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Project description:Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Through comparative transcriptomic analyses, we identified a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in the resistant lines compared to the susceptible lines, predominantly at 8 and 16 hpi. These DEGs were associated with multiple phytohormones, including ethylene, salicylic acid, and jasmonic acid, along with various transcription factors and signaling cascade proteins. Moreover, DE transposable elements (TEs) were predominantly up-regulated after inoculation, and we found that TEs differentially transcribed in a resistant line were enriched near genes. Notably, we identified a long non-coding RNA (lncRNA) that was significantly differentially transcribed after inoculation exclusively in the resistant lines, potentially regulating two flanking LURP-one-related genes, known as key defense mediators in Arabidopsis against oomycete pathogens. Furthermore, DNA methylation analysis revealed increased CHH (H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in the resistant line compared to the susceptible line. Overall, our results provide insights into the molecular mechanisms underlying resistance to P. sansomeana in soybean and underscore the potential role of lncRNAs and epigenetic regulation in plant defense responses.
2023-11-24 | GSE240965 | GEO
Project description:Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Through comparative transcriptomic analyses, we identified a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in the resistant lines compared to the susceptible lines, predominantly at 8 and 16 hpi. These DEGs were associated with multiple phytohormones, including ethylene, salicylic acid, and jasmonic acid, along with various transcription factors and signaling cascade proteins. Moreover, DE transposable elements (TEs) were predominantly up-regulated after inoculation, and we found that TEs differentially transcribed in a resistant line were enriched near genes. Notably, we identified a long non-coding RNA (lncRNA) that was significantly differentially transcribed after inoculation exclusively in the resistant lines, potentially regulating two flanking LURP-one-related genes, known as key defense mediators in Arabidopsis against oomycete pathogens. Furthermore, DNA methylation analysis revealed increased CHH (H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in the resistant line compared to the susceptible line. Overall, our results provide insights into the molecular mechanisms underlying resistance to P. sansomeana in soybean and underscore the potential role of lncRNAs and epigenetic regulation in plant defense responses.
2023-11-24 | GSE240964 | GEO
Project description:Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean
| PRJNA1005984 | ENA
Project description:Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean [WGBS]
| PRJNA1005991 | ENA
Project description:Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean [RNA-seq]
| PRJNA1006160 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-05-25 | GSE203546 | GEO
Project description:Isoflavone reductase (IFR) is an enzyme involved in the biosynthetic pathway of isoflavonoid phytoalexin in plants. IFRs are unique to the plant kingdom and are considered to have crucial roles in plant response to various biotic and abiotic environmental stresses. Here, we report the characterization of a novel member of the soybean isoflavone reductase gene family GmIFR. Overexpression of GmIFR transgenic soybean exhibited enhanced resistance to Phytophthora sojae. Following stress treatments, GmIFR was significantly induced by P. sojae, ethephon (ET), abscisic acid (placeCityABA), salicylic acid (SA). It is located in the cytoplasm when transiently expressed in soybean protoplasts. The daidzein levels reduced greatly for the seeds of transgenic plants, while the relative content of glyceollins in transgenic plants was significantly higher than that of non-transgenic plants. Furthermore, we found that the relative expression levels of reactive oxygen species (ROS) of transgenic soybean plants were significantly lower than those of non-transgenic plants after incubation with P. sojae, suggesting an important role of GmIFR might function as an antioxidant to reduce ROS in soybean. The enzyme activity assay suggested that GmIFR has isoflavone reductase activity.
| S-EPMC4655237 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-06-28 | GSE205994 | GEO
Project description:BackgroundPhytophthora palmivora is a devastating oomycete pathogen in durian, one of the most economically important crops in Southeast Asia. The use of fungicides in Phytophthora management may not be a long-term solution because of emerging chemical resistance issues. It is crucial to develop Phytophthora-resistant durian cultivars, and information regarding the underlying resistance mechanisms is valuable for smart breeding programs.ResultsIn this study, we conducted RNA sequencing (RNA-seq) to investigate early gene expression responses (at 8, 24, and 48 h) after the P. palmivora infection in three durian cultivars, which included one resistant cultivar (Puangmanee; PM) and two susceptible cultivars (Monthong; MT and Kradumthong; KD). We performed co-expression and differential gene expression analyses to capture gene expression patterns and identify the differentially expressed genes. The results showed that genes encoding heat shock proteins (HSPs) were upregulated in all infected durians. The expression levels of genes encoding HSPs, such as ERdj3B, were high only in infected PM. A higher level of P. palmivora resistance in PM appeared to be associated with higher expression levels of various genes encoding defense and chitin response proteins, such as lysM domain receptor-like kinases. MT had a lower resistance level than PM, although it possessed more upregulated genes during P. palmivora infection. Many photosynthetic and defense genes were upregulated in the infected MT, although their expression levels were lower than those in the infected PM. KD, the least resistant cultivar, showed downregulation of genes involved in cell wall organization or biogenesis during P. palmivora infection.ConclusionsOur results showed that the three durian cultivars exhibited significantly different gene expression patterns in response to P. palmivora infection. The upregulation of genes encoding HSPs was common in all studied durians. The high expression of genes encoding chitin response proteins likely contributed to P. palmivora resistance in durians. Durian susceptibility was associated with low basal expression of defense genes and downregulation of several cell wall-related genes. These findings enhance our understanding of durian resistance to Phytophthora infection and could be useful for the development of elite durian cultivars.
| S-EPMC11448271 | biostudies-literature
Project description:Phytophthora root and stem rot of soybean (Glycine max), caused by the oomycete Phytophthora sojae, is an extremely destructive disease worldwide. In this study, we identified GmEIL1, which encodes an ethylene-insensitive3 (EIN3) transcription factor. GmEIL1 was significantly induced following P. sojae infection of soybean plants. Compared to wild-type soybean plants, transgenic soybean plants overexpressing GmEIL1 showed enhanced resistance to P. sojae and GmEIL1-silenced RNA-interference lines showed more severe symptoms when infected with P. sojae. We screened for target genes of GmEIL1 and confirmed that GmEIL1 bound directly to the GmERF113 promoter and regulated GmERF113 expression. Moreover, GmEIL1 positively regulated the expression of the pathogenesis-related gene GmPR1. The GmEIL1-regulated defence response to P. sojae involved both ethylene biosynthesis and the ethylene signalling pathway. These findings suggest that the GmEIL1-GmERF113 module plays an important role in P. sojae resistance via the ethylene signalling pathway.
| S-EPMC11018115 | biostudies-literature