Transcriptomic basis for drought-resistance in Brassica napus L

Transcriptome and metabolome analyses reveal the regulatory role of MdPYL9 in drought resistance in apple

BACKGROUND

The mechanisms by which the apple MdPYL9 gene mediates the response to drought stress remain unclear. Here, transcriptome and metabolome analyses of apple plants under drought were used to investigate the mechanisms by which MdPYL9 regulates the response to drought stress in apple. MdPYL9-overexpressed transgenic and non-transgenic apple histoculture seedlings were rooted, transplanted, and subjected to drought treatments to clarify the mechanisms underlying the responses of apples to drought stress through phenotypic observations, physiological and biochemical index measurements, and transcriptomic and metabolomic analyses.

RESULTS

Under drought stress treatment, transgenic plants were less affected by drought stress than non-transgenic plants. Decreases in the net photosynthetic rate, stomatal conductance, and transpiration rate of transgenic apple plants were less pronounced in transgenic plants than in non-transgenic plants, and increases in the intercellular CO2 concentration were less pronounced in transgenic plants than in non-transgenic plants. The relative electrical conductivity and content of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower in transgenic plants than in non-transgenic plants, and the chlorophyll content and activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) were significantly higher in transgenic plants than in non-transgenic plants. The number of differentially expressed genes (DEGs) involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and the most significant and highly annotated DEGs in the transgenic plants were involved in the flavonoid biosynthesis pathway, and the most significant and highly annotated DEGs in control plants were involved in the phytohormone signal transduction pathway. The number of differentially accumulated metabolites involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and up-regulated metabolites were significantly enriched in apigenin-7-O-glucoside in transgenic plants and in abscisic acid in non-transgenic plants. In the flavonoid biosynthetic pathway, the expression of genes encoding chalcone synthase (CHS) and chalcone isomerase (CHI) was more significantly down-regulated in non-transgenic plants than in transgenic plants, and the expression of the gene encoding 4-coumarate-CoA ligase (4CL) was more significantly up-regulated in transgenic plants than in non-transgenic plants, which resulted in the significant up-regulation of apigenin-7-O-glucoside in transgenic plants.

CONCLUSIONS

The above results indicated that the over-expression of MdPYL9 increased the drought resistance of plants under drought stress by attenuating the down-regulation of the expression of genes encoding CHS and CHI and enhancing the up-regulated expression of the gene encoding 4CL, which enhanced the content of apigenin-7-O-glucoside.

Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes

Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis-antenna proteins, nitrogen metabolism, plant-pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5'-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance.

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

KEY MESSAGE

Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F₁ hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.

Identification of Trehalose-6-Phosphate Synthase (TPS) Genes Associated with Both Source-/Sink-Related Yield Traits and Drought Response in Rapeseed (Brassica napus L.)

Trehalose-6-phosphate synthase (TPS) is an important enzyme for the synthesis of Trehalose-6-phosphate (T6P). In addition to being a signaling regulator of carbon allocation that improves crop yields, T6P also plays essential roles in desiccation tolerance. However, comprehensive studies, such as evolutionary analysis, expression analysis, and functional classification of the TPS family in rapeseed (Brassica napus L.) are lacking. Here, we identified 35 BnTPSs, 14 BoTPSs, and 17 BrTPSs in cruciferous plants, which were classified into three subfamilies. Phylogenetic and syntenic analysis of TPS genes in four cruciferous species indicated that only gene elimination occurred during their evolution. Combined phylogenetic, protein property, and expression analysis of the 35 BnTPSs suggested that changes in gene structures might have led to changes in their expression profiles and further functional differentiation during their evolution. In addition, we analyzed one set of transcriptome data from Zhongshuang11 (ZS11) and two sets of data from extreme materials associated with source-/sink-related yield traits and the drought response. The expression levels of four BnTPSs (BnTPS6, BnTPS8, BnTPS9, and BnTPS11) increased sharply after drought stress, and three differentially expressed genes (BnTPS1, BnTPS5, and BnTPS9) exhibited variable expression patterns among source and sink tissues between yield-related materials. Our findings provide a reference for fundamental studies of TPSs in rapeseed and a framework for future functional research of the roles of BnTPSs in both yield and drought resistance.

Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia

Identifying cold-related genes can provide insights into the cold adaptation mechanism of weeping forsythia. In this study, we compared the changes in gene expressions and physiological and biochemical indices under short-term cold stimulation with the changes in gene sequences under a long-term heterogeneous environment to investigate the cold adaptation mechanism in weeping forsythia. The data of adaptive gene sequence changes, e.g., single nucleotide polymorphisms, were obtained from previous landscape genomics studies. The physiological and biochemical indicators and transcriptome results showed that weeping forsythia initiated a series of programs, including increasing cell osmotic pressures, scavenging ROS, activating the defense mechanism that crosses with pathogen infection, and upregulating CBF/DREB1 transcription factor 1, to cope with short-term cold stress. A reanalysis of landscape genomic data suggested that weeping forsythia responded to long-term heterogeneous cold stress by the differentiation of genes related to synthesis of aromatic substances and adenosine triphosphate. Our results supported the hypothesis that the adaptation mechanisms of species to short-term environmental stimulation and long-term stress in heterogeneous environments are different. The differences in cold tolerance among populations are not necessarily obtained by changing cold-responsive gene sequences. This study provides new insights into the cold adaptation mechanisms of plants.

Exploring drought-responsive crucial genes in Sorghum

Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance.

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We design a method that unites gene rewiring network and Markov random field model

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Drought-responsive genes for five developmental stages of Sorghum are explored

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A multilayer network reveals that Sorghum is very sensitive to pre-flowering drought

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A drought-responsive crucial gene regulatory module is established for Sorghum

Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications

Gene co-expression network (GCN) becomes an increasingly important tool in omics data analysis. A great challenge for GCN construction is that the sample size is far lower than the number of genes. Traditional methods rely on considerable samples. Moreover, association signals are likely weak, nonlinear and stochastic, which are difficult to be identified among thousands of candidates. In this paper, the gray correlation coefficient (GCC) is introduced, and a novel method to construct gene differential co-expression networks (GDCNs) is proposed. Based on the GDCNs, three measures are proposed to explore informative genes. The proposed method can make full use of the information provided by a handful of samples and overcome the shortages of GCNs, which can evaluate the changes of co-expression relationships that are possibly triggered by treatments. Based on RNA-seq data of Brassica napus, GDCNs under multiple experimental conditions are constructed and investigated. It is found that the GCC-based method is very robust to data processing. The GDCNs facilitate the inference of gene functions and the identification of informative genes that are responsible for stress responsiveness. The GDCN-based approaches integrate the 'guilt by association' and the 'guilt by rewiring' rules, which provide alternative tools for omics data analysis.

Leptosphaeria maculans-Brassica napus Battle: A Comparison of Incompatible vs. Compatible Interactions Using Dual RNASeq

Leptosphaeria maculans causes blackleg disease, which is one of the most destructive diseases of canola (Brassica napus L.). Due to the erosion of the current resistance in B. napus, it is pivotal to introduce new resistant genotypes to the growers. This study evaluated the potential of Rlm7 gene as resistance to its corresponding avirulence AvrLm7 gene is abundant. The Rlm7 line was inoculated with L. maculans isolate with AvrLm7; UMAvr7; and the CRISPR/Cas9 knockout AvrLm7 mutant, umavr7, of the same isolate to cause incompatible and compatible interactions, respectively. Dual RNA-seq showed differential gene expressions in both interactions. High expressions of virulence-related pathogen genes-CAZymes, merops, and effector proteins after 7-dpi in compatible interactions but not in incompatible interaction—confirmed that the pathogen was actively virulent only in compatible interactions. Salicyclic and jasmonic acid biosynthesis and signaling-related genes, defense-related PR1 gene (GSBRNA2T00150001001), and GSBRNA2T00068522001 in the NLR gene family were upregulated starting as early as 1- and 3-dpi in the incompatible interaction and the high upregulation of those genes after 7-dpi in compatible interactions confirmed the early recognition of the pathogen by the host and control it by early activation of host defense mechanisms in the incompatible interaction.

Transcriptomic, Metabolomic and Ionomic Analyses Reveal Early Modulation of Leaf Mineral Content in Brassica napus under Mild or Severe Drought

While it is generally acknowledged that drought is one of the main abiotic factors affecting plant growth, how mineral nutrition is specifically and negatively affected by water deficit has received very little attention, other than being analyzed as a consequence of reduced growth. Therefore, Brassica napus plants were subjected to a gradual onset of water deficits (mild, severe, or severe extended), and leaves were analyzed at the ionomic, transcriptomic and metabolic levels. The number of Differentially Expressed Genes (DEGs) and of the most differentially accumulated metabolites increased from mild (525 DEGs, 57 metabolites) to severe (5454 DEGs, 78 metabolites) and severe extended (9346 DEGs, 95 metabolites) water deficit. Gene ontology enrichment analysis of the 11,747 DEGs identified revealed that ion transport was one of the most significant processes affected, even under mild water deficit, and this was also confirmed by the shift in ionomic composition (mostly micronutrients with a strong decrease in Mo, Fe, Zn, and Mn in leaves) that occurred well before growth reduction. The metabolomic data and most of the transcriptomic data suggested that well-known early leaf responses to drought such as phytohormone metabolism (ABA and JA), proline accumulation, and oxidative stress defense were induced later than repression of genes related to nutrient transport.

Transcriptome Analysis Reveals Roles of Anthocyanin- and Jasmonic Acid-Biosynthetic Pathways in Rapeseed in Response to High Light Stress

Rapeseed (Brassica napus) is one of the major important oil crops worldwide and is largely cultivated in the Qinghai-Tibetan plateau (QTP), where long and strong solar-radiation is well-known. However, the molecular mechanisms underlying rapeseed's response to light stress are largely unknown. In the present study, the color of rapeseed seedlings changed from green to purple under high light (HL) stress conditions. Therefore, changes in anthocyanin metabolism and the transcriptome of rapeseed seedlings cultured under normal light (NL) and HL conditions were analyzed to dissect how rapeseed responds to HL at the molecular level. Results indicated that the contents of anthocyanins, especially glucosides of cyanidin, delphinidin, and petunidin, which were determined by liquid chromatography-mass spectrometry (LC-MS), increased by 9.6-, 4.2-, and 59.7-fold in rapeseed seedlings exposed to HL conditions, respectively. Next, RNA-sequencing analysis identified 7390 differentially expressed genes (DEGs), which included 4393 up-regulated and 2997 down-regulated genes. Among the up-regulated genes, many genes related to the anthocyanin-biosynthetic pathway were enriched. For example, genes encoding dihydroflavonol reductase (BnDFR) and anthocyanin synthase (BnANS) were especially induced by HL conditions, which was also confirmed by RT-qPCR analysis. In addition, two PRODUCTION OF ANTHOCYANIN PIGMENTATION 2 (BnPAP2) and GLABRA3 (BnGL3) genes encoding MYB-type and bHLH-type transcription factors, respectively, whose expression was also up-regulated by HL stress, were found to be associated with the changes in anthocyanin biosynthesis. Many genes involved in the jasmonic acid (JA)-biosynthetic pathway were also up-regulated under HL conditions. This finding, which is in agreement with the well-known positive regulatory role of JA in anthocyanin biosynthesis, suggests that the JA may also play a key role in the responses of rapeseed seedlings to HL. Collectively, these data indicate that anthocyanin biosynthesis-related and JA biosynthesis-related pathways mediate HL responses in rapeseed. These findings collectively provide mechanistic insights into the mechanisms involved in the response of rapeseed to HL stress, and the identified key genes may potentially be used to improve HL tolerance of rapeseed cultivars through genetic engineering or breeding strategies.

Identification of WRKY transcription factors responding to abiotic stresses in Brassica napus L

A total of 278 BnWRKYs were identified and analyzed. Ectopic expression of BnWRKY149 and BnWRKY217 suggests that they function in the ABA signaling pathway. WRKY transcription factors play an important role in plant development, however, their function in Brassica napus L. abiotic stress response is still unclear. In this study, a total of 278 BnWRKY transcription factors were identified from the B. napus genome data, and they were subsequently distributed in three main groups. The protein motifs and classification of BnWRKY transcription factors were analyzed, and the locations of their corresponding encoding genes were mapped on the chromosomes of B. napus. Transcriptome analysis of rapeseed seedlings exposed to drought, salt, heat, cold and abscisic acid treatment revealed that 99 BnWRKYs responded to at least one of these stresses. The expression profiles of 12 BnWRKYs were examined with qPCR and the result coincided with RNA-seq analysis. Two genes of interest, BnWRKY149 and BnWRKY217 (homologs of AtWRKY40), were overexpressed in Arabidopsis, and the corresponding proteins were located to the nucleus. Transgene plants of BnWRKY149 and BnWRKY217 were less sensitive to ABA than Arabidopsis Col-0 plants, suggesting they might play important roles in the responses of rapeseed to abiotic stress.

Glutathione, carbohydrate and other metabolites of Larix olgensis A. Henry reponse to polyethylene glycol-simulated drought stress

Drought stress in trees limits their growth, survival, and productivity and it negatively affects the afforestation survival rate. Our study focused on the molecular responses to drought stress in a coniferous species Larix olgensis A. Henry. Drought stress was simulated in one-year-old seedlings using 25% polyethylene glycol 6000. The drought stress response in these seedlings was assessed by analyzing select biochemical parameters, along with gene expression and metabolite profiles. The soluble protein content, peroxidase activity, and malondialdehyde content of L. olgensis were significantly changed during drought stress. Quantitative gene expression analysis identified a total of 8172 differentially expressed genes in seedlings processed after 24 h, 48 h, and 96 h of drought stress treatment. Compared with the gene expression profile of the untreated control, the number of up-regulated genes was higher than that of down-regulated genes, indicating that L. olgensis mainly responded to drought stress through positive regulation. Metabolite analysis of the control and stress-treated samples showed that under drought stress, the increased abundance of linoleic acid was the highest among up-regulated metabolites, which also included some saccharides. A combined analysis of the transcriptome and metabolome revealed that genes dominating the differential expression profile were involved in glutathione metabolism, galactose metabolism, and starch and sucrose metabolism. Moreover, the relative abundance of specific metabolites of these pathways was also altered. Thus, our results indicated that L. olgensis prevented free radical-induced damage through glutathione metabolism and responded to drought through sugar accumulation.

Statistical Identification of Important Nodes in Biological Systems

Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

BACKGROUND

Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology.

RESULTS

Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation-reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations.

CONCLUSIONS

Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

Physiological and transcriptional changes provide insights into the effect of root waterlogging on the aboveground part of Pterocarya stenoptera

Pterocarya stenoptera is a tree species that occurs along rivers and has high tolerance to waterlogging. Identification of waterlogging response genes in the aboveground part of P. stenoptera will increase understanding of tolerance mechanisms under root waterlogging conditions. In this study, we employed four physiological indicators and comparative transcriptome sequencing to investigate the waterlogging tolerance mechanism in P. stenoptera. The physiological results showed that the aboveground part of P. stenoptera was not obviously affected by waterlogging. P. stenoptera enhanced waterlogging tolerance by increasing the synthesis of alpha-Linolenic acids and flavonoids and activating the jasmonic acid, ethylene, and auxin signaling pathways. Our results confirmed our hypothesis that P. stenoptera, a species that is widely distributed along rivers, has evolved a range of mechanisms in response to waterlogging. Our research will provide new insights for understanding the tolerance mechanism of species to waterlogging.

Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC)

Background

Drought is the main stress factor for the cultivation of Pterocarya stenoptera in urban areas, and this factor will cause its dehydration and affect its growth. Identifying drought-related genes will be useful for understanding the drought adaptation mechanism of P. stenoptera.

Results

We used physiological indicator detection, comparative transcriptome sequencing, and reanalysis on the results of previous landscape genomics studies to investigate the drought adaptation mechanism in P. stenoptera. The changes in malondialdehyde content showed that P. stenoptera was remarkably affected by drought stress, and the increase in soluble sugar content suggested its important role in response to drought stress. Results of comparative transcriptome sequencing showed that P. stenoptera initiated a series of programs, such as increasing the gene expression of unsaturated fatty acids, tyrosine, and plant pathogen resistance, to deal with the transient drought stress. According to the annotated results in a previous study, P. stenoptera adapts to the long-term differential drought stress by regulating the thickness of cell walls and expressing upper or lower limits of the downstream genes in the hormone signaling pathway. Through the comparative analysis of drought-responsive and -adaptive genes in P. stenoptera, this study supports the hypothesis that the environment-responsive genes (ERGs) introduced by the transient environmental stresses will be substantially more than the environment-adaptive genes (EAGs) in response to long-term differential environmental stresses, and the EAGs are not necessarily ERGs.

Conclusions

Our study identified drought-responsive and -adaptive genes in P. stenoptera and revealed that P. stenoptera increased the gene expression of unsaturated fatty acids, tyrosine, and plant pathogen resistance in response to transient drought stress. This study reveals the different adaptation mechanism of P. stenoptera under the transient and long-term differential drought stresses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07470-z.

Stress-Related Changes in the Expression and Activity of Plant Carbonic Anhydrases

The data on stress-related changes in the expression and activity of plant carbonic anhydrases (CAs) suggest that they are generally upregulated at moderate stress severity. This indicates probable involvement of CAs in adaptation to drought, high salinity, heat, high light, C_i deficit, and excess bicarbonate. The changes in CA levels under cold stress are less studied and generally represented by the downregulation of CAs excepting βCA2. Excess Cd²⁺ and deficit of Zn²⁺ specifically reduce CA activity and reduce its synthesis. Probable roles of βCAs in stress adaptation include stomatal closure, ROS scavenging and partial compensation for decreased mesophyll CO₂ conductance. βCAs play contrasting roles in pathogen responses, interacting with phytohormone signaling networks. Their role can be either negative or positive, probably depending on the host-pathogen system, pathogen initial titer, and levels of ·NO and ROS. It is still not clear why CAs are suppressed under severe stress levels. It should be noted, that the role of βCAs in the facilitation of CO₂ diffusion and their involvement in redox signaling or ROS detoxication are potentially antagonistic, as they are inactivated by oxidation or nitrosylation. Interestingly, some chloroplastic βCAs may be relocated to the cytoplasm under stress conditions, but the physiological meaning of this effect remains to be studied.

Statistical Identification of Important Nodes in Biological Systems

Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.

Physiological analysis and transcriptome sequencing reveal the effects of drier air humidity stress on Pterocarya stenoptera

Identifying physiological and transcriptomic changes can provide insights into the effects of drier air humidity stress on plants. In this study, we selected 6-month-old seedlings of Pterocarya stenoptera as study materials and used physiological index detection and transcriptome sequencing to investigate the adaptation mechanism of P. stenoptera in response to drier air humidity stress. Proline content, and superoxide dismutase and peroxidase activities did not increase significantly under drier air humidity stress. The physiological results showed that the drier air humidity stress only had slight effects on P. stenoptera. However, transcriptome sequencing showed that P. stenoptera initiated a series of metabolic pathways including L-phenylalanine catabolic process, NAD biosynthetic process, ATP biosynthetic process, and thiamine metabolism under drier air humidity stress. The enriched Kyoto Encyclopedia of Genes and Genomes results at 2 and 4 weeks under the drier air humidity stress showed that the genes THI1 and THIC in thiamine metabolism exhibited significantly differential expression. Previous studies confirmed that the two genes can improve drought tolerance. Our results implicitly indicated that exogenous thiamine might improve drought tolerance and alleviate the yellowing of the P. stenoptera leaves. Our study provides insights into the adaptation mechanism of P. stenoptera in response to drier air humidity stress and important clues into the cultivation and management of P. stenoptera in northern cities in China.

Transcriptome profiles identify the common responsive genes to drought stress in two Elymus species

Elymus, the largest genus of the Triticeae Dumort, is a forage grass in the Qinghai-Tibetan Plateau, where the climate has gradually become increasingly dry in recent years. To understand the mechanisms of the response to drought stress in Elymus species, we first investigated physiological and biochemical responses to polyethylene glycol (PEG-6000) simulated drought stress in two Elymus species, Elymus nutans and Elymus sibiricus, and found that E. nutans was more tolerant to drought stress than E. sibiricus. De novo transcriptome analysis of these two Elymus species treated with or without 10 % PEG-6000 revealed that a total of 1695 unigenes were commonly regulated by drought treatment in these two Elymus species, with 1614 unigenes up-regulated and 81 unigenes down-regulated. The coexpressed differentially expressed genes (DEGs) were enriched in regulation of transcription and gene expression in the GO database. KEGG pathway analysis indicated plant hormone signaling transduction were mostly enriched in co-expressed DEGs. Furthermore, genes annotated in the plant hormone signaling transduction were screened from co-expressed DEGs, and found that abscisic acid plays the major role in the drought stress tolerance of Elymus. Meanwhile, transcription factors screened from co-expressed DEGs were mainly classified into the ERF subfamily and WRKY, DREB, and HSF family members. Our results provide further reference for studying the response mechanism and culturing highly tolerant grasses of the Elymus species under drought stress.

Differentially evolved drought stress indices determine the genetic variation of Brassica napus at seedling traits by genome-wide association mapping

Drought seriously curtails growth, physiology and productivity in rapeseed (Brassica napus). Although drought tolerance is a complex trait, efficient phenotyping and genotyping has led to the identification of novel marker-trait associations underlying drought tolerance. A diverse panel of 228 Brassica accessions was phenotyped under normal (without stress) and water-stress conditions, simulated by polyethylene glycol (PEG-6000) (15% PEG stress) at the seedling stage; stress tolerance index (STI) and stress susceptibility index (SSI) values were acquired. Genome-wide association studies (GWAS) using 201 817 high quality SNPs identified 314 marker-trait associations strongly linked with drought indices and distributed across all nineteen chromosomes in both the A and C genomes. None of these quantitative trait loci (QTL) had been previously identified by other studies. We identified 85 genes underlying these QTL (most within 100 kb of associated SNPs) which were orthologous to Arabidopsis genes known to be associated with drought tolerance. Our study provides a novel resource for breeding drought-tolerant Brassica crops.

Biochar addition alleviate the negative effects of drought and salinity stress on soybean productivity and water use efficiency

BACKGROUND

Environmental stress is a crucial factor restricting plant growth as well as crop productivity, thus influencing the agricultural sustainability. Biochar addition is proposed as an effective management to improve crop performance. However, there were few studies focused on the effect of biochar addition on crop growth and productivity under interactive effect of abiotic stress (e.g., drought and salinity). This study was conducted with a pot experiment to investigate the interaction effects of drought and salinity stress on soybean yield, leaf gaseous exchange and water use efficiency (WUE) under biochar addition.

RESULTS

Drought and salinity stress significantly depressed soybean phenology (e.g. flowering time) and all the leaf gas exchange parameters, but had inconsistent effects on soybean root growth and WUE at leaf and yield levels. Salinity stress significantly decreased photosynthetic rate, stomatal conductance, intercellular CO2 concentration and transpiration rate by 20.7, 26.3, 10.5 and 27.2%, respectively. Lower biomass production and grain yield were probably due to the restrained photosynthesis under drought and salinity stress. Biochar addition significantly enhanced soybean grain yield by 3.1-14.8%. Drought stress and biochar addition significantly increased WUE-yield by 27.5 and 15.6%, respectively, while salinity stress significantly decreased WUE-yield by 24.2%. Drought and salinity stress showed some negative interactions on soybean productivity and leaf gaseous exchange. But biochar addition alleviate the negative effects on soybean productivity and water use efficiency under drought and salinity stress.

CONCLUSIONS

The results of the present study indicated that drought and salinity stress could significantly depress soybean growth and productivity. There exist interactive effects of drought and salinity stress on soybean productivity and water use efficiency, while we could employ biochar to alleviate the negative effects. We should consider the interactive effects of different abiotic restriction factors on crop growth thus for sustainable agriculture in the future.

Selection of reference genes for RT-qPCR normalization in blueberry (Vaccinium corymbosum × angustifolium) under various abiotic stresses

As a small fruit rich in anthocyanins, blueberry (Vaccinium corymbosum × angustifolium) has become a focus of research in recent years for identifying genes related to anthocyanin transport and stress resistance mechanisms based on transcriptome sequencing. However, the lack of validated, stably expressed reference genes greatly limits the functional study of blueberry genes. Therefore, in this study, we selected 14 candidate reference genes from a blueberry transcriptome database and used three algorithms (geNorm, NormFinder and BestKeeper) to evaluate the expression stability of these genes in various organs at different fruit developmental stages under five abiotic stress conditions. EF1α, EIF and TBP were observed to be the most stable and were thus chosen as reference genes for quantitative real-time PCR. Measurement of the relative expression of VcMATE1 (European Nucleotide Archive accession number KF875433) in blueberry further verified the reliability of these reference genes, which may have great utility for determining the accuracy of gene expression analyses in future research on blueberry.

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

BACKGROUND

Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs' response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) responding drought stress and rehydration treatment at the seedling stage.

RESULTS

A total of 5546 down-regulated and 6997 up-regulated mRNAs were detected in Q2 compared with 7824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up- regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA-mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 transcription factors (TFs) corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes. Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response.

CONCLUSIONS

The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

Transcriptome analysis of the molecular mechanism of Chrysanthemum flower color change under short-day photoperiods

Chrysanthemum [Dendranthema morifolium Tzvel.] is an ornamental plant grown under long-term artificial cultivation conditions. In production, early Chrysanthemum blossoms are often promoted by artificial short-day treatment. However, we found that the flower colour of Chrysanthemum blossoms induced by artificial short-day treatment was lighter than those induced by the natural photoperiod. To explore the intrinsic mechanism of colour fading in flowers, we performed full-length transcriptome sequencing of Chrysanthemum morifolium cv. 'Jinbeidahong' using single-molecule real-time sequencing and RNA-sequencing under natural daylight (ND) and short daylight (SD) conditions. The clustered transcriptome sequences were assigned to various databases, such as NCBI, Swiss-Prot, Gene Ontology and so on. The comparative results of digital gene expression analysis revealed that there were differentially expressed transcripts (DETs) in the four stages under ND and SD conditions. In addition, the expression patterns of anthocyanin biosynthesis structural genes were verified by quantitative real-time PCR. The major regulators of the light signalling ELONGATED HYPOCOTYL5 genes were markedly upregulated under ND conditions. The patterns of anthocyanin accumulation were consistent with the expression patterns of CHI1 and 3GT1. The results showed that the anthocyanin synthesis is tightly regulated by the photoperiod, which will be useful for molecular breeding of Chrysanthemum.

Spectral Learning Algorithm Reveals Propagation Capability of Complex Networks

In network science and the data mining field, a long-lasting and significant task is to predict the propagation capability of nodes in a complex network. Recently, an increasing number of unsupervised learning algorithms, such as the prominent PageRank (PR) and LeaderRank (LR), have been developed to address this issue. However, in degree uncorrelated networks, this paper finds that PR and LR are actually proportional to in-degree of nodes. As a result, the two algorithms fail to accurately predict the nodes' propagation capability. To overcome the arising drawback, this paper proposes a new iterative algorithm called SpectralRank (SR), in which the nodes' propagation capability is assumed to be proportional to the amount of its neighbors after adding a ground node to the network. Moreover, a weighted SR algorithm is also proposed to further involve a priori information of a node itself. A probabilistic framework is established, which is provided as the theoretical foundation of the proposed algorithms. Simulations of the susceptible-infected-removed model on 32 networks, including directed, undirected, and binary ones, reveal the advantages of the SR-family methods (i.e., weighted and unweighted SR) over PR and LR. When compared with other 11 well-known algorithms, the indices in the SR-family always outperform the others. Therefore, the proposed measures provide new insights on the prediction of the nodes' propagation capability and have great implications in the control of spreading behaviors in complex networks.

Overexpression of NtabDOG1L promotes plant growth and enhances drought tolerance in Nicotiana tabacum

Drought is one of the major environmental stresses limiting crop growth and production. It is very important to exploit and utilize drought-tolerance genes to improve crop drought-resistance. In this study, we identified two homoeologs of a Nicotiana tabacum (Ntab) DELAY OF GERMINATION (DOG) 1 like gene, named as NtabDOG1L-T and NtabDOG1L-S, respectively. The NtabDOG1L genes were preferentially expressed in roots and their expression levels were induced by polyethylene glycol, high salt, cold, and abscisic acid treatments. Subcellular localization results indicated that NtabDOG1L-T was localized in the nucleus, cytoplasm and cell membrane. Overexpression of NtabDOG1L-T in tobacco resulted in roots growth enhancement in transgenic plants. Furthermore, overexpression of NtabDOG1L-T enhanced drought stress tolerance in transgenic tobacco. The transgenic tobacco lines exhibited lower leaf water loss and electrolyte leakage, lower content of malondialdehyde and reactive oxygen species (ROS), and higher antioxidant enzymes activities after drought treatment when compared with wild type (WT) plants. In addition, the expression levels of several genes encoding key antioxidant enzymes and drought-related proteins were higher in the transgenic plants than in the WT plants under drought stress. Taken together, our results showed that NtabDOG1L functions as a novel regulator that improves plant growth and drought tolerance in tobacco.

Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus

BACKGROUND

Increasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. However, genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions.

RESULTS

High-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor allele frequency (MAF) > 0.05. We identified 17 loci that were significantly associated with seed oil content, among which 12 SNPs were distributed on the A3 (11 loci) and A1 (one loci) chromosomes, and five novel significant SNPs on the C5 (one loci) and C7 (four loci) chromosomes, respectively. Subsequently, we characterized differentially expressed genes (DEGs) between the seeds and silique pericarps on main florescences and primary branches of extremely high- and low-oil content accessions (HO and LO). A total of 64 lipid metabolism-related DEGs were identified, 14 of which are involved in triacylglycerols (TAGs) biosynthesis and assembly. Additionally, we analyzed differences in transcription levels of key genes involved in de novo fatty acid biosynthesis in the plastid, TAGs assembly and lipid droplet packaging in the endoplasmic reticulum (ER) between high- and low-oil content B. napus accessions.

CONCLUSIONS

The combination of GWAS and transcriptome analyses revealed seven candidate genes located within the confidence intervals of significant SNPs. Current findings provide valuable information for facilitating marker-based breeding for higher seed oil content in B. napus.

Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress

BACKGROUND

Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes.

RESULTS

Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame.

CONCLUSION

The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.

Transcriptome Profile Analysis of Winter Rapeseed (Brassica napus L.) in Response to Freezing Stress, Reveal Potentially Connected Events to Freezing Stress

Winter rapeseed is not only an important oilseed crop, but also a winter cover crop in Northern China, where its production was severely limited by freezing stress. As an overwinter crop, the production is severely limited by freezing stress. Therefore, understanding the physiological and molecular mechanism of winter rapeseed (Brassica napus L.) in freezing stress responses becomes essential for the improvement and development of freezing-tolerant varieties of Brassica napus. In this study, morphological, physiological, ultrastructure and transcriptome changes in the Brassica napus line "2016TS(G)10" (freezing-tolerance line) that was exposed to -2 °C for 0 h, 1 h, 3 h and 24 h were characterized. The results showed that freezing stress caused seedling dehydration, and chloroplast dilation and degradation. The content of malondialdehyde (MDA), proline, soluble protein and soluble sugars were increased, as well as the relative electrolyte leakage (REL) which was significantly increased at frozen 24 h. Subsequently, RNA-seq analysis revealed a total of 98,672 UniGenes that were annotated in Brassica napus and 3905 UniGenes were identified as differentially expressed genes after being exposed to freezing stress. Among these genes, 2312 (59.21%) were up-regulated and 1593 (40.79%) were down-regulated. Most of these DEGs were significantly annotated in the carbohydrates and energy metabolism, signal transduction, amino acid metabolism and translation. Most of the up-regulated DEGs were especially enriched in plant hormone signal transduction, starch and sucrose metabolism pathways. Transcription factor enrichment analysis showed that the AP2/ERF, WRKY and MYB families were also significantly changed. Furthermore, 20 DEGs were selected to validate the transcriptome profiles via quantitative real-time PCR (qRT-PCR). In conclusion, the results provide an overall view of the dynamic changes in physiology and insights into the molecular regulation mechanisms of winter Brassica napus in response to freezing treatment, expanding our understanding on the complex molecular mechanism in plant response to freezing stress.

Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L

BACKGROUND

Brassica napus (B. napus) encompasses diverse transcription factors (TFs), but thorough identification and characterization of TF families, as well as their transcriptional responsiveness to multifarious stresses are still not clear.

RESULTS

Totally 2167 TFs belonging to five families were genome-widely identified in B. napus, including 518 BnAP2/EREBPs, 252 BnbZIPs, 721 BnMYBs, 398 BnNACs and 278 BnWRKYs, which contained some novel members in comparison with existing results. Sub-genome distributions of BnAP2/EREBPs and BnMYBs indicated that the two families might have suffered from duplication and divergence during evolution. Synteny analysis revealed strong co-linearity between B. napus and its two ancestors, although chromosomal rearrangements have occurred and 85 TFs were lost. About 7.6% and 9.4% TFs of the five families in B. napus were novel genes and conserved genes, which both showed preference on the C sub-genome. RNA-Seq revealed that more than 80% TFs were abiotic stress inducible and 315 crucial differentially expressed genes (DEGs) were screened out. Network analysis revealed that the 315 DEGs are highly co-expressed. The homologous gene network in A. thaliana revealed that a considerable amount of TFs could trigger the differential expression of targeted genes, resulting in a complex clustered network with clusters of genes responsible for targeted stress responsiveness.

CONCLUSIONS

We identified and characterized five TF families in B. napus. Some crucial members and regulatory networks involved in different abiotic stresses have been explored. The investigations deepen our understanding of TFs for stress tolerance in B. napus.

Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation

In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.

Transcriptomic Profiling and Physiological Analysis of Haloxylon ammodendron in Response to Osmotic Stress

Haloxylon ammodendron, a perennial xero-halophyte, is an essential species for investigating the effects of drought on desert tree. To gain a comprehensive knowledge on the responses of H. ammodendron to drought stress, we specially performed the molecular and physiological analysis of H. ammodendron in response to -0.75 MPa osmotic stress for six and 24 h in lab condition via RNA-seq and digital gene expression (DGE). In total, 87,109 unigenes with a mean length of 680 bp and 13,486 potential simple sequence repeats (SSRs) were generated, and 3353 differentially expressed genes (DEGs) in shoots and 4564 in roots were identified under stress. These DEGs were mainly related to ion transporters, signal transduction, ROS-scavenging, photosynthesis, cell wall organization, membrane stabilization and hormones. Moreover, the physiological changes of inorganic ions and organic solute content, peroxidase (POD) activity and osmotic potential were in accordance with dynamic transcript profiles of the relevant genes. In this study, a detailed investigation of the pathways and candidate genes identified promote the research on the molecular mechanisms of abiotic stress tolerance in the xero-halophytic species. Our data provides valuable genetic resources for future improvement of forage and crop species for better adaptation to abiotic stresses.