Identification of plant hormones and candidate hub genes regulating flag leaf senescence in wheat response to water deficit stress at the grain-filling stage

Molecular mechanism of response to low-temperature during the natural overwintering period of Rosa persica

KEY MESSAGE

The JA and ICE-CBF-COR signaling pathways play important roles in the low-temperature response of Rosa persica, with RpMYC2 interacting with multiple transcription factors and positively regulating tolerance to low-temperature stress. Rosa persica is highly resilient to cold and drought, making it a valuable resource for breeding in the Rosa. However, the response mechanism of R. persica during the overwintering period remains unclear. This study examined root and stem tissues of R. persica over an eight-month natural open field overwintering period, measuring physiological indices of cold tolerance and investigating changes in cold tolerance across different overwintering stages. The values of physiological indicators of cold hardiness of R. persica roots and stems increased and then decreased. Osmoregulatory substances were the primary contributors to cold hardiness of R. persica roots, while antioxidant enzyme systems played a dominant role in cold hardiness of stems. Differential gene enrichment analyses revealed that oxidative reactions, the synthesis of various secondary metabolites, and hormone signaling pathways are crucial in establishing cold tolerance of R. persica at different overwintering stages. Weighted gene co-expression network and time-ordered gene co-expression network analyses identified the gene RpMYC2 as potentially key to cold tolerance in R. persica. Yeast two-hybrid discovery revealed that RpMYC2 interacts with multiple transcription factors to regulate cold stress resistance in R. persica. Based on the transcriptome, key genes involved in response to low temperature were identified in this study, providing the physiological and molecular insights for cold tolerance breeding of Rosa.

Integrated analysis of transcriptomics and defense-related phytohormones to discover hub genes conferring maize Gibberella ear rot caused by Fusarium Graminearum

BACKGROUND

Gibberella ear rot (GER) is one of the most devastating diseases in maize growing areas, which directly reduces grain yield and quality. However, the underlying defense response of maize to pathogens infection is largely unknown.

RESULTS

To gain a comprehensive understanding of the defense response in GER resistance, two contrasting inbred lines 'Nov-82' and 'H10' were used to explore transcriptomic profiles and defense-related phytohormonal alterations during Fusarium graminearum infection. Transcriptomic analysis revealed 4,417 and 4,313 differentially expressed genes (DEGs) from the Nov-82 and H10, respectively, and 647 common DEGs between the two lines. More DEGs were obviously enriched in phenylpropanoid biosynthesis, secondary metabolites biosynthesis, metabolic process and defense-related pathways. In addition, the concentration of the defense-related phytohormones, jasmonates (JAs) and salicylates (SAs), was greatly induced after the pathogen infection. The level of JAs in H10 was more higher than in Nov-82, whereas an opposite pattern for the SA between the both lines. Integrated analysis of the DEGs and the phytohormones revealed five vital modules based on co-expression network analysis according to their correlation. A total of 12 hub genes encoding fatty acid desaturase, subtilisin-like protease, ethylene-responsive transcription factor, 1-aminocyclopropane-1-carboxylate oxidase, and sugar transport protein were captured from the key modules, indicating that these genes might play unique roles in response to pathogen infection, CONCLUSIONS: Overall, our results indicate that large number DEGs related to plant disease resistance and different alteration of defensive phytohormones were activated during F. graminearum infection, providing new insight into the defense response against pathogen invasion, in addition to the identified hub genes that can be further investigated for enhancing maize GER resistance.

Exogenous Cytokinin 4PU-30 Modulates the Response of Wheat and Einkorn Seedlings to Ultraviolet B Radiation

Abiotic stress is responsible for a significant reduction in crop plant productivity worldwide. Ultraviolet (UV) radiation is a natural component of sunlight and a permanent environmental stimulus. This study investigated the distinct responses of young wheat and einkorn plants to excessive UV-B radiation (180 min at λmax 312 nm) following foliar pretreatment with 1 µM synthetic cytokinin 4PU-30. Results demonstrated that UV radiation significantly amplified hydrogen peroxide levels in both wheat and einkorn, with einkorn exhibiting a more pronounced increase compared to wheat. This elevation indicated the induction of oxidative stress by UV radiation in the two genotypes. Intensified antioxidant enzyme activities and the increased accumulation of typical stress markers and non-enzyme protectants were evidenced. Transcriptional activity of genes encoding the key antioxidant enzymes POX, GST, CAT, and SOD was also investigated to shed some light on their genetic regulation in both wheat and einkorn seedlings. Our results suggested a role for POX1 and POX7 genes in the UV-B tolerance of the two wheat species as well as a cytokinin-stimulated UV-B stress response in einkorn involving the upregulation of the tau subfamily gene GSTU6. Based on all our findings, it could be concluded that 4PU-30 had the potential of alleviating oxidative stress by attenuating the symptoms of superfluous UV-B illumination in the two examined plant species.

Screening for drought tolerance and genetic diversity of wheat varieties using agronomic and molecular markers

BACKGROUND

The future predictions for frequent and severe droughts will represent a significant threat to wheat yield and food security. In this context, breeding has proven to be the most efficient approach to enhance wheat productivity in dry environments.

METHODS AND RESULTS

In this study, both agronomic and molecular-based approaches were used to evaluate the response of twenty-eight Tunisian wheat varieties to drought stress. The primary objective was to screen these varieties for drought tolerance using molecular and agro-morphological markers. All varieties were significantly affected by drought stress regarding various traits including total dry matter, straw length, flag leaf area, number of senescent leaves, SPAD value, grain yield and grain number. Furthermore, substantial variability in drought-stress tolerance was observed among wheat genotypes. The cluster analysis and principal component analyses confirmed the existence of genotypic variation in growth and yield impairments induced by drought. The stress susceptibility index (SSI) and tolerance index (TOL) proved to be the most effective indices and were strongly correlated with the varying levels of genotypic tolerance. The genotyping evaluation resulted in the amplification of 101 alleles using highly polymorphic 12 SSR markers, showed an average polymorphism of 74%.

CONCLUSIONS

Taken together, the combination of agronomic and molecular approaches revealed that Karim, Td7, D117 and Utique are the most drought-tolerant wheat varieties. These varieties are particularly promising candidates for genetic improvements and can be utilized as potential genitors for future breeding programs in arid and semi-arid regions.

Comparative transcriptomic data confirm the findings of dehydration stress-induced redox biology of indigenous aromatic rice cultivars

The present work compares the transcriptome data sets of post-imbibitional dehydration stress-raised seedlings of two contrasting indigenous aromatic rice cultivars (Oryza sativa L., Cultivars Jamainadu and Badshabhog) for unfolding genetic regulation of dehydration stress. The result of RNA-seq analysis in Illumina platform in general revealed significant cultivar-specific expression of genes under dehydration stress that substantiate the data of redox metabolic fingerprints (assessed in terms of differential efficacy of ascorbate-glutathione pathway, ROS-antioxidant interaction dynamics and sensitive biomarkers of oxidative stress). Both the cultivars showed a diverse global transcriptomic response under water-deficit condition. Transcripts selected for heatmap generation with proper annotation revealed genes that are significantly expressed and mainly involved in redox functions, signaling, membrane trafficking, replication, protein synthesis, etc. Gene ontology (GO) analysis proposed that dehydration stress in the drought-tolerant cultivar Badshabhog was attributable to the enhanced expression of genes associated with carbon dioxide-concentrating mechanism, peroxysomal biogenesis, protein modification, protein synthesis, mitochondrial electron transport chain functioning, intercellular protein transport, histone demethylation associated with developmental process, regulation of apoptosis, etc. The redox genes that got significantly over-expressed in the IARC Badshabhog vis-à-vis Jamainadu include l-ascorbate oxidase/peroxidase, monothiol glutaredoxin-S1, thioredoxin-like protein AAED1 (chloroplastic), thioredoxin-like protein CXXS1, NADH-dehydrogenase (ubiquinone)-1-beta subcomplex subunit 3-B, NADH-dehydrogenase subunit 6 and K, lipoxygenase 6 isoform-XI, etc. Overall, the results of the RNA-seq analysis led to the identification of cultivar-specific genes, with the cultivar Badshabhog exhibiting significantly greater molecular reprogramming for redox regulation and signaling necessary for combating dehydration stress.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03829-z.

Transcriptome and WGCNA reveal hub genes in sugarcane tiller seedlings in response to drought stress

Drought stress can severely affect sugarcane growth and yield. The objective of this research was to identify candidate genes in sugarcane tillering seedlings in response to drought stress. We performed a comparative phenotypic, physiological and transcriptomic analysis of tiller seedlings of drought-stressed and well-watered "Guire 2" sugarcane, in a time-course experiment (5 days, 9 days and 15 days). Physiological examination reviewed that SOD, proline, soluble sugars, and soluble proteins accumulated in large amounts in tiller seedlings under different intensities of drought stress, while MDA levels remained at a stable level, indicating that the accumulation of osmoregulatory substances and the enhancement of antioxidant enzyme activities helped to limit further damage caused by drought stress. RNA-seq and weighted gene co-expression network analysis (WGCNA) were performed to identify genes and modules associated with sugarcane tillering seedlings in response to drought stress. Drought stress induced huge down-regulated in gene expression profiles, most of down-regulated genes were mainly associated with photosynthesis, sugar metabolism and fatty acid synthesis. We obtained four gene co-expression modules significantly associated with the physiological changes under drought stress (three modules positively correlated, one module negatively correlated), and found that LSG1-2, ERF1-2, SHKA, TIL, HSP18.1, HSP24.1, HSP16.1 and HSFA6A may play essential regulatory roles as hub genes in increasing SOD, Pro, soluble sugar or soluble protein contents. In addition, one module was found mostly involved in tiller stem diameter, among which members of the BHLH148 were important nodes. These results provide new insights into the mechanisms by which sugarcane tillering seedlings respond to drought stress.

Transcriptome-based analysis of key pathways relating to yield formation stage of foxtail millet under different drought stress conditions

Although foxtail millet, as small Panicoid crop, is of drought resilient, drought stress has a significant effect on panicle of foxtail millet at the yield formation stage. In this study, the changes of panicle morphology, photosynthesis, antioxidant protective enzyme system, reactive oxygen species (ROS) system, and osmotic regulatory substance and RNA-seq of functional leaves under light drought stress (LD), heavy drought stress (HD), light drought control (LDCK) and heavy drought control (HDCK) were studied to get a snap-shot of specific panicle morphological changes, physiological responses and related molecular mechanisms. The results showed that the length and weight of panicle had decreased, but with increased empty abortive rate, and then yield dropped off 14.9% and 36.9%, respectively. The photosynthesis of millet was significantly decreased, like net photosynthesis rate, stomatal conductance and transpiration rate, especially under HD treatment with reluctant recovery from rehydration. Under LD and HD treatment, the peroxidase (POD) was increased by 34% and 14% and the same as H₂O₂ by 34.7% and 17.2% compared with LDCK and HDCK. The ability to produce and inhibit O^2- free radicals under LD treatment was higher than HD. The content of soluble sugar was higher under LD treatment but the proline was higher under HD treatment. Through RNA-seq analysis, there were 2,393 and 3,078 different genes expressed under LD and HD treatment. According to the correlation analysis between weighted gene coexpression network analysis (WGCNA) and physiological traits, the co-expression network of several modules with high correlation was constructed, and some hub genes of millet in response to drought stress were found. The expression changes relating to carbon fixation, sucrose and starch synthesis, lignin synthesis, gibberellin synthesis, and proline synthesis of millet were specifically analyzed. These findings provide a full perspective on how drought affects the yield formation of foxtail millet by constructing one work model thereby providing theoretical foundation for hub genes exploration and drought resistance breeding of foxtail millet.

Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1

INTRODUCTION

The soybean cyst nematode (SCN) is a major disease in soybean production thatseriously affects soybean yield. At present, there are no studies on weighted geneco-expression network analysis (WGCNA) related to SCN resistance.

METHODS

Here, transcriptome data from 36 soybean roots under SCN HG Type 0 (race 3) stresswere used in WGCNA to identify significant modules.

RESULTS AND DISCUSSION

A total of 10,000 differentially expressed genes and 21 modules were identified, of which the module most related to SCN was turquoise. In addition, the hub gene GmHg1 with high connectivity was selected, and its function was verified. GmHg1 encodes serine/threonine protein kinase (PK), and the expression of GmHg1 in SCN-resistant cultivars ('Dongnong L-204') and SCN-susceptible cultivars ('Heinong 37') increased significantly after HG Type 0 stress. Soybean plants transformed with GmHg1-OX had significantly increased SCN resistance. In contrast, the GmHg1-RNAi transgenic soybean plants significantly reduced SCN resistance. In transgenic materials, the expression patterns of 11 genes with the same expression trend as the GmHg1 gene in the 'turquoise module' were analyzed. Analysis showed that 11genes were co-expressed with GmHg1, which may be involved in the process of soybean resistance to SCN. Our work provides a new direction for studying the Molecular mechanism of soybean resistance to SCN.

Environmental Stimuli: A Major Challenge during Grain Filling in Cereals

Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable agriculture. Furthermore, soil salinity is another major environmental constraint affecting crop growth and threatening global food security. The grain filling stage is the final stage of growth and is also the most important stage in cereals, directly determining the grain weight and final yield. However, the grain filling process is extremely vulnerable to different environmental stimuli, especially for inferior spikelets. Given the importance of grain filling in cereals and the deterioration of environmental problems, understanding environmental stimuli and their effects on grain filling constitutes a major focus of crop research. In recent years, significant advances made in this field have led to a good description of the intricate mechanisms by which different environmental stimuli regulate grain filling, as well as approaches to adapt cereals to changing climate conditions and to give them better grain filling. In this review, the current environmental stimuli, their dose-response effect on grain filling, and the physiological and molecular mechanisms involved are discussed. Furthermore, what we can do to help cereal crops adapt to environmental stimuli is elaborated. Overall, we call for future research to delve deeper into the gene function-related research and the commercialization of gene-edited crops. Meanwhile, smart agriculture is the development trend of the future agriculture under environmental stimuli.

Transcriptome and metabolome analyses reveal the key genes related to grain size of big grain mutant in Tartary Buckwheat (Fagopyrum tartaricum)

Grain size with high heritability and stability is an important selection target during Tartary buckwheat breeding. However, the mechanisms that regulate Tartary buckwheat grain development are unknown. We generated transcriptome and metabolome sequencing from 10 and 15 days past anthesis (DPA) grains of big grain mutant (bg1) and WT, and identified 4108 differentially expressed genes (DEGs) including 93 significantly up-regulated differential genes and 85 significantly down-regulated genes in both stages, simultaneously. Meanwhile, we identified DEGs involved in ubiquitin-proteasome pathway, HAI-KU (IKU) pathway, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone (auxin, brassinosteroids and cytokinins) transduction pathway and five transcription factor families, including APETALA (AP2), GROWTH-REGULATING FACTORS (GRF), AUXIN RESPONSE FACTOR (ARF), WRKY and MYB. Weighted gene co-expression network analysis (WGCNA) was performed and obtained 9 core DEGs. Conjoint analyses of transcriptome and metabolome sequencing screened out 394 DEGs. Using a combined comprehensive analysis, we identified 24 potential candidate genes that encode E3 ubiquitin-protein ligase HIP1, EMBRYO-DEFECTIVE (EMB) protein, receptor-like protein kinase FERONIA (FER), kinesin-4 protein SRG1, and so on, which may be associated with the big-grain mutant bg1. Finally, a quantitative real-time Polymerase Chain Reaction (qRT-PCR) assay was conducted to validate the identified DEGs. Our results provide additional knowledge for identification and functions of causal candidate genes responsible for the variation in grain size and will be an invaluable resource for the genetic dissection of Tartary buckwheat high-yield molecular breeding.

Integrated physiological and weighted gene co-expression network analysis reveals the hub genes engaged in nitrate-regulated alleviation of ammonium toxicity at the seedling stage in wheat (Triticum aestivum L.)

Wheat has a specific preference for NO₃ ^- and shows toxicity symptoms under high NH₄ ⁺ concentrations. Increasing the nitrate supply may alleviate ammonium stress. Nevertheless, the mechanisms underlying the nitrate regulation of wheat root growth to alleviate ammonium toxicity remain unclear. In this study, we integrated physiological and weighted gene co-expression network analysis (WGCNA) to identify the hub genes involved in nitrate alleviation of ammonium toxicity at the wheat seedling stage. Five NH₄ ⁺/NO₃ ^- ratio treatments, including 100/0 (N_a), 75/25 (N_r1), 50/50 (N_r2), 25/75 (N_r3), and 0/100 (N_n) were tested in this study. The results showed that sole ammonium treatment (N_a) increased the lateral root number but reduced root biomass. Increasing the nitrate supply significantly increased the root biomass. Increasing nitrate levels decreased abscisic acid (ABA) content and increased auxin (IAA) content. Furthermore, we identified two modules (blue and turquoise) using transcriptome data that were significantly related to root physiological growth indicators. TraesCS6A02G178000 and TraesCS2B02G056300 were identified as hub genes in the two modules which coded for plastidic ATP/ADP-transporter and WRKY62 transcription factors, respectively. Additionally, network analysis showed that in the blue module, TraesCS6A02G178000 interacts with downregulated genes that coded for indolin-2-one monooxygenase, SRG1, DETOXIFICATION, and wall-associated receptor kinase. In the turquoise module, TraesCS2B02G056300 was highly related to the genes that encoded ERD4, ERF109, CIGR2, and WD40 proteins, and transcription factors including WRKY24, WRKY22, MYB30, and JAMYB, which were all upregulated by increasing nitrate supply. These studies suggest that increasing the nitrate supply could improve root growth and alleviate ammonium toxicity through physiological and molecular regulation networks, including ROS, hormonal crosstalk, and transcription factors.

Comparative physiological and coexpression network analyses reveal the potential drought tolerance mechanism of peanut

BACKGROUND

Drought stress has negative effects on plant growth and productivity. In this study, a comprehensive analysis of physiological responses and gene expression was performed. The responses and expressions were compared between drought-tolerant (DT) and drought-sensitive (DS) peanut varieties to investigate the regulatory mechanisms and hub genes involved in the impact of drought stress on culture.

RESULTS

The drought-tolerant variety had robust antioxidative capacities with higher total antioxidant capacity and flavonoid contents, and it enhanced osmotic adjustment substance accumulation to adapt to drought conditions. KEGG analysis of differentially expressed genes demonstrated that photosynthesis was strongly affected by drought stress, especially in the drought-sensitive variety, which was consistent with the more severe suppression of photosynthesis. The hub genes in the key modules related to the drought response, including genes encoding protein kinase, E3 ubiquitin-protein ligase, potassium transporter, pentatricopeptide repeat-containing protein, and aspartic proteinase, were identified through a comprehensive combined analysis of genes and physiological traits using weighted gene co-expression network analysis. There were notably differentially expressed genes between the two varieties, suggesting the positive roles of these genes in peanut drought tolerance.

CONCLUSION

A comprehensive analysis of physiological traits and relevant genes was conducted on peanuts with different drought tolerances. The findings revealed diverse drought-response mechanisms and identified candidate genes for further research.

Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator

Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and hyperaccumulation. In this regard, understanding of interacting genes can be a crucial aspect as these interactions regulate several biological functions at molecular level in response to multiple signals. In this current study, we applied a weighted gene co-expression network analysis (WGCNA) on root and shoot RNA-seq data of A. halleri to predict the related scale-free organ specific co-expression networks, for the first time. A total of 19,653 genes of root and 18,081 genes of shoot were grouped into 14 modules and subjected to GO and KEGG enrichment analysis. "Photosynthesis" and "photosynthesis-antenna proteins" were identified as the most enriched and common pathway to both root and shoot. Whereas "glucosinolate biosynthesis," "autophagy," and "SNARE interactions in vesicular transport" were specific to root, and "circadian rhythm" was found to be enriched only in shoot. Later, hub and bottleneck genes were identified in each module by using cytoHubba plugin based on Cytoscape and scoring the relevance of each gene to the topology of the network. The modules with the most significant differential expression pattern across control and treatment (Cd-Zn treatment) were selected and their hub and bottleneck genes were screened to validate their possible involvement in heavy metal stress. Moreover, we combined the analysis of co-expression modules together with protein-protein interactions (PPIs), confirming some genes as potential candidates in plant heavy metal stress and as biomarkers. The results from this analysis shed the light on the pivotal functions to the hyperaccumulative trait of A. halleri, giving perspective to new paths for future research on this species.

TaWRKY13-A Serves as a Mediator of Jasmonic Acid-Related Leaf Senescence by Modulating Jasmonic Acid Biosynthesis

Leaf senescence is crucial for crop yield and quality. Transcriptional regulation is a key step for integrating various senescence-related signals into the nucleus. However, few regulators of senescence implicating transcriptional events have been functionally characterized in wheat. Based on our RNA-seq data, we identified a WRKY transcription factor, TaWRKY13-A, that predominately expresses at senescent stages. By using the virus-induced gene silencing (VIGS) method, we manifested impaired transcription of TaWRKY13-A leading to a delayed leaf senescence phenotype in wheat. Moreover, the overexpression (OE) of TaWRKY13-A accelerated the onset of leaf senescence under both natural growth condition and darkness in Brachypodium distachyon and Arabidopsis thaliana. Furthermore, by physiological and molecular investigations, we verified that TaWRKY13-A participates in the regulation of leaf senescence via jasmonic acid (JA) pathway. The expression of JA biosynthetic genes, including AtLOX6, was altered in TaWRKY13-A-overexpressing Arabidopsis. We also demonstrated that TaWRKY13-A can interact with the promoter of AtLOX6 and TaLOX6 by using the electrophoretic mobility shift assay (EMSA) and luciferase reporter system. Consistently, we detected a higher JA level in TaWRKY13-A-overexpressing lines than that in Col-0. Moreover, our data suggested that TaWRKY13-A is partially functional conserved with AtWRKY53 in age-dependent leaf senescence. Collectively, this study manifests TaWRKY13-A as a positive regulator of JA-related leaf senescence, which could be a new clue for molecular breeding in wheat.

Gene co-expression network analysis of the heat-responsive core transcriptome identifies hub genes in Brassica rapa

Gene co-expression network analysis of the heat-responsive core transcriptome in two contrasting Brassica rapa accessions reveals the main metabolic pathways, key modules and hub genes, are involved in long-term heat stress. Brassica rapa is a widely cultivated and economically important vegetable in Asia. High temperature is a common stress that severely impacts leaf head formation in B. rapa, resulting in reduced quality and production. The purpose of this study was thus to identify candidate heat tolerance genes by comparative transcriptome analysis of two contrasting B. rapa accessions in response to long-term heat stress. Two B. rapa accessions, '268' and '334', which showed significant differences in heat tolerance, were used for RNA sequencing analysis. We identified a total of 11,055 and 8921 differentially expressed genes (DEGs) in '268' and '334', respectively. Functional enrichment analyses of all of the identified DEGs, together with the genes identified from weighted gene co-expression network analyses (WGCNA), revealed that the autophagy pathway, glutathione metabolism, and ribosome biogenesis in eukaryotes were significantly up-regulated, whereas photosynthesis was down-regulated, in the heat resistance of B. rapa '268'. Furthermore, when B. rapa '334' was subjected to long-term high-temperature stress, heat stress caused significant changes in the expression of certain functional genes linked to protein processing in the endoplasmic reticulum and plant hormone signal transduction pathways. Autophagy-related genes might have been induced by persistent heat stress and remained high during recovery. Several hub genes like HSP17.6, HSP17.6B, HSP70-8, CLPB1, PAP1, PYR1, ADC2, and GSTF11 were discussed in this study, which may be potential candidates for further analyses of the response to long-term heat stress. These results should help elucidate the molecular mechanisms of heat stress adaptation in B. rapa.

Roles of Phytohormones and Their Signaling Pathways in Leaf Development and Stress Responses

Phytohormones participate in various processes over the course of a plant's lifecycle. In addition to the five classical phytohormones (auxins, cytokinins, gibberellins, abscisic acid, and ethylene), phytohormones such as brassinosteroids, jasmonic acid, salicylic acid, strigolactones, and peptides also play important roles in plant growth and stress responses. Given the highly interconnected nature of phytohormones during plant development and stress responses, it is challenging to study the biological function of a single phytohormone in isolation. In the current Review, we describe the combined functions and signaling cascades (especially the shared points and pathways) of various phytohormones in leaf development, in particular, during leaf primordium initiation and the establishment of leaf polarity and leaf morphology as well as leaf development under various stress conditions. We propose a model incorporating the roles of multiple phytohormones in leaf development and stress responses to illustrate the underlying combinatorial signaling pathways. This model provides a reference for breeding stress-resistant crops.

Transcriptional and Physiological Analyses to Assess the Effects of a Novel Biostimulant in Tomato

This work aimed to study the effects in tomato (Solanum lycopersicum L.) of foliar applications of a novel calcium-based biostimulant (SOB01) using an omics approach involving transcriptomics and physiological profiling. A calcium-chloride fertilizer (SOB02) was used as a product reference standard. Plants were grown under well-watered (WW) and water stress (WS) conditions in a growth chamber. We firstly compared the transcriptome profile of treated and untreated tomato plants using the software RStudio. Totally, 968 and 1,657 differentially expressed genes (DEGs) (adj-p-value < 0.1 and |log2(fold change)| ≥ 1) were identified after SOB01 and SOB02 leaf treatments, respectively. Expression patterns of 9 DEGs involved in nutrient metabolism and osmotic stress tolerance were validated by real-time quantitative reverse transcription PCR (RT-qPCR) analysis. Principal component analysis (PCA) on RT-qPCR results highlighted that the gene expression profiles after SOB01 treatment in different water regimes were clustering together, suggesting that the expression pattern of the analyzed genes in well water and water stress plants was similar in the presence of SOB01 treatment. Physiological analyses demonstrated that the biostimulant application increased the photosynthetic rate and the chlorophyll content under water deficiency compared to the standard fertilizer and led to a higher yield in terms of fruit dry matter and a reduction in the number of cracked fruits. In conclusion, transcriptome and physiological profiling provided comprehensive information on the biostimulant effects highlighting that SOB01 applications improved the ability of the tomato plants to mitigate the negative effects of water stress.

Transcriptome divergence between developmental senescence and premature senescence in Nicotiana tabacum L

Senescence is a degenerative process triggered by intricate and coordinated regulatory networks, and the mechanisms of age-dependent senescence and stress-induced premature senescence still remain largely elusive. Thus we selected leaf samples of developmental senescence (DS) and premature senescence (PS) to reveal the regulatory divergence. Senescent leaves were confirmed by yellowing symptom and physiological measurement. A total of 1171 and 309 genes (DEGs) were significantly expressed respectively in the whole process of DS and PS. Up-regulated DEGs in PS were mostly related to ion transport, while the down-regulated DEGs were mainly associated with oxidoreductase activity and sesquiterpenoid and triterpenoid biosynthesis. In DS, photosynthesis, precursor metabolites and energy, protein processing in endoplasmic reticulum, flavonoid biosynthesis were notable. Moreover, we found the vital pathways shared by DS and PS, of which the DEGs were analyzed further via protein-protein interaction (PPI) network analysis to explore the alteration responding to two types of senescence. In addition, plant hormone transduction pathway was mapped by related DEGs, suggesting that ABA and ethylene signaling played pivotal roles in formulating the distinction of DS and PS. Finally, we conducted a model containing oxidative stress and ABA signaling as two hub points, which highlighted the major difference and predicted the possible mechanism under DS and PS. This work gained new insight into molecular divergence of developmental senescence and premature senescence and would provide reference on potential mechanism initiating and motivating senescence for further study.

Identification and genetic analysis of EMS-mutagenized wheat mutants conferring lesion-mimic premature aging

BACKGROUND

Lesion-mimic and premature aging (lmpa) mutant lmpa1 was identified from the ethyl methane sulfonate (EMS) mutant library in the bread wheat variety Keda 527 (KD527) background. To reveal the genetic basis of lmpa1 mutant, phenotypic observations and analyses of chlorophyll content and photosynthesis were carried out in lmpa1, KD527 and their F1 and F2 derivatives. Further, bulked segregation analysis (BSA) in combination with a 660 K SNP array were conducted on the F2 segregation population of lmpa1/Chinese spring (CS) to locate the lmpa1 gene.

RESULTS

Most agronomic traits of lmpa1 were similar to those of KD527 before lesion-like spots appeared. Genetic analysis indicated that the F1 plants from the crossing of lmpa1 and KD527 exhibited the lmpa phenotype and the F2 progenies showed a segregation of normal (wild type, WT) and lmpa, with the ratios of lmpa: WT = 124:36(χ2 = 1.008 < =3.841), indicating that lmpa is a dominant mutation. The combination of BSA and the SNP array analysis of CS, lmpa1 and lmpa1/CS F2 WT pool (50 plants) and lmpa pool (50 plants) showed that polymorphic SNPs were enriched on chromosome 5A, within a region of 30-40 Mb, indicating that the wheat premature aging gene Lmpa1 was probably located on the short arm of chromosome 5A.

CONCLUSIONS

EMS-mutagenized mutant lmpa1 deriving from elite wheat line KD527 conferred lmpa. Lmpa phenotype of lmpa1 mutant is controlled by a single dominant allele designated as Lmpa1, which affected wheat growth and development and reduced the thousand grain weight (tgw) of single plant in wheat. The gene Lmpa1 was tentatively located within the region of 30-40 Mb near to the short arm of chromosome 5A.