Ethylene-responsive Transcription Factor Research Articles

PvERF104 confers cadmium tolerance in Arabidopsis: Evidence for metal-responsive element-binding transcription factors

Cadmium (Cd) is highly toxic to all organisms including plants, and transcription factors are essential regulators for Cd-responsive genes. In animals, metal-responsive transcription factor-1 (MTF-1) is a unique and main transcriptional activator for heavy metal detoxification through binding metal-responsive elements (MREs). However, plants have no homologs of MTF-1, and whether there are MRE-binding transcription factors in plants remain largely unknown. Previously, we identified an MRE-binding transcription factor 1 (PvMTF-1) from the bean (Phaseolus vulgaris). Unfortunately, PvMTF-1 is an orphan protein and cannot represent a conserved MRE-binding transcription factor family in plants. Here, we isolated and characterized bean ethylene response transcription factor (ERF) 104 (PvERF104) as a functional MRE-binding transcription factor. PvERF104 was isolated from the bean by yeast one-hybrid screens using the MRE as a bait. PvERF104 acted as an MRE-dependent transcriptional repressor. Expression of PvERF104 relieved Cd-induced lipid peroxidation and reduced Cd accumulation, and then moderately improved Cd tolerance in Arabidopsis. Further analyses showed that PvERF104 directly or indirectly regulated the expression of MRE-containing Cd stress-related genes, and subsequently influenced Cd tolerance. Thus, PvERF104 represents a member of ERF-type MRE-binding transcription factors. Our findings thereby provide new insights into the roles and mechanisms of MRE-binding transcription factors in plants against Cd. Data AvailabilityData will be made available on request.

Comparative proteome and transcriptome analyses of the response of postharvest pears to Penicillium expansum infection

Penicillium expansum causes blue mold disease in pears during storage and transportation, causing huge economic losses. However, researches on the defense mechanisms of pears against P. expansum are still in the early stages. Therefore, many unknown disease-resistant factors have yet to be excavated, severely limiting the breakthrough progress of pear blue mold control strategies. The current study used transcriptome and proteome approaches to evaluate pear defense mechanisms following infection with P. expansum. 96% of pear proteins were associated with the transcriptome data. Gene Ontology (GO) enrichment analysis determined that the remaining associated genes/proteins were significantly enriched in 80 GO terms. The significantly enriched GO terms included oxyacid metabolism, aldehyde-lyase activity, transition metal ion binding, terpenoid metabolic process, response to stimulus, etc. An enrichment analysis conducted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that 122 metabolic pathways were enriched, of which 11 were closely related to other metabolic pathways. In these 11 metabolic pathways, the genes/proteins (such as peroxidase, histidinol-phosphate aminotransferase (hisC), prephenate dehydratase (ADT), etc.) related to the biosynthesis of plant secondary metabolites, and the genes/proteins (such as ethylene-responsive transcription factor 1 (ERF), BR-signaling kinase (BSK), brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1), etc.) related to plant hormones were significantly enriched. Overall, this study provides a deep understanding of pear’s defense response, which could be used in future research to develop strategies to control fungal diseases.

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.

Genome-Wide Identification of AP2/ERF Transcription Factor Family and Functional Analysis of DcAP2/ERF#96 Associated with Abiotic Stress in Dendrobium catenatum.

APETALA2/Ethylene Responsive Factor (AP2/ERF) family plays important roles in reproductive development, stress responses and hormone responses in plants. However, AP2/ERF family has not been systematically studied in Dendrobium catenatum. In this study, 120 AP2/ERF family members were identified for the first time in D. catenatum, which were divided into four groups (AP2, RAV, ERF and DREB subfamily) according to phylogenetic analysis. Gene structures and conserved motif analysis showed that each DcAP2/ERF family gene contained at least one AP2 domain, and the distribution of motifs varied among subfamilies. Cis-element analysis indicated that DcAP2/ERF genes contained abundant cis-elements related to hormone signaling and stress response. To further identify potential genes involved in drought stress, 12 genes were selected to detect their expression under drought treatment through qRT-PCR analysis and DcAP2/ERF#96, a nuclear localized ethylene-responsive transcription factor, showed a strong response to PEG treatment. Overexpression of DcAP2/ERF#96 in Arabidopsis showed sensitivity to ABA. Molecular, biochemical and genetic assays indicated that DcAP2ERF#96 interacts with DREB2A and directly inhibits the expression of P5CS1 in response to the ABA signal. Taken together, our study provided a molecular basis for the intensive study of DcAP2/ERF genes and revealed the biological function of DcAP2ERF#96 involved in the ABA signal.

MusaNAC29-like transcription factor improves stress tolerance through modulation of phytohormone content and expression of stress responsive genes

Understanding the molecular mechanisms governed by genes and cross-talks among stress signaling pathways is vital for generating a broad view on stress responses in plants. Here, we analysed the effects of MusaNAC29-like transcription factor of banana on stress responses and report the quantitative modulation of phytohormone and flavonoid content and analysed the growth parameters and yield trait in transgenic banana plants. Expression of MusaNAC29-like transcription factor was strongly altered in responses to stress conditions and application of signaling molecules. Under control conditions, PMusaNAC29-like-GUS is activated in cells bordering xylem vessel elements and is strongly triggered in other cells types after influence of salicylic acid and abscisic acid. Transgenic banana plants of cultivar Rasthali and Grand Naine overexpressing MusaNAC29-like transcription factor displayed superior tolerance towards drought and salinity stress. LC-MS analysis indicated elevated levels of jasmonic acid and salicylic acid while content of zeatin was significantly reduced in leaves of transgenic banana lines. Transgenic banana lines displayed increased levels of gallic acid, coumaric acid, naringenin, chlorogenic acid while levels of vanillic acid and piperine were significantly reduced. Expression of stress related genes coding for antioxidants, thiol peptidase proteins, cold-regulated proteins, late embryogenesis abundant proteins, ethylene-responsive transcription factors, bHLH proteins, jasmonate-zim-domain proteins and WRKY transcription factors were significantly induced in transgenic banana lines. Though MusaNAC29-like transcription factor improved stress tolerance, its overexpression resulted in retarded growth of transgenic lines resulting in reduced yield of banana fruits.

Identification of QTLs and candidate genes controlling berry size in table grape by integrating QTL and transcriptomic analysis

• QTLs for berry weight were stably identified on Chrs5, 11, and 17, respectively. • QTLs for berry length were stably identified on Chrs5, 8, 15, and 17, respectively. • 6 potential candidate genes underlying the stable QTLs were highlighted. • VIT_05s0020g03980, VIT_08s0032g01110 and VIT_15s0021g02460 belonging to the IQD, YABBY, and CNR families could have a significant effect on the berry size variation in grapevine. Grape berry size is one of important external quality attributes affecting consumers’ preference, but also a component of yield, and thus one of the major concerns of grapevine breeders. However, as a complex quantitative trait under polygenic control, its genetic mechanism is still not fully understood. In the present work, berry weight, berry length and berry diameter of the grapes of 160 F1 progenies from an interspecific cross between ‘Moldova’ ( V. labruscana × V. vinifera ) and ‘Ruiduxiangyu’ ( V. vinifera ) were evaluated at the mature stage over four consecutive years. The significant QTLs and the underlying candidate genes for berry size related traits were identified by integrating with QTL mapping, RNA-seq, phylogenetic, and allelic variants analyses. 15 QTLs mainly on the Chr5, 11, and 17 linked to the trait of berry weight, 17 QTLs contributed to the trait of berry length, and 8 QTLs associated with berry diameter were detected based on high density genetic linkage maps over four years respectively. 6 prominent candidate genes including VIT_05s0020g03980 (protein IQ-DOMAIN 14-like), VIT_08s0032g01110 (putative axial regulator YABBY 2-like), VIT_15s0021g02460 (putative cell number regulator 6), VIT_17s0053g00700 (unnamed protein), VIT_17s0053g00990 (predicted expansin-A15) and VIT_11s0052g00840 (PREDICTED AP2-like ethylene-responsive transcription factor AIL5-like) were further highlighted underlying the QTLs. The results obtained in this study provide new insights into berry size variation in grapevine.

CmERF5-CmRAP2.3 transcriptional cascade positively regulates waterlogging tolerance in Chrysanthemum morifolium.

Waterlogging stress affects plant growth by limiting root respiration and reducing yield and economic value. Therefore, identifying genes involved in regulating waterlogging stress is vital. This study reports the ethylene-responsive VII transcription factor (CmRAP2.3) in the chrysanthemum. Subcellular localization and transactivation assay analyses revealed that CmRAP2.3 was localized in the nucleus and possessed transactivation activity. Overexpression of CmRAP2.3 in chrysanthemum was found to enhance waterlogging tolerance by decreasing reactive oxygen species (ROS) levels. Furthermore, we found that the transcription factor CmERF5 binds to GCC-like motifs in the CmRAP2.3 promoter region and activates CmRAP2.3 expression. Additionally, CmERF5 overexpression maintained a low ROS level and improved chrysanthemum waterlogging tolerance. Taken together, this study shows a molecular mechanism by which CmERF5 transcriptionally activates CmRAP2.3 to reduce waterlogging stress via the ROS pathway in the chrysanthemum.

A Novel Locus for Bakanae Disease Resistance, qBK4T, Identified in Rice

Bakanae disease caused by Fusarium fujikuroi causes crop failure and yield losses in the majority of rice-growing countries. In this study, we employed a joint strategy quantitative trait locus (QTL) mapping–Genome-Wide Association Study (GWAS) to investigate novel genetic loci associated with Bakanae disease resistance using a population of 143 BC1F8 RILs derived from a cross between Ilpum × Tung Tin Wan Hien1. The phenotypic data from the bioassay and the genotypic data generated using a DNA chip were utilized to perform QTL mapping and GWAS study. Our results identified a novel genetic locus qBK4T associated with Bakanae disease resistance, which was mapped on chromosome 4 and flanked by AX-116847364 (33.12 Mbp) and AX-115752415 (33.44 Mbp) markers covering a region of 324kbp. There were 34 genes in this region including Os04g55920 (encoding a zinc-finger protein, OsJAZ1), Os04g55970 (encoding AP2-like ethylene-responsive transcription factor), etc. This study proposes qBK4T as a novel locus for Bakanae disease resistance. The identification of qBK4T and its flanking marker information could be useful for marker-assisted breeding and functional characterization of resistance genes against bakanae disease.

A Comparative Analysis of Metabolome Reveals the Regulation of the Anthocyanin Biosynthesis Branch in Potatoes

A comparative metabolomic analysis was performed using purple potato tubers and derived red mutant tubers to investigate the regulation of anthocyanin biosynthesis. The metabolome analysis revealed 19 key differential metabolites including 10 flavonoids and 4 nucleotides. As a differential metabolite, pelargonidin was responsible for the mutant, and other metabolites had a correlation with it. To further analyse the regulatory mechanism of the differential metabolites, correlation analyses of metabolome and transcriptome were done. Among the differential metabolites, seven flavonoids and F3′5′H were in the flavonoid metabolic pathway. F3′5′H is responsible for the anthocyanin biosynthesis branch in potato tubers. To further analyse the regulatory mechanism of F3′5′H, the transcriptome analysis identified 63 differentially expressed genes, which highly correlated with F3'5'H. Furthermore, correlations among the key differential metabolites and the differentially expressed genes indicated that 11 differential genes and 10 differential metabolites presented 76 significant correlations. These 11 genes mainly encoded serine/threonine protein kinase, UMP-CMP kinase, MADS-box transcription factor, and WD repeat-containing protein. The 10 differential metabolites were involved in pelargonidin, luteolin, kaempferol-3-O-rutinoside, eriodictyol-7-O-glucoside, and uridine monophosphate. Through yeast one-hybrid experiments, the proteins interacting with the promoter of F3'5'H were screened: ethylene-responsive transcription factor ERF011, gibberellin-regulated protein 9-like, and serine-threonine protein kinase, transcription factor LHW bHLH. These results will provide valuable insights into the regulation mechanism of the anthocyanin biosynthesis branch in potatoes.

Teosinte confers specific alleles and yield potential to maize improvement.

Teosinte improves maize grain yield and broadens the maize germplasm. Seventy-one quantitative trait loci associated with 24 differential traits between maize and teosinte were identified. Maize is a major cereal crop with a narrow germplasm that has limited its production and breeding progress. Teosinte, an ancestor of maize, provides valuable genetic resources for maize breeding. To identify the favorable alien alleles in teosinte and its yield potential for maize breeding, 4 backcrossed maize-teosinte recombinant inbred line (RIL) populations were cultivated under five conditions. A North Carolina mating design II experiment was conducted on inbred lines with B73 and Mo17 pedigree backgrounds to analyze their combining ability. Abundant phenotypic variation on 26 traits of four RIL populations were found, of which barren tip length, kernel height, and test weight showed positive genetic improvement potential. The hybrid FM132 (BD138/MP116) showed a superior grain yield to that of the check, with an average yield gain of 4.86%. Moreover, inbred lines BD138 and MP048 showed a higher general grain yield combining ability than those of their corresponding checks. We screened 4,964,439 high-quality single-nucleotide polymorphisms in the BD (B73/Zea diploperennis) RIL population for bin construction and used 2322 bin markers for genetic map construction and quantitative trait loci (QTL) mapping. Via inclusivecomposite interval mapping, 71 QTL associated with 24 differential traits were identified. Gene annotation and transcriptional expression suggested that Zm00001eb352570 and Zm00001eb352580, both annotated as ethylene-responsive transcription factors, were key candidate genes that regulate ear height and the ratio of ear to plant height. Our results indicate that teosinte could broaden the narrow maize germplasm, improve yield potential, and provide desirable alleles for maize breeding.

Role of chlorine dioxide and chloroxyanions residue in yellowing alleviation of ready-to-eat broccoli: Insights from transcriptomic evidence

Chlorine dioxide (ClO2) unexpectedly contributed to the yellowing alleviation of ready-to-eat broccoli. Herein, we employed phenotypic and transcriptomic analyses for the first time to investigate the molecular mechanism of yellowing alleviation in the presence of ClO2. In our study, ClO2 and chloroxyanions were mainly distributed in floret bud and the content of ClO2 residue in the bud was over 50 % higher than that in stem and pedicel. Besides, the correlation analysis represented the yellowing process correlated strongly with the ClO3- residue in ready-to-eat broccoli. Further transcriptomic analyses and genes expression validation demonstrated that the endogenous ethylene biosynthesis in broccoli was noticeably inhibited by intrusive ClO2 and chloroxyanions. Ethylene biosynthesis was supposed to associate with chlorophyll degradation via the expression of ethylene-responsive transcription factor (ERF) in broccoli senescence based on transcriptomic data. This study not only carries out the novel and systematical investigation of ClO2 distribution, but also provides the deeper understanding of the quality maintenance of ready-to-eat produce.

Jasmonate signaling and remodeling of cell wall metabolism induced by boron deficiency in pea shoots

Boron (B) is an essential element for plant growth but its cellular functions are poorly defined. We conducted transcriptome analysis of shoot apices of pea ( Pisum sativum L.) growing for up to 18 days in the presence or absence of borate. Shoots of B deficient plants exhibited impaired elongation of the apex but increased growth of lateral shoots. Transcriptome analysis at days 10, 14 and 18 revealed 42, 517 and 2684 differentially expressed genes (DEGs), respectively, relating to diverse aspects of cell growth, metabolism, membrane function and cell signaling. Genes involved in jasmonate signaling and cell wall metabolism were upregulated in the B deficient plants. Many DEGs encoded transcription factors (TFs) potentially involved in these responses including many MYB and ethylene-responsive transcription factor (ERF) proteins and two orthologs of MYC2 which has been implicated in jasmonate signaling. Treatment of detached apices with B or jasmonic acid (JA) led to rapid changes in the expression of several of these DEGs. These results are consistent with a major role for borate in cell wall structure, perturbation of which can activate jasmonate signaling and cell wall remodeling. Such changes can help to explain how B deficiency leads to changes in shoot growth and architecture. • Boron deficiency leads to impaired growth of the shoot apex in pea plants. • Boron deficiency activates jasmonate signaling. • Boron deficiency causes widescale changes in expression of genes for cell wall components and metabolism.

Simulated microgravity contributed to modification of callogenesis performance and secondary metabolite production in CannabisIndica

In vitro plant culture paves the way for meeting the industrial demand of pharmaceutically valuable secondary metabolites. This study intends to monitor how callus cells of Cannabis indica respond to the simulated microgravity (clinorotation; a Man-made technology). Callus initiation resulted from the culture of the leaf explant in a medium supplemented with kinetin (0.5 mgL−1) and 2, 4-D (2 mgL−1). Calli were treated with microgravity at three exposure times (0, 3, and 5 days). The microgravity treatments increased callus biomass about 2.5-fold. The clinorotation treatments transcriptionally induced the olivetolic acid cyclase (OAC) and olivetol synthase (OLS) genes about 6.2-fold. The tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes displayed a similar upward trend in response to microgravity. The applied treatments also stimulated the expression of the ethylene-responsive element-binding proteins (ERF1B) and WRKY1 transcription factors by an average of 7.6-fold. Moreover, the simulated microgravity triggered epigenetic modification in the DNA methylation profile. The HPLC-based assessment validated the high efficacy of the clinorotation treatments to increase the concentration of cannabinoids, including Cannabigerol (CBG) and Cannabidiol (CBD). However, the clinorotated calli contained a lower concentration of Tetrahydrocannabinol (THC) than the control group. The microgravity treatments increased concentrations of proline (79%), soluble sugars (61.3%), and proteins (21.4%) in calli. The biochemical assessment revealed that the clinorotation treatments slightly increased H2O2 concentration. The upregulation in the activities of peroxidase, catalase, and phenylalanine ammonia-lyase enzymes resulted from the microgravity treatments. Both HPLC and molecular assessments validated the significant efficacy of microgravity to enhance the production of cannabinoids.

Comparative Physiological and Transcriptome Analysis Reveal the Molecular Mechanism of Melatonin in Regulating Salt Tolerance in Alfalfa (Medicago sativa L.).

As a high-quality legume forage, alfalfa is restricted by various abiotic stresses during its growth and development. Melatonin is a multifunctional signaling molecule that involves in plant defense against multiple stresses. However, little is known about its downstream signaling pathway and regulatory mechanisms in salt stress of alfalfa. In this study, we investigated the protective effects and key regulatory pathways of melatonin on alfalfa under salt tolerance. The results showed that melatonin promoted the growth of alfalfa seedlings under salt stress, as demonstrated by higher plant height, leaf area, and fresh weight. Melatonin treatment resulted in an increase in the photosynthetic capacity and starch content of alfalfa. Moreover, melatonin decreased cell membrane damage and reactive oxygen species (ROS) accumulation by enhancing antioxidant defense activity under salt stress conditions. Transcriptome sequencing (RNA-seq) analysis revealed that melatonin mainly induced the transcription of genes involved in Ca2+ signaling (cyclic nucleotide gated channel, CNGCs; cam modulin/calmodulin-like protein, CAM/CMLs and calcium-dependent protein kinase, CDPKs), starch and sucrose metabolism (α-amylase, AMYs; β-amylase, BAMs; starch synthase, SSs and sucrose synthase, SUSs), plant hormone signal transduction (auxin/indole acetic acid protein, AUX/IAAs; ABA receptor, PYL4; protein phosphatase 2C, PP2Cs; scarecrow-like protein, SCLs and ethylene-responsive transcription factor 1B, ERF1B), and key transcription factors (C3Hs, MYBs, ERFs, and WRKYs). Specifically, we focused on starch and sucrose metabolism and plant hormone signal transduction pathways. The interactions between melatonin and other phytohormones occurred via regulation of the expression of genes involved in hormone signaling pathways. In addition, melatonin increased the contents of endogenous melatonin, auxin, gibberellic acid (GA3), salicylic acid, brassinosteroids, and ethylene, while decreasing the abscisic acid content under salt stress. In summary, this study established a regulatory network for melatonin-induced key signaling pathways and functional genes under salt stress and provided a theoretical basis for salt tolerance breeding in alfalfa.

Screening for seedling stage salinity tolerance and comparative transcriptome analysis in Rice (Oryza sativa L.)

Soil salinity is one of the major abiotic stresses which affect crop productivity including rice, Oryza sativa L. Developing salt tolerant varieties gained considerable attention accordingly. Here, we studied salinity tolerance in rice crop. We screened ten rice genotypes for saline tolerance at different concentrations of 0 dSm-1, 2 dSm-1, 4 dSm-1, 6 dSm-1, 8 dSm-1,10 dSm-1, 12 dSm-1 and 14 dSm-1, respectively. Among the ten genotypes studied, CARIDhan-7 tolerated salt stress up to 6dSm-1 of irrigated water. Comparative transcriptome analysis was done with the genotypes by treating with saline water at 0dSm-1 and 6 dSm-1. A total of 1013 genes were differentially expressed under simulated stress conditions. Out of which, 551 genes were upregulated and 462 genes were downregulated. Based on the metabolic pathway analysis, the MAPK signaling pathway, along with the other 9 pathways were found to be enriched in the stressed sample. Nine ion transporter genes, 1potassium channel, 1 protein phosphatase gene, IAA homologs OsIAA9, two ROS scavenging-related genes, and 4 stress regulated genes identified were found to be significantly up-regulated along with some functional proteins previously reported under salt stress. An AP2-like ethylene-responsive transcription factor PLETHORA 2 was found to be downregulated. The results suggested that the CARIDhan-7 genotype undergoes various saline tolerant mechanisms and pathways in response to the stress imposed when compared to non-stressed seedlings.

Transcriptome changes associated with apple (Malus domestica) root defense response after Fusarium proliferatum f. sp. malus domestica infection

BackgroundApple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves in apple seedlings, leading to plant death. A comparative transcriptome analysis was conducted using the Illumina Novaseq platform to identify the molecular defense mechanisms of the susceptible M.26 and the resistant M9T337 apple rootstocks to Fpmd MR5 infection.ResultsApproximately 518.1 million high-quality reads were generated using RNA sequencing (RNA-seq). Comparative analysis between the mock-inoculated and Fpmd MR5 infected apple rootstocks revealed 28,196 significantly differentially expressed genes (DEGs), including 14,572 up-regulated and 13,624 down-regulated genes. Among them, the transcriptomes in the roots of the susceptible genotype M.26 were reflected by overrepresented DEGs. MapMan analysis indicated that a large number of DEGs were involved in the response of apple plants to Fpmd MR5 stress. The important functional groups identified via gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were responsible for fundamental biological regulation, secondary metabolism, plant-pathogen recognition, and plant hormone signal transduction (ethylene and jasmonate). Furthermore, the expression of 33 up-regulated candidate genes (12 related to WRKY DNA-binding proteins, one encoding endochitinase, two encoding beta-glucosidases, ten related to pathogenesis-related proteins, and eight encoding ethylene-responsive transcription factors) were validated by quantitative real-time PCR.ConclusionRNA-seq profiling was performed for the first time to analyze response of apple root to Fpmd MR5 infection. We found that the production of antimicrobial compounds and antioxidants enhanced plant resistance to pathogens, and pathogenesis-related protein (PR10 homologs, chitinase, and beta-glucosidase) may play unique roles in the defense response. These results provide new insights into the mechanisms of the apple root response to Fpmd MR5 infection.

Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress.

Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can withstand high salinity levels without showing signs of harm to the plant. However, the plant is more prone to salinity stress at the germination stage and a poor germination as well as poor crop stand lead to a weak productivity. It is possible to obtain a comprehensive picture of the cotton seedling germination and establishment against salt stress by examining dynamic changes in the transcriptomic and metabolomic profiles. The reported study employed a pretreatment of cotton seeds by soaking them in 0.2% Magnesium Sulphate (MgSO4) solution at room temperature for 4, 8, and 12 h. The analysis of variance based on the studied traits emergence rate, above and underground plant parts’ fresh weight measured, displayed significant differences of the three treatments compared with the control. A total of 28,801 and 264 differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were discovered to code for biological processes such as response to salt stress, cellular response to salt stress, abscisic acid receptor PYR/PYL, regulation of seed growth and germination, and auxin-activated signaling pathways. A large amount of ethylene-responsive transcription factors (ERF) was identified (1235) as differentially expressed, followed by bHLH (252), WRKY (96), MYB (202), GATA (81), RABA (64), DIVARICATA (28), and MADs-box (26) in treated seedling samples. Functional enrichment analysis revealed the significant roles in the hormones and signal transduction, carbohydrates metabolism, and biosynthesis of amino acids, promoting salt stress tolerance. Our results indicated positive effects of MgSO4 at 4 h treatment on seedling germination and growth, seemingly by activating certain growth-regulating enzymes (auxins, gibberellins, jasmonates, abscisic acid, and salicylic acid) and metabolites (phenolic acids, flavonoids, and akaloids). Such pretreatment of MgSO4 on seeds would be beneficial in future cotton management under saline conditions to enhance good crop stand and productivity.

GWAS Reveals a Novel Candidate Gene CmoAP2/ERF in Pumpkin (Cucurbita moschata) Involved in Resistance to Powdery Mildew.

Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also a good source of quality oils. However, pumpkin is susceptible to the fungus Podosphaera xanthii, an obligate biotrophic pathogen, which usually causes powdery mildew (PM) on both sides of the leaves and reduces photosynthesis. The fruits of infected plants are often smaller than usual and unpalatable. This study identified a novel gene that involves PM resistance in pumpkins through a genome-wide association study (GWAS). The allelic variation identified in the CmoCh3G009850 gene encoding for AP2-like ethylene-responsive transcription factor (CmoAP2/ERF) was proven to be involved in PM resistance. Validation of the GWAS data revealed six single nucleotide polymorphism (SNP) variations in the CmoAP2/ERF coding sequence between the resistant (IT 274039 [PMR]) and the susceptible (IT 278592 [PMS]). A polymorphic marker (dCAPS) was developed based on the allelic diversity to differentiate these two haplotypes. Genetic analysis in the segregating population derived from PMS and PMR parents provided evidence for an incomplete dominant gene-mediated PM resistance. Further, the qRT-PCR assay validated the elevated expression of CmoAP2/ERF during PM infection in the PMR compared with PMS. These results highlighted the pivotal role of CmoAP2/ERF in conferring resistance to PM and identifies it as a valuable molecular entity for breeding resistant pumpkin cultivars.

Identification and Validation of Quantitative Trait Loci for Grain Size in Bread Wheat (Triticum aestivum L.)

Grain width (GW) and grain length (GL) are crucial components affecting grain weight. Dissection of their genetic control is essential for improving yield potential in wheat breeding. Yangmai 12 (YM12) and Yanzhan 1 (YZ1) are two elite cultivars released in the Middle and Lower Yangtze Valleys Wheat Zone (MLYVWZ) and the Yellow-Huai River Valleys Wheat Zone (YRVWZ), respectively. One biparental population derived from YM12/YZ1 cross was employed to perform QTL mapping based on the data from four environments over two years to detect quantitative trait loci (QTL) for GW and GL. A total of eight QTL were identified on chromosomes 1B, 2D, 3B, 4B, 5A, and 6B. Notably, QGW.yz.2D was co-located with QGL.yz.2D, and QGW.yz.4B was co-located with QGL.yz.4B, respectively. QGW.yz.2D and QGL.yz.2D, with the increasing GW/GL allele from YZ1, explained 12.36–18.27% and 13.69–26.53% of the phenotypic variations for GW and GL, respectively. QGW.yz.4B and QGL.yz.4B, with the increasing GW/GL allele from YM12, explained 10.34–11.95% and 10.35–16.04% of the phenotypic variation for GW and GL, respectively. QGL.yz.5A, with the increasing GL allele from YM12, explained 10.04–12.48% of the phenotypic variation for GL. Moreover, the positive alleles of these three QTL regions could significantly increase thousand-grain weight, and QGW.yz.4B/QGL.yz.4B and QGL.yz.5A did not show significant negative effects on grain number per spike. QGL.yz.2D, QGW.yz.4B/QGL.yz.4B, and QGL.yz.5A have not been reported. These three QTL regions were then further validated using Kompetitive Allele-Specific PCR (KASP) markers in 159 wheat cultivars/lines from MLYVWZ and YRVWZ. Combining the positive alleles of the major QTL significantly increased GW and GL. Eleven candidate genes associated with encoding ethylene-responsive transcription factor, oleosin, osmotin protein, and thaumatin protein were identified. Three major QTL and KASP markers reported here will be helpful in developing new wheat cultivars with high and stable yields.

The coordination of melatonin and anti-bacterial activity by EIL5 underlies ethylene-induced disease resistance in cassava.

Ethylene and melatonin are widely involved in plant development and environmental stress responses. However, the role of their direct relationship in the immune response and the underlying molecular mechanisms in plants remain elusive. Here, we found that Xanthomonas axonopodis pv. manihotis (Xam) infection increased endogenous ethylene levels, which positively modulated plant disease resistance through activating melatonin accumulation in cassava. In addition, the ethylene-responsive transcription factor ETHYLENE INSENSITIVE LIKE5 (MeEIL5), a positive regulator of disease resistance, was essential for ethylene-induced melatonin accumulation and disease resistance in cassava. Notably, the identification of heat stress transcription factor 20 (MeHsf20) as an interacting protein of MeEIL5 indicated the association between ethylene and melatonin in plant disease resistance. MeEIL5 physically interacted with MeHsf20 to promote the transcriptional activation of the gene encoding N-acetylserotonin O-methyltransferase 2 (MeASMT2), thereby improving melatonin accumulation. Moreover, MeEIL5 promoted the physical interaction of MeHsf20 and pathogen-related gene 3 (MePR3), resulting in improved anti-bacterial activity of MePR3. This study illustrates the dual roles of MeEIL5 in fine-tuning MeHsf20-mediated coordination of melatonin biosynthesis and anti-bacterial activity, highlighting the ethylene-responsive MeEIL5 as the integrator of ethylene and melatonin signals in the immune response in cassava.