Identification of transcriptional regulatory nodes in soybean defense networks using transient co-transactivation assays

Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids

BACKGROUND

Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation.

RESULTS

A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene.

CONCLUSIONS

The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.

Knockdown of GmVQ58 encoding a VQ motif-containing protein enhances soybean resistance to the common cutworm (Spodoptera litura Fabricius)

Plants have evolved complex defense mechanisms to withstand insect attack. Identification of plant endogenous insect resistance genes is of great significance for understanding plant-herbivore interactions and improving crop insect resistance. Soybean (Glycine max (L.) Merr.) is an important crop that is often attacked by the common cutworm (CCW) (Spodoptera litura Fabricius). In this study, based on our transcriptomic data, the gene GmVQ58, encoding a FxxxVQxxTG (VQ) motif-containing protein, was cloned and characterized. This gene showed the highest expression in the leaves and roots and was up-regulated significantly after CCW attack. Constitutive expression of GmVQ58 rescued the susceptibility of an Arabidopsis mutant to CCW, and interference of GmVQ58 in soybean hairy roots enhanced the resistance to CCW. Furthermore, GmVQ58 was localized to the nucleus and physically interacted with the transcription factor GmWRKY32. The expression of two defense-related genes, GmN:IFR and GmVSPβ, was up-regulated in GmVQ58-RNAi lines. Additionally, the promoter region of GmVQ58 was likely selected during domestication, resulting in different expression patterns in cultivated soybeans relative to wild soybeans. These results suggest that silencing GmVQ58 confers soybean resistance to CCW.

RNA-Seq analysis reveals transcript diversity and active genes after common cutworm (Spodoptera litura Fabricius) attack in resistant and susceptible wild soybean lines

BACKGROUND

Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

RESULTS

The transcriptomes of two wild accessions (W11 and W99) with different resistance to CCW were analyzed at early- and late-induction time points. After induction, the susceptible accession W11 differentially expressed 1268 and 508 genes at the early and late time points, respectively. Compared with W11, the resistant accession W99 differentially expressed 1270 genes at the early time point and many more genes (2308) at the late time point. In total, 3836 non-redundant genes were identified in both lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) in W99 at the late time point were mostly associated with specific processes and pathways. Among the non-redundant genes, 146 genes were commonly up-regulated in the treatment condition compared with the control condition at the early- and late-induction time points in both accessions used in this experiment. Approximately 40% of the common DEGs were related to secondary metabolism, disease resistance, and signal transduction based on their putative function. Excluding the common DEGs, W99 expressed more unique DEGs than W11. Further analysis of the 3836 DEGs revealed that the induction of CCW not only up-regulated defense-related genes, including 37 jasmonic acid (JA)-related genes, 171 plant-pathogen-related genes, and 17 genes encoding protease inhibitors, but also down-regulated growth-related genes, including 35 photosynthesis-related genes, 48 nutrition metabolism genes, and 28 auxin metabolism genes. Therefore, representative defense-related and growth-related genes were chosen for binding site prediction via co-expression of transcription factors (TFs) and spatial expression pattern analyses. In total, 53 binding sites of 28 TFs were identified based on 3 defense-related genes and 3 growth-related genes. Phosphate transporter PT1, which is a representative growth-related gene, was transformed into soybean, and the transgenic soybean plants were susceptible to CCW.

CONCLUSIONS

In summary, we described transcriptome reprograming after herbivore induction in wild soybean, identified the susceptibility of growth-related genes, and provided new resources for the breeding of herbivore-resistant cultivated soybeans.

A Novel Transcription Factor CaSBP12 Gene Negatively Regulates the Defense Response against Phytophthora capsici in Pepper (Capsicum annuum L.)

SBP-box (Squamosa-promoter binding protein) genes are a type of plant-specific transcription factor and play important roles in plant growth, signal transduction and stress response. However, little is known about the SBP-box genes in pepper (CaSBP), especially in the process of Phytophthora capsici infection. In this study, a novel gene (CaSBP12) was selected from the CaSBP gene family, which was isolated from the pepper genome database in our previous study. The CaSBP12 gene was located in the nucleus of the cell and its silencing in the pepper plant enhanced the defense response against Phytophthora capsici infection. After inoculation with Phytophthora capsici, the root activity of the CaSBP12-silenced plants is compared to control plants, while malondialdehyde (MDA) content is compared viceversa. Additionally, the expression of defense related genes (CaPO1, CaSAR8.2, CaBPR1, and CaDEF1) in the silenced plants were induced to different degrees and the peak of CaSAR8.2 and CaBPR1 were higher than that of CaDEF1. The CaSBP12 over-expressed Nicotiana benthamiana plants were more susceptible to Phytophthora capsici infection with higher EC (electrical conductivity) and MDA contents as compared to the wild-type. The relative expression of defense related genes (NbDEF, NbNPR1, NbPR1a, and NbPR1b) in transgenic and wild-type Nicotiana benthamiana plants were induced, especially the NbPR1a and NbPR1b. In conclusion, these results indicate that CaSBP12 gene negative regulates the defense response against Phytophthora capsici infection which suggests their potentially significant role in plant defense. To our knowledge, this is the first report on CaSBP gene which negative regulate defense response.

Capsicum annuum HsfB2a Positively Regulates the Response to Ralstonia solanacearum Infection or High Temperature and High Humidity Forming Transcriptional Cascade with CaWRKY6 and CaWRKY40

The responses of pepper (Capsicum annuum) plants to inoculation with the pathogenic bacterium Ralstonia solanacearum and to high-temperature-high-humidity (HTHH) conditions were previously found to be coordinated by the transcription factors CaWRKY6 and CaWRKY40; however, the underlying molecular mechanism was unclear. Herein, we identified and functionally characterized CaHsfB2a, a nuclear-localized heat shock factor involved in pepper immunity to R. solanacearum inoculation (RSI) and tolerance to HTHH. CaHsfB2a is transcriptionally induced in pepper plants by RSI or HTHH and by exogenous application of salicylic acid (SA), methyl jasmonate (MeJA), ethylene (ETH), or abscisic acid (ABA). Virus-induced gene silencing (VIGS) of CaHsfB2a significantly impaired pepper immunity to RSI, hampered HTHH tolerance, and curtailed expression of immunity- and thermotolerance-associated marker genes such as CaHIR1, CaNPR1, CaABR1, and CaHSP24. Likewise, transient overexpression of CaHsfB2a in pepper leaves induced hypersensitive response (HR)-like cell death and H2O2 accumulation and upregulated the above-mentioned marker genes as well as CaWRKY6 and CaWRKY40. Chromatin immunoprecipitation (ChIP) and microscale thermophoresis (MST) analysis revealed that CaHsfB2a bound the promoters of both CaWRKY6 and CaWRKY40. In a parallel experiment, we determined by ChIP-PCR and MST that CaHsfB2a was regulated directly by CaWRKY40 but indirectly by CaWRKY6. Cumulatively, our results suggest that CaHsfB2a positively regulates plant immunity against RSI and tolerance to HTHH, via transcriptional cascades and positive feedback loops involving CaWRKY6 and CaWRKY40.

CaHDZ27, a Homeodomain-Leucine Zipper I Protein, Positively Regulates the Resistance to Ralstonia solanacearum Infection in Pepper

Homeodomain-leucine zipper class I (HD-Zip I) transcription factors have been functionally characterized in plant responses to abiotic stresses, but their roles in plant immunity are poorly understood. Here, a HD-Zip I gene, CaHZ27, was isolated from pepper (Capsicum annum) and characterized for its role in pepper immunity. Quantitative real-time polymerase chain reaction showed that CaHDZ27 was transcriptionally induced by Ralstonia solanacearum inoculation and exogenous application of methyl jasmonate, salicylic acid, or ethephon. The CaHDZ27-green fluorescent protein fused protein was targeted exclusively to the nucleus. Chromatin immunoprecipitation demonstrated that CaHDZ27 bound to the 9-bp pseudopalindromic element (CAATAATTG) and triggered β-glucuronidase expression in a CAATAATTG-dependent manner. Virus-induced gene silencing of CaHDZ27 significantly attenuated the resistance of pepper plants against R. solanacearum and downregulated defense-related marker genes, including CaHIR1, CaACO1, CaPR1, CaPR4, CaPO2, and CaBPR1. By contrast, transient overexpression of CaHDZ27 triggered strong cell death mediated by the hypersensitive response and upregulated the tested immunity-associated marker genes. Ectopic CaHDZ27 expression in tobacco enhances its resistance against R. solanacearum. These results collectively suggest that CaHDZ27 functions as a positive regulator in pepper resistance against R. solanacearum. Bimolecular fluorescence complementation and coimmunoprecipitation assays indicate that CaHDZ27 monomers bind with each other, and this binding is enhanced significantly by R. solanacearum inoculation. We speculate that homodimerization of CaHZ27 might play a role in pepper response to R. solanacearum, further direct evidence is required to confirm it.

Genetic Architecture of Charcoal Rot (Macrophomina phaseolina) Resistance in Soybean Revealed Using a Diverse Panel

Charcoal rot (CR) disease caused by Macrophomina phaseolina is responsible for significant yield losses in soybean production. Among the methods available for controlling this disease, breeding for resistance is the most promising. Progress in breeding efforts has been slow due to the insufficient information available on the genetic mechanisms related to resistance. Genome-wide association studies (GWAS) enable unraveling the genetic architecture of resistance and identification of causal genes. The aims of this study were to identify new sources of resistance to CR in a collection of 459 diverse plant introductions from the USDA Soybean Germplasm Core Collection using field and greenhouse screenings, and to conduct GWAS to identify candidate genes and associated molecular markers. New sources for CR resistance were identified from both field and greenhouse screening from maturity groups I, II, and III. Five significant single nucleotide polymorphism (SNP) and putative candidate genes related to abiotic and biotic stress responses are reported from the field screening; while greenhouse screening revealed eight loci associated with eight candidate gene families, all associated with functions controlling plant defense response. No overlap of markers or genes was observed between field and greenhouse screenings suggesting a complex molecular mechanism underlying resistance to CR in soybean with varied response to different environments; but our findings provide useful information for advancing breeding for CR resistance as well as the genetic mechanism of resistance.

Identification of Two bZIP Transcription Factors Interacting with the Promoter of Soybean Rubisco Activase Gene (GmRCAα)

Rubisco activase (RCA), a key photosynthetic protein, catalyses the activation of Rubisco and thus plays an important role in photosynthesis. Although the RCA gene has been characterized in a variety of species, the molecular mechanism regulating its transcription remains unclear. Our previous studies on RCA gene expression in soybean suggested that expression of this gene is regulated by trans-acting factors. In the present study, we verified activity of the GmRCAα promoter in both soybean and Arabidopsis and used a yeast one-hybrid (Y1H) system for screening a leaf cDNA expression library to identify transcription factors (TFs) interacting with the GmRCAα promoter. Four basic leucine zipper (bZIP) TFs, GmbZIP04g, GmbZIP07g, GmbZIP1, and GmbZIP71, were isolated, and GmbZIP04g and GmbZIP07g were confirmed as able to bind to a 21-nt G-box-containing sequence. Additionally, the expression patterns of GmbZIP04g, GmbZIp07g, and GmRCAα were analyzed in response to abiotic stresses and during a 24-h period. Our study will help to advance elucidation of the network regulating GmRCAα transcription.