Ontology highlight
ABSTRACT:
PROVIDER: PRJNA882865 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR21684764_1.fastq.gz | Fastqsanger.gz | |||
| SRR21684765_1.fastq.gz | Fastqsanger.gz |
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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:Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions. Soybean seedlings mRNA profiles inoculated with a non-pathogenic and pathogenic isolates of F. oxysporum and collected at 72 and 96 hpi, were generated using Illumina HiSeq 2500. Control seedlings were also included for each time of inoculation. Three biological replicates were considered for each condition, 18 samples in total.
2016-03-31 | E-GEOD-66861 | biostudies-arrayexpress
Project description:Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practicalapproach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 conferring broad spectra of resistance to P. sojae isolates, were identified in a landrace PI 567139B and mapped to a 6.5-cM region on chromosome 3 and a 3.0-cM region on chromosome 16, corresponding to 840 kb and 600 kb of sequences, respectively,of the soybean reference genome. By analyzing ten and nine recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines of the mapping populations, RpsUN1 and RpsUN2 were further narrowed to a 151-kb region that harbors five genes including three NBS-LRR genes, and a 36-kb region that contains four genes including five NBS-LRR genes, respectively, according to the reference genome. Analysis of expressional changes of these nine genes before and after inoculation with the pathogen suggest that the counterparts of Glyma.03g034600 in the RpsUN1 region and the counterparts of Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between different NBS-LRR genes in the mapped regions may have occurred, resulting in the formation of two recombinants with inconsistent genotypes and phenotypes detected by molecular markers within the fine-mapped regions. The haplotypes of genomic regions surrounding RpsUN1 and RpsUN2 in the entire soybean germplasm deposited in the US soybean germplasm collection were analyzed towards a better understanding of the origins of these two novel sources of resistance and screening of effective markers for marker-assisted selectionof these two resistance genes for soybean breeding.
2017-06-04 | GSE82240 | GEO
Project description:Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions.
2016-03-31 | GSE66861 | GEO
Project description:Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean
| PRJNA1005984 | ENA
Project description:Soybean is a self-pollinating crop species that has relatively low nucleotide polymorphism rates compared to other crop plant species. Despite the appearance of a low intervarietal nucleotide polymorphism rate, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some varieties. ‘Williams 82,’ the soybean variety used to produce the reference genome sequence, was derived from backcrossing a phytophthora root rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’ To explore the genetic basis of intravarietal variation, we investigated the nucleotide, structural and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. Collectively, these findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intravarietal genetic heterogeneity may be much greater than previously assumed. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are utilizing or working towards developing a reference genome sequence.
2010-12-14 | GSE25294 | GEO
Project description:Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean [WGBS]
| PRJNA1005991 | ENA
Project description:Affymetrix soybean genome arrays were used to identify genes differentially expressed in the immune resistance response at 6, 12, 24, and 48 hours after inoculation with Phakopsora pachyrhizi isolates TW72-1 or HW94-1 soybean + HW94-1 = resistant; soybean + TW72-1 = susceptible Keywords: time course
2008-01-31 | GSE8432 | GEO