, A. duranensis-A. hypogaea (AA) and A. ipaensis-A. hypogaea (BB), were homologous, and their physical locations were consistent. The Ka/Ks results indicated that nine FAD genes underwent a purifying selection, and Ah|FAD3.2 experienced positive selection during tetraploid peanut speciation. Various cis-acting elements related to hormone signaling and stress responsiveness in promoters and the predicted miRNA targeting Ah|FADs suggested that these genes play crucial roles in drought tolerance. The expression profiles of Ah|FADs in 22 tissues and drought-tolerant and -sensitive cultivars under drought stress suggested that 4 and 6 FADs were putative genes related to oil accumulation and drought, respectively. These findings will help provide insight into the potential functional roles of the FAD genes, which may aid in dealing with plant drought stress.

A novel online analyzer for accurate and rapid measurement of volatile fatty acids in anaerobic wastewater treatment.

Volatile fatty acids (VFAs), which are largely generated during the anaerobic acidification process, are considered to be reliable indicators of the stable process operation. However, the common methods for monitoring VFAs are offline, and they are typically manual requiring time-consuming, costly and complex instruments. This study aims to develop a novel online analyzer for automatic measuring VFAs, which was based on the 5-pH point titration, embedded with a proportional-integral-derivative (PID) feedback control system. The results show that it can achieve accurate and rapid monitoring of VFAs ranging between 0-400 mg/L (<9 min/sample) but simultaneously faces the problems of overtitration and interference of complex characteristics of wastewater. In order to improve its accuracy and stability, the effects of three general coefficients (KI,KP, and KD) of PID on the titration were investigated, and the optimal values of KI, KP, and KD were found to be 1.5, 1.0, and -1.0~0.5, respectively. Besides, the initial titration speed was set at 0.06 mL/min, equal to the minimum speed of the peristaltic pump, and the dichotomy approach was integrated into the PID feedback controller. Owing to the above improvements, the relative mean deviation and standard deviation of measuring VFAs in both synthetic and real wastewaters were mostly lower than 5.0% and 5.0 mg/L, proving the online analyzer is rapid, accurate and reliable.

Identification of the glutamine synthetase (GS) gene family in four wheat species and functional analysis of Ta4D.GSe in Arabidopsis thaliana.

Drought stress can negatively impact crop yield and quality. Improving wheat yields under drought stress is a major objective of agronomic research. Glutamine synthetase (GS) is a key enzyme of nitrogen metabolism that is critical to plant growth and development in abiotic stress response. However, to date, no systemic characterization of the GS genes has yet been conducted in wheat and its close relatives. We identified a total of 15 GS genes in Triticum aestivum (2n = 6x = 42; AABBDD), as well as 9 GS genes in Triticum dicoccoides (2n = 4x = 28; AABB), 6 in Aegilops tauschii (2n = 2x = 14; DD), and 5 in Triticum urartu (2n = 2x = 14; AA). The 35 GSs were further clustered into five lineages according to the phylogenetic tree. Synteny analysis revealed that the three subgenomes in bread wheat retained extensive synteny between bread wheat and its three relative species. We identified three up-regulated TaGSs (Ta4A.GSe, Ta4B.GSe, and Ta4D.GSe) from transcriptome data after drought and salt stress. Ta4D.GSe was subsequently used for further functional studies, and its subcellular localization were determined in Arabidopsis protoplasts. Its overexpression in Arabidopsis enhanced drought tolerance by increasing the ability of scavenging of reactive oxygen species (ROS) and osmotic adjustment. We identified GS gene family in four wheat species and performed comparative analyses of their relationships, chromosome locations, conserved motif, gene structure, and synteny. The subcellular localization of Ta4D.GSe was detected and its drought tolerance function was demonstrated. Taken together, these findings provide insight into the potential functional roles of the GS genes in abiotic stress tolerance. KEY MESSAGE: This report clearly shows detailed characterization of GS gene family in four wheat species and demonstrates that Ta4D.GSe plays an important role in enhancing drought tolerance by improving the scavenging of ROS and osmotic adjustment ability in Arabidopsis.

CSM-Net: Automatic joint segmentation of intima-media complex and lumen in carotid artery ultrasound images.

The intima-media thickness (IMT) is an effective biomarker for atherosclerosis, which is commonly measured by ultrasound technique. However, the intima-media complex (IMC) segmentation for the IMT is challenging due to confused IMC boundaries and various noises. In this paper, we propose a flexible method CSM-Net for the joint segmentation of IMC and Lumen in carotid ultrasound images. Firstly, the cascaded dilated convolutions combined with the squeeze-excitation module are introduced for exploiting more contextual features on the highest-level layer of the encoder. Furthermore, a triple spatial attention module is utilized for emphasizing serviceable features on each decoder layer. Besides, a multi-scale weighted hybrid loss function is employed to resolve the class-imbalance issues. The experiments are conducted on a private dataset of 100 images for IMC and Lumen segmentation, as well as on two public datasets of 1600 images for IMC segmentation. For the private dataset, our method obtain the IMC Dice, Lumen Dice, Precision, Recall, and F1 score of 0.814 ± 0.061, 0.941 ± 0.024, 0.911 ± 0.044, 0.916 ± 0.039, and 0.913 ± 0.027, respectively. For the public datasets, we obtain the IMC Dice, Precision, Recall, and F1 score of 0.885 ± 0.067, 0.885 ± 0.070, 0.894 ± 0.089, and 0.885 ± 0.067, respectively. The results demonstrate that the proposed method precedes some cutting-edge methods, and the ablation experiments show the validity of each module. The proposed method may be useful for the IMC segmentation of carotid ultrasound images in the clinic. Our code is publicly available at https://github.com/yuanyc798/US-IMC-code.

Genome-wide identification and analysis of Oleosin gene family in four cotton species and its involvement in oil accumulation and germination.

BACKGROUND: Cotton is not only a major textile fiber crop but also a vital oilseed, industrial, and forage crop. Oleosins are the structural proteins of oil bodies, influencing their size and the oil content in seeds. In addition, the degradation of oleosins is involved in the mobilization of lipid and oil bodies during seed germination. However, comprehensive identification and the systematic analysis of the Oleosin gene (OLEOs) family have not been conducted in cotton. RESULTS: An in-depth analysis has enabled us to identify 25 and 24 OLEOs in tetraploid cotton species G. hirsutum and G. barbadense, respectively, while 12 and 13 OLEOs were identified in diploid species G. arboreum and G. raimondii, respectively. The 74 OLEOs were further clustered into three lineages according to the phylogenetic tree. Synteny analysis revealed that most of the OLEOs were conserved and that WGD or segmental duplications might drive their expansion. The transmembrane helices in GhOLEO proteins were predicted, and three transmembrane models were summarized, in which two were newly proposed. A total of 24 candidate miRNAs targeting GhOLEOs were predicted. Three highly expressed oil-related OLEOs, GH_A07G0501 (SL), GH_D10G0941 (SH), and GH_D01G1686 (U), were cloned, and their subcellular localization and function were analyzed. Their overexpression in Arabidopsis increased seed oil content and decreased seed germination rates. CONCLUSION: We identified OLEO gene family in four cotton species and performed comparative analyses of their relationships, conserved structure, synteny, and gene duplication. The subcellular localization and function of three highly expressed oil-related OLEOs were detected. These results lay the foundation for further functional characterization of OLEOs and improving seed oil content.

Chilling and gibberellin acids hyperinduce ß-1,3-glucanases to reopen transport corridor and break endodormancy in tree peony (Paeonia suffruticosa).

Bud endodormancy is accompanied by transport channel apertures blockage through callose deposition, and its resume to growth requires evoking ß-1,3-glucanases (BGs) to unchoke the conduit. To understand out its working manner, the statuses of the transport channels were evaluated and candidate BGs were identified during chilling and gibberellin acids (GA) induced dormancy release in tree peony. Calcein reflects plasmodesmata permeability, and no calcein was observed in the bud together with density aniline blue fluorescent around the stem phloem at 0 d chilling. With the increase of chilling accumulation, the contents of glucan declined and the activities of gulcanase increased gradually in buds, and the calcein reached the top of flower primordia at 21 d chilled bud. Both GA3 and GA4 feedings promoted bud sprouting and growth along with rapidly unchoking the transport channels, and GA3 was more effective. Several candidate ß-1,3-glucanase genes were detected, combining transcriptional profiling and quantitative PCR analysis. PsBG1, PsBG3, PsBG6, PsBG8 and PsBG9 were inducible by chilling accumulation and presented laminarin hydrolyzing activities after prokaryotically expression, while PsBG1, PsBG3, PsBG8 and PsBG9 responded to GAs application. Subcellular localizations revealed that PsBG6 and PsBG9 were plasmodesmata residents. It was concluded that PsBG6 played a vital role in chilling accumulation response and PsBG9 was central in GAs-induced dormancy release, and they could be used as marker genes for dormancy release in tree peony. These results were of great value to understand the mechanism of dormancy regulation and as an important fundamental for forcing culture technology in tree peony.

Changes of DNA Methylation Patterns Reveal Epigenetic Modification of Dormancy Release-Related Genes Is Induced by Chilling in Tree Peony.

DNA methylation is an important epigenetic regulator of gene expression. Application of 5-azacytidine (a methylation inhibitor) significantly promoted bud sprouting rate and the elongation of branches and leaves in "Luhehong" and "Fengdanbai." In total, 11,166 and 11,443 fragments were obtained by methylation-sensitive amplified polymorphism (MSAP) analysis during chilling-induced dormancy release in the two varieties, respectively. Total methylation levels were high in dormant buds, mainly for hemimethylation, which were slowly increased by short-term chilling (7 days) and decreased by long-term chilling. Compared with 0 day, the ratio of the methylation downregulated group increased during dormancy release, whereas that of the upregulated group declined gradually. These variations were consistent with the dynamic expressions of DNA methyltransferase/demethylase genes and their enzyme activity changes. In total, 13 polymorphic MSAP fragments were similar to known proteins (E-value <1e-5), and their methylation statuses were consistent with their expression patterns. The expression change of PsCWH, encoding cell wall hydrolase, might be due to DNA methylation ratios of CpG sites identified by bisulfite sequencing. These results indicated that chilling accumulation promoted bud dormancy release and sprouting through DNA methylation modification of specific genes. This study would provide new insights into the molecular mechanism underlying dormancy release in tree peony.

Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony.

BACKGROUND: Bud dormancy is a sophisticated strategy which plants evolve to survive in tough environments. Endodormancy is a key obstacle for anti-season culture of tree peony, and sufficient chilling exposure is an effective method to promote dormancy release in perennial plants including tree peony. However, the mechanism of dormancy release is still poorly understood, and there are few systematic studies on the metabolomics during chilling induced dormancy transition. RESULTS: The tree peony buds were treated with artificial chilling, and the metabolmics analysis was employed at five time points after 0-4 °C treatment for 0, 7, 14, 21 and 28 d, respectively. A total of 535 metabolites were obtained and devided into 11 groups including flavonoids, amino acid and its derivatives, lipids, organic acids and its derivates, nucleotide and its derivates, alkaloids, hydroxycinnamoyl derivatives, carbohydrates and alcohols, phytohormones, coumarins and vitamins. Totally, 118 differential metabolites (VIP ≥ 1, P < 0.05) during chilling treatment process were detected, and their KEGG pathways involved in several metabolic pathways related to dormancy. Sucrose was the most abundant carbohydrate in peony bud. Starch was degradation and Embden Meyerhof Parnas (EMP) activity were increased during the dormancy release process, according to the variations of sugar contents, related enzyme activities and key genes expression. Flavonoids synthesis and accumulation were also promoted by prolonged chilling. Moreover, the variations of phytohormones (salicylic acid, jasmonic acid, abscisic acid, and indole-3-acetic acid) indicated they played different roles in dormancy transition. CONCLUSION: Our study suggested that starch degradation, EMP activation, and flavonoids accumulation were crucial and associated with bud dormancy transition in tree peony.

Application of 5-azacytidine induces DNA hypomethylation and accelerates dormancy release in buds of tree peony.

Release of bud dormancy is a prerequisite for the growth resumption and production in perennial plants such as tree peony. DNA methylation plays a pivotal role in regulating gene expression. In this study, combination of morphologic observation and DNA methylation analysis indicated that 5-azacytidine (5-azaC) application for 7 d declined 5 mC quantities and promoted dormancy release. After 5-azaC treatment, total 174,341 unigenes and 1818 differentially expression genes (DEGs) were obtained by RNA-seq, of which there were 1194 DEGs after 1 d 5-azaC treatment (AD1 vs CD1), and 624 DEGs after 7 d (AD7 vs CD7), respectively. The KEGG pathway analysis identified that totally 10 DEGs annotated in DNA replication pathway were enriched when AD7 compared with CD7. Furthermore, the expression patterns of several DEGs by real-time quantitative RT-PCR were consistent with that of RNA-seq data. 5-azaC application significantly decreased the expression levels of DNA methyltransferase genes, PsCMT3, PsMET1 and PsDRM2, and increased the transcript of demethylase gene PsROS1. Simultaneously, total methyltransferases activity decreased, and demethylase activity was induced by 5-azaC. In summary, application of 5-azaC inhibited the expression of the genes related to growth and development in short-term, indicating a possible toxic effect to plant, and its long-term effect was to induce hypomethylation by increasing demethylase genes transcripts and decreasing the expressions of methyltransferase genes, and then activate cell cycle, DNA replication and glycol-metabolism processes, which subsequently accelerated dormancy release. All these would provide a new strategy to further understand the molecular mechanism of dormancy release in tree peony.

Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage.

BACKGROUND: Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. RESULTS: In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. CONCLUSIONS: These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.