scholarly journals MiR1885 Regulates Disease Tolerance Genes in Brassica rapa during Early Infection with Plasmodiophora brassicae

2021 ◽  
Vol 22 (17) ◽  
pp. 9433
Author(s):  
Parameswari Paul ◽  
Sushil Satish Chhapekar ◽  
Jana Jeevan Rameneni ◽  
Sang Heon Oh ◽  
Vignesh Dhandapani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Quantitative Trait ◽  
Plasmodiophora Brassicae ◽  
Severe Disease ◽  
Pcr Analysis ◽  
Post Inoculation ◽  
Clubroot Resistance ◽  
Trait Locus

Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreases crop quality and productivity. Several clubroot resistance-related quantitative trait loci and candidate genes have been identified. However, the underlying regulatory mechanism, the interrelationships among genes, and how genes are regulated remain unexplored. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. The main objective of this study was to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down-regulated the expression of the TIR-NBS genes Bra019412 and Bra019410, which are located at a clubroot resistance-related quantitative trait locus. The Bra-miR1885-mediated down-regulation of both genes was detected for up to 15 days post-inoculation in the clubroot-resistant line CR Shinki and in the clubroot-susceptible line 94SK. A qRT-PCR analysis revealed Bra019412 expression was negatively regulated by miR1885. Both Bra019412 and Bra019410 were more highly expressed in CR Shinki than in 94SK; the same expression pattern was detected in multiple clubroot-resistant and clubroot-susceptible inbred lines. A 5′ rapid amplification of cDNA ends analysis confirmed the cleavage of Bra019412 by Bra-miR1885b. Thus, miR1885s potentially regulate TIR-NBS gene expression during P. brassicae infections of B. rapa.

scholarly journals Expression Quantitative Trait Locus Mapping of Toxoplasma Genes Reveals Multiple Mechanisms for Strain-Specific Differences in Gene Expression

2008 ◽  
Vol 7 (8) ◽  
pp. 1403-1414 ◽  
Author(s):  
Jon P. Boyle ◽  
Jeroen P. J. Saeij ◽  
Scott Y. Harada ◽  
Jim W. Ajioka ◽  
John C. Boothroyd
Keyword(s):  
Gene Expression ◽  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Severe Disease ◽  
Expression Quantitative Trait Locus ◽  
Specific Hybridization ◽  
Hybridization Intensity ◽  
Specific Variation ◽  
Trait Locus ◽  
Locus Mapping

ABSTRACT Toxoplasma gondii is an intracellular parasite with a significant impact on human health, especially in cases where individuals are immunocompromised (e.g., due to human immunodeficiency virus/AIDS). In Europe and North America, only a few clonal genotypes appear to be responsible for the vast majority of Toxoplasma infections, and these clonotypes have been intensely studied to identify strain-specific phenotypes that may play a role in the manifestation of more-severe disease. To identify and genetically map strain-specific differences in gene expression, we have carried out expression quantitative trait locus analysis on Toxoplasma gene expression phenotypes by using spotted cDNA microarrays. This led to the identification of 16 Toxoplasma genes that had significant and mappable strain-specific variation in hybridization intensity. While the analysis should identify both cis- and trans-mapping hybridization profiles, we identified only loci with strain-specific hybridization differences that are most likely due to differences in the locus itself (i.e., cis mapping). Interestingly, a larger number of these cis-mapping genes than would be expected by chance encode either confirmed or predicted secreted proteins, many of which are known to localize to the specialized secretory organelles characteristic of members of the phylum Apicomplexa. For six of the cis-mapping loci, we determined if the strain-specific hybridization differences were due to true transcriptional differences or rather to strain-specific differences in hybridization efficiency because of extreme polymorphism and/or deletion, and we found examples of both scenarios.

scholarly journals Optimizing expression quantitative trait locus mapping workflows for single-cell studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna S. E. Cuomo ◽  
Giordano Alvari ◽  
Christina B. Azodi ◽  
Davis J. McCarthy ◽  
Marc Jan Bonder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait Locus ◽  
Single Cell ◽  
Quantitative Trait ◽  
Cell Types ◽  
Expression Quantitative Trait Locus ◽  
Eqtl Mapping ◽  
Trait Locus ◽  
The Impact

Abstract Background Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for sample multiplexing improving, population-scale scRNA-seq, and thus single-cell expression quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping of sc-eQTL provides additional resolution to study the regulatory role of common genetic variants on gene expression across a plethora of cell types and states and promises to improve our understanding of genetic regulation across tissues in both health and disease. Results While previously established methods for bulk eQTL mapping can, in principle, be applied to sc-eQTL mapping, there are a number of open questions about how best to process scRNA-seq data and adapt bulk methods to optimize sc-eQTL mapping. Here, we evaluate the role of different normalization and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines. We use both real and simulated datasets across single-cell technologies to systematically assess the impact of these different statistical approaches. Conclusion We provide recommendations for future single-cell eQTL studies that can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

scholarly journals A compendium of uniformly processed human gene expression and splicing quantitative trait loci

2021 ◽  
Vol 53 (9) ◽  
pp. 1290-1299
Author(s):  
Nurlan Kerimov ◽  
James D. Hayhurst ◽  
Kateryna Peikova ◽  
Jonathan R. Manning ◽  
Peter Walter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Cell Types ◽  
Summary Statistics ◽  
Genome Wide ◽  
Cell Type Specific ◽  
Trait Locus ◽  
Complex Human Traits

AbstractMany gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues.

scholarly journals Transcriptome patterns and blood physiology associated with homing success of sockeye salmon during their final stage of marine migration

2018 ◽  
Vol 75 (9) ◽  
pp. 1511-1524 ◽  
Author(s):  
S. Matthew Drenner ◽  
Scott G. Hinch ◽  
Nathan B. Furey ◽  
Timothy D. Clark ◽  
Shaorong Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Sockeye Salmon ◽  
Protein Biosynthesis ◽  
Infected Fish ◽  
Pcr Analysis ◽  
Biological Processes ◽  
Marine Migration ◽  
Polymerase Chain ◽  
Marine Survival

To better understand the mechanisms that lead to marine mortality of homing adult sockeye salmon (Oncorhynchus nerka), gill and blood biopsies were used in combination with biotelemetry to demonstrate how survival to freshwater entry is related to gene expression and physiological indices of stress. Microarray analysis of gene expression indicated multiple biological processes, including immune and stress responses, protein biosynthesis, and metabolism. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) analysis indicated fish with upregulation of genes related to stress and infection had higher marine survival compared with fish without this genomic signature. We proposed that higher marine survival of potentially stressed and immune compromised fish can be explained by stressed and infected fish being highly motivated to enter fresh water, leading to enhanced marine survival. However, once in a river, stressed and immune compromised fish could suffer higher mortality because of premature river entry. Overall, this study supports the idea that infection and stress are important biological processes influencing behaviour and fate of sockeye salmon during homing migrations.

scholarly journals Effect of Host Resistance and Fungicide Application on Clubroot Pathotype 6 in Green Cabbage and Napa Cabbage

2012 ◽  
Vol 22 (3) ◽  
pp. 311-319 ◽  
Author(s):  
Catarina Saude ◽  
Alan McKeown ◽  
Bruce D. Gossen ◽  
Mary Ruth McDonald
Keyword(s):  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Host Resistance ◽  
Plasmodiophora Brassicae ◽  
Field Trials ◽  
Organic Soils ◽  
Southern Ontario ◽  
Clubroot Resistance ◽  
Mineral Soils ◽  
Standard Cultivar

Field trials were conducted to evaluate resistance to clubroot (Plasmodiophora brassicae, pathotype 6) in green cabbage (Brassica oleracea var. capitata) and napa cabbage (Brassica rapa ssp. pekinensis) at sites in southern Ontario in 2009 and 2010. The reaction of green cabbage cultivars Kilaton, Tekila, Kilaxy, and Kilaherb and the commercial standard cultivars, Bronco or Atlantis, were evaluated on organic (two site-years) and mineral soils (two site-years) that were naturally infested with the clubroot pathogen. In addition, fluazinam fungicide was drench applied to one treatment of the commercial standard cultivar immediately after transplanting. The napa cabbage cultivars Yuki, Deneko, Bilko, and Mirako (in 2009) and Emiko, Mirako, Yuki, and China Gold (in 2010) were evaluated only on organic soils (two site-years). At harvest, the roots of each plant were assessed for clubroot incidence and severity. Also, plant and head characteristics of the resistant green cabbage cultivars were evaluated at one site in 2010. The green cabbage cultivars Kilaton, Tekila, Kilaxy, and Kilaherb were resistant to pathotype 6 (0% to 3.8% incidence), but ‘Bronco’ was susceptible (64% to 100% incidence). Application of fluazinam reduced clubroot severity on ‘Bronco’ by 6% at one of three sites. Resistance was more effective in reducing clubroot than application of fluazinam. Plant and head characteristics of the resistant cultivars were similar to those of ‘Bronco’ treated with fluazinam. Napa cabbage cultivars Yuki, Deneko, Bilko, Emiko, and China Gold were resistant to clubroot (0% to 13% incidence), and ‘Mirako’ was highly susceptible (87% to 92% incidence). We conclude that the clubroot resistance available in several cultivars of green and napa cabbage was effective against P. brassicae pathotype 6.

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