scholarly journals The disease progression and molecular defense response in Chenopodium quinoa infected with Peronospora variabilis, the causal agent of quinoa downy mildew

2019 ◽  
Author(s):  
Oscar M. Rollano-Peñaloza ◽  
Valeria Palma-Encinas ◽  
Susanne Widell ◽  
Allan G. Rasmusson ◽  
Patricia Mollinedo
Keyword(s):  
Gene Expression ◽  
Disease Progression ◽  
Downy Mildew ◽  
Defense Response ◽  
Chenopodium Quinoa ◽  
Gene Markers ◽  
Environmental Threat ◽  
Jasmonic Acid Response ◽  
Andean Highlands ◽  
Downy Mildew Disease

AbstractThe downy mildew disease, caused by the biotrophic oomycete Peronospora variabilis, is the largest environmental threat to quinoa (Chenopodium quinoa Willd.) cultivation in the Andean highlands. However, so far no molecular information on the quinoa-Peronospora interaction has been reported. Here, we have developed tools to study the downy mildew disease in quinoa at gene expression level. Living P. variabilis could be isolated and maintained in the presence of a fungicide, allowing the characterization of downy mildew disease progression in two differently susceptible quinoa cultivars under controlled conditions. Quinoa gene expression changes induced by P. variabilis were analysed by qRT-PCR for quinoa homologues of Arabidopsis thaliana pathogen-associated genes. Overall, we observed a slower disease progression and higher tolerance in the quinoa cultivar Kurmi than in the cultivar Maniquena Real. We also observed that quinoa orthologs of A. thaliana genes involved in the salicylic acid defense response pathway (AtCAT2 and AtEP3) did not have changes in its gene expression. In contrast, quinoa orthologs of A. thaliana gene markers of the induction of the jasmonic acid response pathway (AtWRKY33 and AtHSP90) were significantly induced in plants infected with P. variabilis. These genes could be used as defense response markers to select quinoa cultivars that are more tolerant to P. variabilis infection.

scholarly journals The Incidence and Severity of Downy Mildew Disease on Local Madurese Maize Crops in Sumenep district, East Java, Indonesia

Agrologia ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Syaiful Khoiri ◽  
Abdiatun Abdiatun ◽  
Khairatul Muhlisa ◽  
Achmad Amzeri ◽  
Dita Megasari
Keyword(s):  
Disease Progression ◽  
Downy Mildew ◽  
Disease Severity ◽  
Sampling Method ◽  
Plant Sample ◽  
Progression Rate ◽  
Plant Pests ◽  
Local Cultivars ◽  
Disease Progression Rate ◽  
Downy Mildew Disease

In Madura island, corn is the main commodity that is widely planted with an area of 301,725 ha or about 30% of the area of maize in East Java. Madura Island has local cultivars, such as: Tambin, Talango, Guluk-guluk, Manding, and Kretek. Efforts to increase production are continuously being made, starting from improving varieties until managing plant pests. One of the main diseases in maize is downy mildew. However, information about the incidence, incidence, severity, and species that cause downy mildew in local cultivars has not been reported. So, this study aims to identify the causes of downy mildew in local cultivars of Madura and disease severity in the field. The research method is a survey on local maize centers. Sampling was done by using the diagonal sampling method. Each plant sample was observed for symptoms of disease and scoring to calculate the value of disease severity. Fungi identification was carried out by microscopic observation of the fungus. The results showed that the cause of downy mildew in Madura local maize in Sumenep Regency was P. maydis. The highest incidence, disease severity, and AUDPC value after 4 MST were found in Guluk-guluk cultivars in Padangdangan Village, but had the lowest disease progression rate values. Meanwhile, the highest rate of disease progression was found in the Manding cultivar in Mandala Village. Based on the resistance category, Talango cultivar had the best resistance when compared to other cultiva.Keywords: AUDPC, downy mildew, disease progress, Madurese maize, Peronosclerospora maydis

scholarly journals Expression Profile of New Gene Markers and Signaling Pathways Involved in Immunological Processes in Human Cumulus-Oophorus Cells

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1369
Author(s):  
Błażej Chermuła ◽  
Greg Hutchings ◽  
Wiesława Kranc ◽  
Małgorzata Józkowiak ◽  
Karol Jopek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Markers ◽  
Immune System ◽  
Defense Response ◽  
Expression Profiles ◽  
Cumulus Cells ◽  
Cytokine Signaling ◽  
Gene Markers ◽  
Local Inflammatory Response

The function of the immune system extends from defense against external pathogens to the recognition and elimination of mutated or dying cells, aiding elimination of malignant potential and/or maintaining homeostasis. The many cell types of the immune system secrete a broad range of factors to enable cellular signaling that is vital to physiological processes. Additionally, in the ovary, follicular selection and maturation, as well as ovulation, are directly regulated by the nearby immune cells. Additionally, ovulation and rupture of the follicle have been observed to resemble a local inflammatory response. Cells of the cumulus–oocyte complex (COC) show evolving gene expression profiles throughout the oocytes’ lifespan, including genes associated with immunological processes. Analysis of these genes allows the identification of useful molecular markers, as well as highlighting gene functions and interactions in these cells. Cumulus cells were obtained from hormonally stimulated patients undergoing an in vitro fertilization procedure and studied under long-term culture conditions. The microarray technique made it possible to compare the level of CCs’ gene expression on the 1st, 7th, 15th and 30th day of cultivation. Additionally, RNA microarray analysis was performed to map gene expression in these cells, associated with immunological processes and associated cytokine signaling. Subsequently, the use of DAVID software allowed us to identify the “defense response to other organism”, “defense response”, “defense response to virus”, “cytokine secretion”, “cytokine production” and “cytokine-mediated signaling pathway” GO BP terms, as well as allowing further analysis of the most differentially expressed genes associated with these processes. Of the 122 genes involved, 121 were upregulated and only one was downregulated. The seven most upregulated genes related to the abovementioned terms were ANXA3, IFIT1, HLA-DPA1, MX1, KRT8, HLA-DRA and KRT18. Therefore, genes involved in immunological defense processes are upregulated in CC cultures and could serve as useful molecular markers of growth and development in the COC, as well as the proliferation of granulosa and cumulus cells.

scholarly journals First report of Peronospora variabilis causing downy mildew disease in cañahua (Chenopodium pallidicaule) in Bolivia

2021 ◽  
Author(s):  
Oscar Miguel Rollano-Peñaloza ◽  
Valeria D. Palma-Encinas ◽  
Paola M. Nogales-Ascarrunz ◽  
Susanne Widell ◽  
Allan G. Rasmusson ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Nutritional Value ◽  
Large Scale ◽  
Artificial Infection ◽  
Potential Threat ◽  
Disease Symptoms ◽  
Sequence Identification ◽  
Visual Confirmation ◽  
Andean Highlands ◽  
Downy Mildew Disease

Abstract Cañahua (Chenopodium pallidicaule Aellen) is a semi-domesticated grain cultivated in the Andean highlands for millennia. Cañahua seeds have high nutritional value and it has become attractive because of its high resistance to frost, drought and saline soils. In May 2018, cañahua plants showed symptoms of the downy mildew disease caused by Peronospora variabilis which is known to heavily affect its tetraploid-relative quinoa. Besides the typical symptoms in the plant, visual confirmation of P. variabilis reproductive structures by microscopy was achieved. In order to verify the ability of P. variabilis to infect cañahua, an artificial infection in three cañahua varieties was performed. The three cañahua varieties were infected by P. variabilis and developed downy mildew disease symptoms. The pathogen identity was confirmed by PCR and Sanger sequencing of the PvCox2 and PvITS region. DNA sequence identification confirmed that the P. variabilis that usually infects quinoa can also infect cañahua plants. Therefore, cañahua when grown next to quinoa must be carefully watched for downy mildew disease symptoms because P. variabilis can be a potential threat for future large scale cañahua agriculture.

Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis

2021 ◽  
Author(s):  
Alicia Balbín-Suárez ◽  
Samuel Jacquiod ◽  
Annmarie-Deetja Rohr ◽  
Benye Liu ◽  
Henryk Flachowsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Defense ◽  
Defense Response ◽  
Soil Column ◽  
Soil Layer ◽  
Soil Microbiome ◽  
Control Soil ◽  
Apple Rootstocks ◽  
Apple Replant Disease ◽  
Replant Disease

Abstract A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD) causing agents to spread in soil. ‘M26’ apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of OTUs affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production, and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.

scholarly journals Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

2020 ◽  
Vol 21 (S18) ◽  
Author(s):  
Sudipta Acharya ◽  
Laizhong Cui ◽  
Yi Pan
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Selection ◽  
Marker Gene ◽  
Biological Data ◽  
Protein Interaction Data ◽  
Marker Genes ◽  
Data Sets ◽  
Gene Markers ◽  
Multi Objective

Abstract Background In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting knowledge from multiple potential biological resources may be an effective way to understand the spectrum of cancer or other diseases with applications in specific epidemiology for a particular population. Results In the current article, we design the feature selection and marker gene detection as a multi-view multi-objective clustering problem. Regarding that, we propose an Unsupervised Multi-View Multi-Objective clustering-based gene selection approach called UMVMO-select. Three important resources of biological data (gene ontology, protein interaction data, protein sequence) along with gene expression values are collectively utilized to design two different views. UMVMO-select aims to reduce gene space without/minimally compromising the sample classification efficiency and determines relevant and non-redundant gene markers from three cancer gene expression benchmark data sets. Conclusion A thorough comparative analysis has been performed with five clustering and nine existing feature selection methods with respect to several internal and external validity metrics. Obtained results reveal the supremacy of the proposed method. Reported results are also validated through a proper biological significance test and heatmap plotting.

scholarly journals GhKWL1 Upregulates GhERF105 but Its Function Is Impaired by Binding with VdISC1, a Pathogenic Effector of Verticillium dahliae

2021 ◽  
Vol 22 (14) ◽  
pp. 7328
Author(s):  
Yang Chen ◽  
Mi Zhang ◽  
Lei Wang ◽  
Xiaohan Yu ◽  
Xianbi Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgenic Plants ◽  
Gossypium Hirsutum ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Defense Response ◽  
Upland Cotton ◽  
Effector Protein ◽  
Positive Regulator ◽  
Its Gene

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease for many important crops, including cotton. Kiwellins (KWLs), a group of cysteine-rich proteins synthesized in many plants, have been shown to be involved in response to various phytopathogens. To evaluate genes for their function in resistance to Verticillium wilt, we investigated KWL homologs in cotton. Thirty-five KWL genes (GhKWLs) were identified from the genome of upland cotton (Gossypium hirsutum). Among them, GhKWL1 was shown to be localized in nucleus and cytosol, and its gene expression is induced by the infection of V. dahliae. We revealed that GhKWL1 was a positive regulator of GhERF105. Silencing of GhKWL1 resulted in a decrease, whereas overexpression led to an increase in resistance of transgenic plants to Verticillium wilt. Interestingly, through binding to GhKWL1, the pathogenic effector protein VdISC1 produced by V. dahliae could impair the defense response mediated by GhKWL1. Therefore, our study suggests there is a GhKWL1-mediated defense response in cotton, which can be hijacked by V. dahliae through the interaction of VdISC1 with GhKWL1.

scholarly journals Screening of gene markers related to the prognosis of metastatic skin cutaneous melanoma based on Logit regression and survival analysis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Guoliang Jia ◽  
Zheyu Song ◽  
Zhonghang Xu ◽  
Youmao Tao ◽  
Yuanyu Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cutaneous Melanoma ◽  
Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Training Dataset ◽  
Validation Dataset ◽  
Survival Prognosis ◽  
Gene Markers ◽  
Clinical Prognosis ◽  
Logit Regression

Abstract Background Bioinformatics was used to analyze the skin cutaneous melanoma (SKCM) gene expression profile to provide a theoretical basis for further studying the mechanism underlying metastatic SKCM and the clinical prognosis. Methods We downloaded the gene expression profiles of 358 metastatic and 102 primary (nonmetastatic) CM samples from The Cancer Genome Atlas (TCGA) database as a training dataset and the GSE65904 dataset from the National Center for Biotechnology Information database as a validation dataset. Differentially expressed genes (DEGs) were screened using the limma package of R3.4.1, and prognosis-related feature DEGs were screened using Logit regression (LR) and survival analyses. We also used the STRING online database, Cytoscape software, and Database for Annotation, Visualization and Integrated Discovery software for protein–protein interaction network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses based on the screened DEGs. Results Of the 876 DEGs selected, 11 (ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C) were screened using LR analysis. The survival prognosis of nonmetastatic group was better compared to the metastatic group between the TCGA training and validation datasets. The 11 DEGs were involved in 9 KEGG signaling pathways, and of these 11 DEGs, CALML5 was a feature DEG involved in the melanogenesis pathway, 12 targets of which were collected. Conclusion The feature DEGs screened, such as CALML5, are related to the prognosis of metastatic CM according to LR. Our results provide new ideas for exploring the molecular mechanism underlying CM metastasis and finding new diagnostic prognostic markers.

Sign in / Sign up

Export Citation Format

Share Document