Hormone Signal Transduction Pathways Research Articles

Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis).

Chinese cabbage tipburn is characterized by the formation of necrotic lesions on the margin of leaves, including on the insides of the leafy head. This physiological disorder is associated with a localized calcium deficiency during leaf development. However, little information is available regarding the molecular mechanisms governing Ca-deficiency-triggered tipburn. This study comprehensively analysed the transcriptomic comparison between control and calcium treatments (CK and 0 mM Ca) in Chinese cabbage to determine its molecular mechanism in tipburn. Our analysis identified that the most enriched gene ontology (GO) categories are photosynthesis, thylakoid and cofactor binding. Moreover, the KEGG pathway was most enriched in photosynthesis, carbon metabolism and carbon fixation. We also analyzed the co-expression network by functional categories and identified ten critical hub differentially expressed genes (DEGs) in each gene regulatory network (GRN). These DEGs might involve abiotic stresses, developmental processes, cell wall metabolism, calcium distribution, transcription factors, plant hormone biosynthesis and signal transduction pathways. Under calcium deficiency, CNX1, calmodulin-binding proteins and CMLs family proteins were downregulated compared to CK. In addition, plant hormones such as GA, JA, BR, Auxin and ABA biosynthesis pathways genes were downregulated under calcium treatment. Likewise, HATs, ARLs and TCP transcription factors were reported as inactive under calcium deficiency, and potentially involved in the developmental process. This work explores the specific DEGs' significantly different expression levels in 0 mM Ca and the control involved in plant hormones, cell wall developments, a light response such as chlorophylls and photosynthesis, transport metabolism and defence mechanism and redox. Our results provide critical evidence of the potential roles of the calcium signal transduction pathway and candidate genes governing Ca-deficiency-triggered tipburn in Chinese cabbage.

New Insights into MdSPS4-Mediated Sucrose Accumulation under Different Nitrogen Levels Revealed by Physiological and Transcriptomic Analysis.

Nitrogen nutrition participates in many physiological processes and understanding the physiological and molecular mechanisms of apple responses to nitrogen is very significant for improving apple quality. This study excavated crucial genes that regulates sugar metabolism in response to nitrogen in apples through physiology and transcriptome analysis, so as to lay a theoretical foundation for improving fruit quality. In this paper, the content of sugar and organic acid in apple fruit at different developmental periods under different nitrogen levels (0, 150, 300, and 600 kg·hm-2) were determined. Then, the transcriptomic analysis was performed in 120 days after bloom (DAB) and 150 DAB. The results showed that the fructose and glucose content were the highest at 120 DAB under 600 kg·hm-2 nitrogen level. Meanwhile, different nitrogen treatments decreased malate content in 30 and 60 DAB. RNA-seq analysis revealed a total of 4537 UniGenes were identified as differentially expressed genes (DEGs) under nitrogen treatments. Among these DEGs, 2362 (52.06%) were up-regulated and 2175 (47.94%) were down-regulated. The gene co-expression clusters revealed that most DEGs were significantly annotated in the photosynthesis, glycolysis/gluconeogenesis, pyruvate metabolism, carbon metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction pathways. The key transcription factor genes (ERF, NAC, WRKY, and C2H2 genes) were differentially expressed in apple fruit. Sugar and acid metabolism-related genes (e.g., HXK1, SPS4, SS2, PPC16-2, and MDH2 genes) exhibited significantly up-regulated expression at 120 DAB, whereas they were down-regulated at 150 DAB. Furthermore, the MdSPS4 gene overexpression positively promoted sucrose accumulation in apple callus and fruit. In conclusion, the combinational analysis of transcriptome and the functional validation of the MdSPS4 gene provides new insights into apple responses to different nitrogen levels.

Transcriptome and metabolome analyses reveal novel insights into the seed germination of Michelia chapensis, an endangered species in China

Michelia chapensis Dandy, a well-known medicinal woody plant endemic to China, is endangered and seriously constricted by seed dormancy-induced low-regeneration in natural conditions. Cold stratification can effectively reduce seed dormancy and promote the seed germination of M. chapensis. However, the molecular events and systematic changes that occurred during seed germination in M. chapensis remain largely unknown. In this study, we carried out transcriptomic and metabolomic analyses to elucidate the potential molecular mechanisms underlying seed germination in M. chapensis under cold stratification. The results showed that the embryo cells became bigger and looser with increasing stratification time. Moreover, the endosperm appeared reduced due to the consumption of nutrients. Seventeen phytohormones were examined by the metabolome targeted for hormones. Compared with the ES (no stratification), the levels of indole-3-acetic acid (IAA) and gibberellin A3 (GA3) were increased in the MS (stratification for 45 days), while the abscisic acid (ABA) was downregulated in both MS and LS (stratification for 90 days). The transcriptome profiling identified 24975 differentially expressed genes (DEGs) in the seeds during germination. The seed germination of M. chapensis was mainly regulated by the biological pathways of plant hormone signal transduction, energy supply, secondary metabolite biosynthesis, photosynthesis-related metabolism, and transcriptional regulation. This study reveals the biological evidence of seed germination at the transcriptional level and provides a foundation for unraveling molecular mechanisms regulating the seed germination of M. chapensis.

Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus.

Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called "Wild Jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack.

Physiological and transcriptome profiling revealed defense networks during Cladosporium fulvum and tomato interaction at the early stage.

Tomato leaf mold caused by Cladosporium fulvum (C. fulvum) is a serious fungal disease which results in huge yield losses in tomato cultivation worldwide. In our study, we discovered that ROS (reactive oxygen species) burst was triggered by C. fulvum treatment in tomato leaves. RNA-sequencing was used to identify differentially expressed genes (DEGs) induced by C. fulvum inoculation at the early stage of invasion in susceptible tomato plants. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to annotate functions of DEGs in tomato plants. Based on our comparative analysis, DEGs related to plant-pathogen interaction pathway, plant hormone signal transduction pathway and the plant phenylpropanoid pathway were further analyzed. Our results discovered that a number of core defense genes against fungal invasion were induced and plant hormone signal transduction pathways were impacted by C. fulvum inoculation. Further, our results showed that SA (salicylic acid) and ABA (abscisic acid) contents were accumulated while JA (jasmonic acid) content decreased after C. fulvum inoculation in comparison with control, and quantitative real-time PCR to detect the relative expression of genes involved in SA, ABA and JA signaling pathway further confirmed our results. Together, results will contribute to understanding the mechanisms of C. fulvum and tomato interaction in future.

Putative genes and pathways for Vascular Streak Dieback resistance in cocoa (Theobroma cacao L.) identified through the characterization of linked markers

Vascular Streak Dieback (VSD) caused by the fungus Ceratobasidium theobromae inflicts heavy yield losses in cocoa. Our previous study has identified and validated five ISSR and one SSR markers co-segregating with resistance and shown that they are efficient to select the resistant lines. In this work, to identify the genes and pathways involved in the resistance mechanisms, the ISSR markers for resistance, generated with UBC811, UBC826 and UBC857, were cloned and sequence characterized. The sequences had shown that the resistance loci lie in the chromosomes III and V. Eight disease resistance related proteins, TCM024428 Ankyrin repeat family protein/BTB/POZ domain-containing protein, TCM024455 Calcium-binding EF-hand family protein, TCM011959 Disease resistance protein, TCM012042 Kinase super family protein isoform 2, TCM012044 Basic helix-loop-helix DNA-binding superfamily protein, TCM014828 NBS-LRR resistance protein, TCM014842 Disease resistance family protein/LRR family, and TCM012034 NB-ARC domain-containing disease resistance protein, have been identified along with their partner defence proteins, domains and biological functions. KEGG analysis revealed tcc04075 plant hormone signal transduction pathway and tcc04626 plant-pathogen interaction pathway, having roles in the VSD resistance mechanism. • Molecular markers linked with VSD resistance in cocoa were cloned and sequenced. • Flanking regions of markers had 175 proteins including 8 resistance proteins. • Hormone signal transduction and pathogen interaction pathways were identified. • Protein partners and interaction patterns of resistance proteins were illustrated. • Domains of resistance protein and their roles in defence were predicted.

Regulation of salt tolerance in the roots of Zea mays by L-histidine through transcriptome analysis.

Soil salinization is an important worldwide environmental problem and the main reason to reduce agricultural productivity. Recent findings suggested that histidine is a crucial residue that influences the ROS reduction and improves the plants' tolerance to salt stress. Herein, we conducted experiments to understand the underlying regulatory effects of histidine on maize root system under salt stress (100 mM NaCl solution system). Several antioxidant enzymes were determined. The related expressed genes (DEGs) with its pathways were observed by Transcriptome technologies. The results of the present study confirmed that histidine can ameliorate the adverse effects of salt stress on maize root growth. When the maize roots exposed to 100 mM NaCl were treated with histidine, the accumulation of superoxide anion radicals, hydrogen peroxide, and malondialdehyde, and the content of nitrate nitrogen and ammonium nitrogen were significantly reduced; while the activities of superoxide dismutase, peroxidase, catalase, nitrate reductase, glutamine synthetase, and glutamate synthase were significantly increased. Transcriptome analysis revealed that a total of 454 (65 up-regulated and 389 down-regulated) and 348 (293 up-regulated and 55 down-regulated) DEGs were observed when the roots under salt stress were treated with histidine for 12 h and 24 h, respectively. The pathways analysis of those DEGs showed that a small number of down-regulated genes were enriched in phytohormone signaling and phenylpropanoid biosynthesis at 12 h after histidine treatment, and the DEGs involved in the phytohormone signaling, glycolysis, and nitrogen metabolism were significantly enriched at 24 h after treatment. These results of gene expression and enzyme activities suggested that histidine can improve the salt tolerance of maize roots by enriching some DEGs involved in plant hormone signal transduction, glycolysis, and nitrogen metabolism pathways.

Regeneration pattern and genome-wide transcription profile of rhizome axillary buds after perennial rice harvest.

Perennial rice is a new type of rice that allows the harvest of rice for multiple years without growing new seedlings annually. This technology represents a green and sustainable agricultural production mode with many advantages for balancing agricultural ecology and food security. However, the differences in regeneration patterns between perennial and annual rice and the gene regulatory pathways of the apical dominance in axillary bud growth after harvest in perennial rice are still unclear. In this study, perennial rice (PR23) and annual rice (Chugeng28) were used to investigate axillary bud growth patterns before and after apical spike removal. After elimination of apical dominance at different development stages, perennial rice rhizome axillary buds at the compression nodes germinated more rapidly than others and developed into new seedlings. The axillary buds at the high-position nodes in annual rice grew faster than those at other nodes. Furthermore, the global gene expression patterns of PR23 rhizome buds at compression nodes grown for 1, 3, 4, and 5 days after apical spike removal were analyzed by transcriptome sequencing. Compared with the control buds without apical removal, 264, 3,484, 2,095, and 3,398 genes were up-regulated, and 674, 3,484, 1,594, and 1,824 genes were down-regulated in the buds grown for 1, 3, 4, and 5 days after apical spike removal, respectively. Trend analysis of the expressed genes at different time points was performed and co-expression network was constructed to identify key genes in rhizome axillary bud regrowth. The results showed that 85 hub genes involved in 12 co-regulatory networks were mainly enriched in the light system, photosynthesis-antenna protein, plant hormone signal transduction, ABC transporter and metabolic pathways, which suggested that hormone and photosynthetic signals might play important roles in the regulation of rhizome axillary bud regeneration in perennial rice. Overall, this study clarified the differences in the regeneration patterns of axillary buds between perennial and annual rice and provided insight into the complex regulatory networks during the regeneration of rhizome axillary buds in perennial rice.

Genome-scale investigation and identification of variations associated with early flowering based on whole genome resequencing and transcriptome integrated analysis in tree peony

Tree peony, a traditional ornamental flower and candidate national flower of China, has thousands of varieties with different flower colors and types after a long history of natural selection and artificial breeding. However, the short and concentrated florescence period and a shortage of early- and late-flowering varieties limit the enhancement of ornamental values. Single nucleotide polymorphisms (SNPs) and insertion/deletion mutations (InDels) are important factors for mutant genotypes generation. Whole genome resequencing and transcriptome integrated analysis was conducted using early-flowering genotype Paeonia ostii ‘Fengdan’ (FD), early-flowering mutant of Paeonia ostii ‘Fengdan’ (MU), and late-flowering genotype Paeonia suffruticosa ‘Lianhe’ (LH) to identify variants related to the early-flowering phenotype. Comparison of FD vs LH, MU vs LH, and MU vs FD revealed 1,488 SNPs, 1,261 InDels, and 1,912 differential expressed genes (DEGs) specific to early-flowering genotype FD and MU, respectively. Additionally, 329 DEGs affected by SNPs and InDels variants were differentially expressed in three tree peony genotypes at the full-blooming stage. Furthermore, 37 DEGs affected by SNP variants and 44 DEGs affected by InDel variants were identified in the early-flowering genotype FD and its corresponding MU at the full-blooming stage. Most of these genes were related to phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, RNA degradation, and MAPK signaling pathway. Additionally, four SNPs were validated in FD, MU, and LH by Sanger sequencing. Expression profiles of 25 DEGs containing SNP/Indels associated with the early-flowering trait were verified by RT-qPCR. The abundant genetic variations identified in this study offer valuable genomic resources for ongoing functional and molecular breeding research for the early-flowering breeding of tree peony.

A 2-bp deletion in the protein kinase domain region of the ERECTA-like receptor kinase gene in cucumber results in short internode phenotype

Cucumber varieties with shortend internodes require less space than regular vining varieties, thus have great significance for germplasm improvement. Here, we found a novel spontaneous cucumber mutant si107 that exhibited short intenodes (si), smaller leaves, fruits, and seeds. The decrease in longitudinal cell length led to the shortened internodes of si107. The genetic analysis revealed a single recessive gene si-2 that was responsible for the mutation. Through multiple lines of evidence, we demonstrated that CsSI is the possible candidate gene for si-2, which encodes an ERECTA leucine-rich repeat receptor-like kinase. The shortened internode in si107 is attributed to a 2-bp deletion in the protein kinase domain region of this gene. The expression of CsSI was higher in the internodes, petioles, and fruit peels of si107 than in the wild type (WT). The transcriptome analysis between the si107 mutant and WT indicated that differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway, in which auxin signal genes comprised the largest group, and all were downregulated in si107. Phytohormone quantitation confirmed that endogenous auxin levels in the stems of si107 were decreased. Our results provide new insights into the molecular mechanisms underlying the internode length control in cucumber.

Low Temperature Inhibits the Defoliation Efficiency of Thidiazuron in Cotton by Regulating Plant Hormone Synthesis and the Signaling Pathway.

Thidiazuron (TDZ) is the main defoliant used in production to promote leaf abscission for machine-picked cotton. Under low temperatures, the defoliation rate of cotton treated with TDZ decreases and the time of defoliation is delayed, but there is little information about this mechanism. In this study, RNA-seq and physiological analysis are performed to reveal the transcriptome profiling and change in endogenous phytohormones upon TDZ treatment in abscission zones (AZs) under different temperatures (daily mean temperatures: 25 °C and 15 °C). Genes differentially expressed in AZs between TDZ treatment and control under different temperatures were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to compare the enriched GO terms and KEGG pathways between the two temperature conditions. The results show that, compared with the corresponding control group, TDZ induces many differentially expressed genes (DEGs) in AZs, and the results of the GO and KEGG analyses show that the plant hormone signaling transduction pathway is significantly regulated by TDZ. However, under low temperature, TDZ induced less DEGs, and the enriched GO terms and KEGG pathways were different with those under normal temperature condition. Many genes in the plant hormone signal transduction pathway could not be induced by TDZ under low temperature conditions. In particular, the upregulated ethylene-signaling genes and downregulated auxin-signaling genes in AZs treated with TDZ were significantly affected by low temperatures. Furthermore, the expression of ethylene and auxin synthesis genes and their content in AZs treated with TDZ were also regulated by low temperature conditions. The upregulated cell wall hydrolase genes induced by TDZ were inhibited by low temperatures. However, the inhibition of low temperature on genes in AZs treated with TDZ was relieved with the extension of the treatment time. Together, these results indicate that the responses of ethylene and auxin synthesis and the signaling pathway to TDZ are inhibited by low temperatures, which could not induce the expression of cell wall hydrolase genes, and then inhibit the separation of AZ cells and the abscission of cotton leaves. This result provides new insights into the mechanism of defoliation induced by TDZ under low temperature conditions.

Mining for genes related to pistil abortion in Prunus sibirica L.

In Prunus sibirica, the phenomenon of pistil abortion is very common and seriously affects its fruit quality and yield; however, the molecular mechanisms of pistil abortion remains unclear. In this study, we identified differentially expressed genes (DEGs) and pathways associated with pistil abortion using transcriptome sequencing. After comparative analysis, a total of 1,950 DEGs were identified, of which 1,000 were upregulated, and 950 were downregulated. Gene Ontology (GO) functional enrichment analysis of DEGs showed that metabolic process, cellular process, single-organism process, membrane, membrane part, cell, binding, catalytic activity, and transporter activity contained the largest number of DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the plant-pathogen interaction, starch and sucrose metabolism, and plant hormone signal transduction pathways contained the largest number of DEGs. The NAC, bHLH, and B3 transcription factor families contained the largest number of DEGs. qRT-PCR detection confirmed that the gene expression levels were consistent with the transcriptome sequencing results. This study provides a theoretical basis and scientific basis for further research on the molecular mechanisms of P. sibirica pistil abortion.

Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment

BackgroundDendrobium officinale Kimura et Migo, which contains rich polysaccharides, flavonoids and alkaloids, is a Traditional Chinese Medicine (TCM) with important economic benefits, while various pathogens have brought huge losses to its industrialization. NBS gene family is the largest class of plant disease resistance (R) genes, proteins of which are widely distributed in the upstream and downstream of the plant immune systems and are responsible for receiving infection signals and regulating gene expression respectively. It is of great significance for the subsequent disease resistance breeding of D. officinale to identify NBS genes by using the newly published high-quality chromosome-level D. officinale genome.ResultsIn this study, a total of 655 NBS genes were uncovered from the genomes of D. officinale, D. nobile, D. chrysotoxum, V. planifolia, A. shenzhenica, P. equestris and A. thaliana. The phylogenetic results of CNL-type protein sequences showed that orchid NBS-LRR genes have significantly degenerated on branches a and b. The Dendrobium NBS gene homology analysis showed that the Dendrobium NBS genes have two obvious characteristics: type changing and NB-ARC domain degeneration. Because the NBS-LRR genes have both NB-ARC and LRR domains, 22 D. officinale NBS-LRR genes were used for subsequent analyses, such as gene structures, conserved motifs, cis-elements and functional annotation analyses. All these results suggested that D. officinale NBS-LRR genes take part in the ETI system, plant hormone signal transduction pathway and Ras signaling pathway. Finally, there were 1,677 DEGs identified from the salicylic acid (SA) treatment transcriptome data of D. officinale. Among them, six NBS-LRR genes (Dof013264, Dof020566, Dof019188, Dof019191, Dof020138 and Dof020707) were significantly up-regulated. However, only Dof020138 was closely related to other pathways from the results of WGCNA, such as pathogen identification pathways, MAPK signaling pathways, plant hormone signal transduction pathways, biosynthetic pathways and energy metabolism pathways.ConclusionOur results revealed that the NBS gene degenerations are common in the genus Dendrobium, which is the main reason for the diversity of NBS genes, and the NBS-LRR genes generally take part in D. officinale ETI system and signal transduction pathways. In addition, the D. officinale NBS-LRR gene Dof020138, which may have an important breeding value, is indirectly activated by SA in the ETI system.

Enhanced Resistance to Sclerotinia sclerotiorum in Brassica rapa by Activating Host Immunity through Exogenous Verticillium dahliae Aspf2-like Protein (VDAL) Treatment.

Sclerotinia stem rot caused by Sclerotinia sclerotiorum is one of the most destructive diseases in Brassica rapa. Verticillium dahliae Aspf2-like protein (VDAL) is a secretory protein of V. dahliae which has been shown to enhance the resistance against fungal infections in several plants. Nonetheless, the molecular mechanisms of VDAL-primed disease resistance are still poorly understood. In this study, we performed physiological, biochemical, and transcriptomic analyses of Brassica rapa in order to understand how VDAL confers resistance to S. sclerotiorumn infections in plants. The results showed that foliar application of VDAL significantly reduced the plaque area on leaves inoculated with S. sclerotiorum. It also enhanced antioxidant capacity by increasing activities of superoxide dismutase (SOD), peroxidase (POD), peroxidase (APX), glutathione reductase (GR), protoporphyrinogen oxidase (PPO), and defense-related enzymes β-1,3-glucanase and chitinase during the infection periods. This occurred in parallel with significantly reduced relative conductivity at different periods and lower malondialdehyde (MDA) content as compared to sole S. sclerotiorum inoculation. Transcriptomic analysis showed a total of 146 (81 up-regulated and 65 down-regulated) differentially expressed genes (DEGs) in VDAL-treated leaves compared to the control. The most enriched three Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction, all of which were associated with plant immunity. DEGs associated with MAPK and hormone signal transduction pathways were ethylene response sensor ERS2, EIN3 (Ethylene Insensitive3)-binding F-box protein 2 (EBF2), ethylene-responsive transcription factor ERF94, MAPK 9 (MKK9), protein phosphatase 2C (PP2C37), auxin-responsive proteins (AUX/IAA1 and 19), serine/threonine-protein kinase CTR1, and abscisic acid receptors (PLY 4 and 5). Among the DEGs linked with the plant-pathogen interaction pathway were calmodulin-like proteins (CML5, 24, 27), PTI1-like tyrosine protein kinase 3 (Pti13) and transcription factor MYB30, all of which are known to play key roles in pathogen-associated molecular pattern (PAMP)-triggered immunity and effector-triggered immunity (ETI) for hypersensitive response (HR), cell wall reinforcement, and stomatal closure in plants. Overall, VDLA treatment triggered repression of the auxin and ABA signaling pathways and de-repression of the ethylene signaling pathways in young B. rapa seedlings to increase plant innate immunity. Our results showed that VDAL holds great potential to enhance fungal disease resistance in B. rapa crop.

Study on the interaction mechanism between Crocus sativus and Fusarium oxysporum based on dual RNA-seq.

The saffron phenylpropane synthesis pathway and Fusarium oxysporum cell wall-degrading enzymes play key roles in their early interactions. Saffron (Crocus sativus) is a highly important crop with diverse medicinal properties. F. oxysporum is a widely-distributed soil-borne fungus, causing the serious saffron rot disease. Currently, there is no effective management strategy to control this disease because of no resistant cultivars and limited information about the resistance and pathogenic mechanisms. In this study, we first characterized the infection process and physiological responses of saffron infected by F. oxysporum. The molecular mechanism of these infection interactions was revealed by dual RNA-seq analysis. On the 3rd day of infection, the hyphae completely entered, colonized and spread in the corm cells; while on the 6th day of infection, hyphae had appeared in the xylem cells, blocking these vessels. Transcriptome results indicate that within the host, phenylpropanoid metabolism, plant hormone signal transduction and plant pathogen interaction pathways were activated during infection. These pathways were conducive to the enhancement of cell wall, the occurrence of hypersensitivity, and the accumulation of various antibacterial proteins and phytoantitoxins. Meanwhile, in the fungus, many up-regulated genes were related to F. oxysporum cell wall degrading enzymes, toxin synthesis and pathogenicity gene, showing its strong pathogenicity. This study provides new ideas for the control of saffron corm rot, and also provides a theoretical basis for mining the key functional genes.

Spatiotemporal and Transcriptional Characterization on Tanshinone Initial Synthesis in Salvia miltiorrhiza Roots.

Tanshinones are the bioactive constituents of Danshen (Salvia miltiorrhiza Bunge), which is used in Traditional Chinese Medicine to treat cardiovascular and other diseases, and they synthesize and accumulate in the root periderm of S. miltiorrhiza. However, there is no relevant report on the initial stage of tanshinone synthesis, as well as the root structure and gene expression characteristics. The present study aims to provide new insights into how these bioactive principles begin to synthesize by characterizing possible differences in their biosynthesis and accumulation during early root development from both spatial and temporal aspects. The morphological characteristics and the content of tanshinones in roots of S. miltiorrhiza were investigated in detail by monitoring the seedlings within 65 days after germination (DAGs). The ONT transcriptome sequencing was applied to investigate gene expression patterns. The periderm of the S. miltiorrhiza storage taproot initially synthesized tanshinone on about 30 DAGs. Three critical stages of tanshinone synthesis were preliminarily determined: preparation, the initial synthesis, and the continuous rapid synthesis. The difference of taproots in the first two stages was the smallest, and the differentially expressed genes (DEGs) were mainly enriched in terpene synthesis. Most genes involved in tanshinone synthesis were up regulated during the gradual formation of the red taproot. Plant hormone signal transduction and ABC transport pathways were widely involved in S. miltiorrhiza taproot development. Five candidate genes that may participate in or regulate tanshinone synthesis were screened according to the co-expression pattern. Moreover, photosynthetic ferredoxin (FD), cytochrome P450 reductase (CPR), and CCAAT binding transcription factor (CBF) were predicted to interact with the known downstream essential enzyme genes directly. The above results provide a necessary basis for analyzing the initial synthesis and regulation mechanism of Tanshinones.

Physiological and Transcriptomic Analysis Revealed the Molecular Mechanism of Pinus koraiensis Responses to Light.

Korean pine (Pinus koraiensis Sieb. et Zucc.), as the main tree species in northeast China, has important economic and ecological values. Currently, supplementary light has been widely used in plant cultivation projects. However, the studies about different supplementary light sources on the growth and development of Korean pine are few. In this study, the one with no supplementary light was used as the control, and two kinds of light sources were set up: light-emitting diode (LED) and incandescent lamp, to supplement light treatment of Korean pine. The spectrum and intensity of these two light sources were different. The results showed that the growth and physiological-biochemical indicators were significantly different under different supplementary light treatments. The biomass of supplementary light treatment was significantly lower than the control. Compared with the control, IAA and GA were lower, and JA, ABA, ZT, and ETH were higher under supplementary light conditions. Photosynthetic parameters in supplementary light conditions were significantly lower than the control. Supplemental light induces chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid accumulation. From RNA-seq data, differentially expressed genes (DEGs) were observed in all the comparison groups, and there were 487 common DEGs. The expression levels of DEGs encoding transcription factors were also changed. According to GO and KEGG analysis, the plant hormone signal transduction, circadian rhythm-plant, and flavonoid biosynthesis pathways were the most enriched. These results provided a theoretical basis for the response of Korean pine to different supplementary lights.

Small RNA and degradome analyses reveal regulatory roles of miRNAs in vascular cambium development in Cryptomeria fortunei

The vascular cambium activity of trees directly affects the yield and quality of forest products . Therefore, studying the laws governing vascular cambium activity in Cryptomeria fortunei , a species mainly used for wood production, is important. miRNAs regulate target gene expression and play an important role in plant growth and development, but the role of miRNAs in C. fortunei vascular cambium growth remains poorly understood. Here, small RNA (sRNA) and degradome libraries were constructed for C. fortunei vascular cambium at five different growth stages. A total of 1064 miRNAs (859 known and 205 novel miRNAs), including 266 differentially expressed miRNAs (DEMs), were identified by sRNA sequencing , and 4215 targets of 843 miRNAs were identified by degradome analysis. These targets were enriched in metabolism (e.g., phenylpropanoid biosynthesis), genetic information processing and signal transduction (e.g., plant hormone signal transduction) pathways during vascular cambium development. We obtained 365 differentially expressed target pairs and constructed a regulatory network of 111 annotated negatively regulated target pairs. The blue module was identified as a key module through weighted DEM coexpression network analysis, and seven negatively regulated target pairs (pab-miR159g/aly-miR397a-5p/pab-miR397a/novel23_mature- MYB , novel12_star- UGT72B1 and smo-miR1083/pab-miR1083- GARP-ARR-B ) were considered as key regulators of C. fortunei vascular cambium growth. This study provides important miRNA and target data related to C. fortunei vascular cambium growth. These results increase the understanding of the posttranscriptional regulatory mechanisms of vascular cambium development in conifers and provide important references for the genetic improvement of wood production in plants. • In Chinese cedar vascular cambium, 859 known and 205 novel miRNAs were identified. • A degradome analysis identified 4215 targets of 843 miRNAs. • Differentially expressed miRNAs and target pairs were identified. • A negatively regulated target pair network was constructed. • A key blue module was obtained through WGCNA, and key target pairs were identified.

Infection by Endophytic Epichloë sibirica Was Associated with Activation of Defense Hormone Signal Transduction Pathways and Enhanced Pathogen Resistance in the Grass Achnatherum sibiricum.

Epichloë endophytes can improve the resistance of host grasses to pathogenic fungi, but the underlying mechanisms remain largely unknown. Here, we used phytohormone quantifications, gene expression analysis, and pathogenicity experiments to investigate the effect of Epichloë sibirica on the resistance of Achnatherum sibiricum to Curvularia lunata pathogens. Comparison of gene expression patterns between endophyte-infected and endophyte-free leaves revealed that endophyte infection was associated with significant induction of 1,758 and 765 differentially expressed genes in the host before and after pathogen inoculation, respectively. Functional analysis of the differentially expressed genes suggested that endophyte infection could activate the constitutive resistance of the host by increasing photosynthesis, enhancing the ability to scavenge reactive oxygen species, and actively regulating the expression of genes with function related to disease resistance. We found that endophyte infection was associated with induction of the expression of genes involved in the biosynthesis pathways of jasmonic acid, ethylene, and pipecolic acid and amplified the defense response of the jasmonic acid/ethylene co-regulated EIN/ERF1 transduction pathway and Pip-mediated TGA transduction pathway. Phytohormone quantifications showed that endophyte infection was associated with significant accumulation of jasmonic acid, ethylene, and pipecolic acid after pathogen inoculation. Exogenous phytohormone treatments confirmed that the disease index of plants was negatively related to both jasmonic acid and ethylene concentrations. Our results demonstrate that endophyte infection can not only improve the constitutive resistance of the host to phytopathogens before pathogen inoculation but also be associated with enhanced systemic resistance of the host to necrotrophs after C. lunata inoculation.

Regulatory network of ginsenoside biosynthesis under Ro stress in the hairy roots of Panax ginseng revealed by RNA sequencing.

P. ginseng C.A. Meyer is a valuable Chinese herbal medicine that belongs to the Araliaceae family. Major obstacles to the continuous cropping of ginseng have severely restricted the sustainable development of the ginseng industry. The allelopathic effects of triterpenoid saponins play an important role in disorders related to continuous cropping; however, the mechanisms underlying the allelopathic autotoxicity of triterpenoid ginsenosides remain unknown. In this study, we performed mRNA and miRNA sequencing analyses to identify candidate genes and miRNAs that respond differentially to ginsenoside Ro stress in ginseng and their targets. The growth of the ginseng hairy roots was significantly inhibited under Ro stress (0.5mg/L, Ro-0.5). The inhibition of root growth and injury to root-tip cells promoted the accumulation of the endogenous hormones indole-3-acetic acid and salicylic acid and inhibited the accumulation of abscisic acid and jasmonate acid. The accumulation of ginsenosides, except Rg3, was significantly inhibited under Ro-0.5 stress. An mRNA analysis of the Ro-0.5 and control groups showed that differentially expressed genes were mostly concentrated in the hormone signal transduction pathway. ARF7 and EFM were upregulated, whereas XTH23 and ZOX1 were downregulated. These genes represent important potential candidates for hormone-responsive continuous cropping diseases. In total, 74 differentially expressed miRNAs were identified based on the miRNA sequencing analysis, of which 22 were upregulated and 52 were downregulated. The target genes of ptc-miR156k_L + 1, mtr-miR156b-5p, gma-miR156a_R + 1, and mtr-miR156e all belonged to TRINITY_DN14567_c0_g4, which is a gene in the plant hormone signal transduction pathway. These four miRNAs were all negatively correlated with mRNA, indicating their likely involvement in the response of ginseng to continuous cropping disorders and the regulation of ginsenoside synthesis. Our findings provide useful insights for removing the barriers to continuous ginseng cropping and have important implications in the genetic engineering of plant stress responses.