ArticleBMC genomics2014
Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed, 85 citations in OpenAlex.
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- Targeted capture and cloning of Rps6 reveal redundancy in soybean resistance genes.BMC plant biology · 2026Article
- Transcriptome Comparison between Resistant and Susceptible Soybean Cultivars in Response to Inoculation of Phytophthora sojae.The plant pathology journal · 2024Article
- Transcription-Aided Selection (TAS) for Crop Disease Resistance: Strategy and Evidence.International journal of molecular sciences · 2024Article
- Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana.The plant genome · 2024Article
- Integrated Transcriptome and Metabolome Analysis Reveals Molecular Mechanisms Underlying Resistance toPlants (Basel, Switzerland) · 2024Article
- The soybean plasma membrane GmDR1 protein conferring broad-spectrum disease and pest resistance regulates several receptor kinases and NLR proteins.Scientific reports · 2024Article
- Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change.BMC plant biology · 2024Article
- Article
- Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance against Diaporthe caulivora.Scientific reports · 2023Article
- Comparative Transcriptome Profiling Unfolds a Complex Defense and Secondary Metabolite Networks ImpartingInternational journal of molecular sciences · 2023Article
- A genome-wide analysis of the USDA Soybean Isoline Collection.The plant genome · 2023Article
- Molecular mechanisms underpinning quantitative resistance toFrontiers in plant science · 2023Article
- Article
- Progress and Challenges in Elucidating the Functional Role of Effectors in the Soybean-Journal of fungi (Basel, Switzerland) · 2022Review
- Breeding for disease resistance in soybean: a global perspective.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- Comprehensive Analysis of Cytochrome P450 Monooxygenases Reveals Insight Into Their Role in Partial Resistance AgainstFrontiers in plant science · 2022Article
- CRISPR/Cas9-mediated targeted mutagenesis of GmTCP19L increasing susceptibility to Phytophthora sojae in soybean.PloS one · 2022Article
- Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance toFrontiers in plant science · 2022Article
- Progress and prospectus in genetics and genomics ofFrontiers in genetics · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen.
resultsA total of 4,330 differentially expressed genes (DEGs) were identified in Williams versus 2,014 to 5,499 DEGs in individual NILs upon inoculation with the pathogen. Comparisons of the DEGs between the NILs and Williams identified incompatible interaction genes (IIGs) and compatible interaction genes (CIGs). Hierarchical cluster and heatmap analyses consistently grouped the NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6), suggesting an overlap in Rps-induced defense signaling among certain NILs. Gene ontology (GO) analysis revealed associations between members of the WRKY family and incompatible reactions and between a number of phytohormone signaling pathways and incompatible/compatible interactions. These associations appear to be distinguished according to the NIL clusters.
conclusionsThis study characterized genes and multiple branches of putative regulatory networks associated with resistance to P. sojae in ten soybean NILs, and depicted functional "fingerprints" of individual Rps-mediated resistance responses through comparative transcriptomic analysis. Of particular interest are dramatic variations of detected DEGs, putatively involved in ethylene (ET)-, jasmonic acid (JA)-, (reactive oxygen species) ROS-, and (MAP-kinase) MAPK- signaling, among these soybean NILs, implicating their important roles of these signaling in differentiating molecular defense responses. We hypothesize that different timing and robustness in defense signaling to the same pathogen may be largely responsible for such variations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.