scholarly journals Leveraging RNA-Seq to Characterize Resistance to Brown Stem Rot and the Rbs3 Locus in Soybean

2018 ◽  
Vol 31 (10) ◽  
pp. 1083-1094 ◽  
Author(s):  
Chantal E. McCabe ◽  
Silvia R. Cianzio ◽  
Jamie A. O’Rourke ◽  
Michelle A. Graham
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Iron Homeostasis ◽  
Complex Disease ◽  
Stem Rot ◽  
Infected Leaf ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Brown Stem Rot ◽  
Phialophora Gregata

Brown stem rot, caused by the fungus Phialophora gregata, reduces soybean yield by up to 38%. Although three dominant resistance loci have been identified (Rbs1 to Rbs3), the gene networks responsible for pathogen recognition and defense remain unknown. Further, identification and characterization of resistant and susceptible germplasm remains difficult. We conducted RNA-Seq of infected and mock-infected leaf, stem, and root tissues of a resistant (PI 437970, Rbs3) and susceptible (Corsoy 79) genotype. Combining historical mapping data with genotype expression differences allowed us to identify a cluster of receptor-like proteins that are candidates for the Rbs3 resistance gene. Reads mapping to the Rbs3 locus were used to identify potential novel single-nucleotide polymorphisms within candidate genes that could improve phenotyping and breeding efficiency. Comparing responses to infection revealed little overlap in differential gene expression between genotypes or tissues. Gene networks associated with defense, DNA replication, and iron homeostasis are hallmarks of resistance to P. gregata. This novel research demonstrates the utility of combining contrasting genotypes, gene expression, and classical genetic studies to characterize complex disease resistance loci.

scholarly journals Brown Stem Rot Resistance in Soybean Germ Plasm from Central China

Plant Disease ◽  
1997 ◽  
Vol 81 (8) ◽  
pp. 953-956 ◽  
Author(s):  
M. S. Bachman ◽  
C. D. Nickell ◽  
P. A. Stephens ◽  
A. D. Nickell
Keyword(s):  
Germplasm Collection ◽  
Central China ◽  
Stem Rot ◽  
Disease Assessment ◽  
Sources Of Resistance ◽  
University Of Illinois ◽  
Brown Stem Rot ◽  
Phialophora Gregata ◽  
Foliar Symptoms ◽  
Resistant Lines

Soybean accessions from China were screened in an attempt to identify unique sources of resistance to Phialophora gregata, the cause of brown stem rot. In 1994, over 500 accessions from the USDA Soybean Germplasm Collection, University of Illinois, Urbana-Champaign, were evaluated in the field at Urbana, IL, for reaction to brown stem rot. The accessions originated from nine provinces in central China and ranged in maturity from groups II to IV. Disease assessment was based on incidence of foliar symptoms and severity of stem symptoms produced by infection with natural inoculum. Based on field results, 64 putatively resistant lines were selected and evaluated in the greenhouse by a root-dip inoculation method. Thirteen accessions with levels of resistance equal to those of resistant standards were identified from five provinces. These lines may have value as donors of unique sources of resistance to brown stem rot.

scholarly journals Characterization and Distribution of Two Races of Phialophora gregata in the North-Central United States

2003 ◽  
Vol 93 (7) ◽  
pp. 901-912 ◽  
Author(s):  
T. C. Harrington ◽  
J. Steimel ◽  
F. Workneh ◽  
X. B. Yang
Keyword(s):  
Genetic Variation ◽  
Stem Rot ◽  
North Central ◽  
Brown Stem Rot ◽  
Phialophora Gregata ◽  
The North ◽  
Foliar Symptoms ◽  
Central United States ◽  
Soybean Plants ◽  
Xylem Discoloration

Genetic variation and variation in aggressiveness in Phialophora gregata f. sp. sojae, the cause of brown stem rot of soybean, was characterized in a sample of 209 isolates from the north-central region. The isolates were collected from soybean plants without regard to symptoms from randomly selected soybean fields. Seven genotypes (A1, A2, A4, A5, A6, M1, and M2) were distinguished based on DNA fingerprinting with microsatellite probes (CAT)5 and (CAC)5, with only minor genetic variation within the A or M genotypes. Only the A1, A2, and M1 genotypes were represented by more than one isolate. The A genotypes dominated in the eastern Iowa, Illinois, and Ohio samples, whereas the M genotypes were dominant in samples from western Iowa, Minnesota, and Missouri. In growth chamber experiments, isolates segregated into two pathogenicity groups based on their aggressiveness toward soybean cvs. Kenwood and BSR101, which are relatively susceptible and resistant, respectively, to brown stem rot. In both root dip inoculation and inoculation by injecting spores into the stem near the ground line (stab inoculations), isolates of the A genotypes caused greater foliar symptoms and more vascular discoloration than isolates of the M genotypes on both cultivars of soybean. All isolates caused foliar symptoms in both cultivars and in three additional cultivars of soybean with resistance to brown stem rot. Greater differences between the A and M genotypes were seen in foliar symptoms than in the linear extent of xylem discoloration, and greater differences were seen in Kenwood than in BSR101. Inoculation of these genotypes into five cultivars of soybean with different resistance genes to brown stem rot showed a genotype × cultivar interaction. A similar distinction was found in an earlier study of the adzuki bean pathogen, P. gregata f. sp. adzukicola, and consistent with the nomenclature of that pathogen, the soybean pathogens are named the aggressive race (race A) and the mild race (race M) of P. gregata f. sp. sojae.

scholarly journals Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage

2017 ◽  
Vol 77 (3) ◽  
pp. 423-423 ◽  
Author(s):  
Jamie Soul ◽  
Sara L Dunn ◽  
Sanjay Anand ◽  
Ferdinand Serracino-Inglott ◽  
Jean-Marc Schwartz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Complex Disease ◽  
Calcium Signalling ◽  
Rna Seq ◽  
Knee Cartilage ◽  
Knee Oa ◽  
Genome Wide ◽  
Group A ◽  
Group B ◽  
Patient Subgroups

IntroductionOsteoarthritis (OA) is a heterogeneous and complex disease. We have used a network biology approach based on genome-wide analysis of gene expression in OA knee cartilage to seek evidence for pathogenic mechanisms that may distinguish different patient subgroups.MethodsResults from RNA-Sequencing (RNA-Seq) were collected from intact knee cartilage at total knee replacement from 44 patients with OA, from 16 additional patients with OA and 10 control patients with non-OA. Results were analysed to identify patient subsets and compare major active pathways.ResultsThe RNA-Seq results showed 2692 differentially expressed genes between OA and non-OA. Analysis by unsupervised clustering identified two distinct OA groups: Group A with 24 patients (55%) and Group B with 18 patients (41%). A 10 gene subgroup classifier was validated by RT-qPCR in 16 further patients with OA. Pathway analysis showed increased protein expression in both groups. PhenomeExpress analysis revealed group differences in complement activation, innate immune responses and altered Wnt and TGFβ signalling, but no activation of inflammatory cytokine expression. Both groups showed suppressed circadian regulators and whereas matrix changes in Group A were chondrogenic, in Group B they were non-chondrogenic with changes in mechanoreceptors, calcium signalling, ion channels and in cytoskeletal organisers. The gene expression changes predicted 478 potential biomarkers for detection in synovial fluid to distinguish patients from the two groups.ConclusionsTwo subgroups of knee OA were identified by network analysis of RNA-Seq data with evidence for the presence of two major pathogenic pathways. This has potential importance as a new basis for the stratification of patients with OA for drug trials and for the development of new targeted treatments.

scholarly journals A Molecular Marker Identifying Subspecific Populations of the Soybean Brown Stem Rot Pathogen, Phialophora gregata

2000 ◽  
Vol 90 (8) ◽  
pp. 875-883 ◽  
Author(s):  
Weidong Chen ◽  
Craig R. Grau ◽  
Eric A. Adee ◽  
Xiangqi Meng
Keyword(s):  
Molecular Marker ◽  
Direct Detection ◽  
Point Mutations ◽  
Variable Region ◽  
Stem Rot ◽  
Specific Primers ◽  
Brown Stem Rot ◽  
Phialophora Gregata ◽  
Genotype C ◽  
Genotype A

A molecular marker was developed to separate and identify subspecific populations of Phialophora gregata, the causal agent of soybean brown stem rot. A variable DNA region in the intergenic spacer of the nuclear rDNA was identified. Two specific primers flanking the variable region were developed for easy identification of the genotypes using polymerase chain reaction (PCR). These two specific primers amplified three DNA products. The three PCR products were used to separate isolates of P. gregata into distinct genotypes: A (1,020 bp), B (830 bp), and C (660 bp). Genotype C was found in isolates obtained from Adzuki beans from Japan, whereas all 292 isolates obtained from soybean and the 8 isolates from mung bean belonged to either genotype A or B. The original nondefoliating (type II) strain ATCC 11073 (type culture of P. gregata) belonged to genotype B. The difference between genotypes A and B was due only to an 188-bp insertion or deletion; genotype C, however, differs from genotypes A and B at 58 point mutations, in addition to the length difference. Isolates of both genotypes A and B were widespread in seven Midwestern states. Genotype A was found mostly in certain susceptible soybean cultivars like Sturdy and Pioneer 9305, whereas genotype B was found predominately in brown stem rot-resistant soybean cvs. Bell, IA 3003, and Seiben SS282N. The specific primers were also used to directly detect cultivar-preferential infection by the two genotypes in infected soybean stems growing in the same field. Data from direct detection in soybean stems showed that cultivar-preferential infection by the two genotypes of P. gregata was significant.

scholarly journals Soybean Stem Colonization by Genotypes A and B of Cadophora gregata Increases with Increasing Population Densities of Heterodera glycines

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1297-1301 ◽  
Author(s):  
G. M. Tabor ◽  
G. L. Tylka ◽  
C. R. Bronson
Keyword(s):  
Population Density ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Cyst Nematode ◽  
Stem Rot ◽  
Population Densities ◽  
Brown Stem Rot ◽  
Phialophora Gregata ◽  
Soybean Genotypes ◽  
Genotype A

Growth chamber experiments were conducted to investigate whether parasitism by increasing population densities of Heterodera glycines, the soybean cyst nematode, increases the incidence and severity of stem colonization by the aggressive genotype A and the mild genotype B of Cadophora gregata (Phialophora gregata), causal agents of brown stem rot of soybeans. Soybean genotypes with three combinations of resistance and susceptibility to H. glycines and genotype A of C. gregata were inoculated with each genotype of C. gregata alone or each genotype with two population densities of H. glycines eggs, 1,500 or 10,000 per 100 cm3 of soil. Stems of two H. glycines-susceptible soybeans were more colonized by both aggressive and mild genotypes of C. gregata in the presence of high than in the presence of low H. glycines population density.

scholarly journals Mapping eQTLs With RNA-Seq Reveals Novel SLE Susceptibility Genes, Non-Coding RNAs, and Alternative-Splicing Events That Are Concealed Using Microarrays

2016 ◽  
Author(s):  
Christopher A. Odhams ◽  
Andrea Cortini ◽  
Lingyan Chen ◽  
Amy L. Roberts ◽  
Ana Vinuela ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lupus Erythematosus ◽  
Molecular Mechanisms ◽  
Complex Disease ◽  
Splice Junction ◽  
Susceptibility Genes ◽  
Eqtl Analysis ◽  
Rna Seq ◽  
Control Of Gene Expression ◽  
Non Coding Rnas

AbstractStudies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered a greater frequency of candidate-causal eQTLs using RNA-Seq, and identified novel SLE susceptibility genes that were concealed using microarrays (e.g. NADSYN1, SKP1, and TCF7). Many of these eQTLs were found to influence the expression of several genes, suggesting risk haplotypes may harbour multiple functional effects. We pinpointed eQTLs modulating expression of four non-coding RNAs; three of which were replicated in whole-blood. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, the autophagy-related gene WDFY4, and the redox coenzyme NADSYN1, through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. In doing so, we have identified novel SLE candidate genes and specific molecular mechanisms that will serve as the basis for targeted follow-up studies.

Detecting Orobanche minor Seeds in Soil Using PCR

2003 ◽  
Vol 4 (1) ◽  
pp. 4 ◽  
Author(s):  
Megan E. Patzoldt ◽  
Weidong Chen ◽  
Brian W. Diers
Keyword(s):  
Southern China ◽  
Germplasm Collection ◽  
Central China ◽  
Stem Rot ◽  
Brown Stem Rot ◽  
Phialophora Gregata ◽  
South Central ◽  
Resistant Sources ◽  
Preliminary Study ◽  
Orobanche Minor

A new set of soybean accessions from south-central China were added to the USDA germplasm collection in 1996. Previous studies have shown that accessions with high levels of resistance to brown stem rot (BSR) can be found in germplasm collected from central and southern China. The objective of this study was to screen these accessions and identify those with resistance to BSR. In a preliminary study, 85 of 623 accessions tested were identified as resistant to BSR. In the second study, these 85 accessions were challenged with multiple biotypes of Phialophora gregata f. sp. sojae to identify those accessions with the strongest resistance. From these two studies, ten accessions were identified that had BSR resistance equal to or greater than the current resistant sources. Accepted for publication 10 June 2003. Published 1 July 2003.

scholarly journals Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190341 ◽  
Author(s):  
Judit Salces-Ortiz ◽  
Carlos Vargas-Chavez ◽  
Lain Guio ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Organophosphate Insecticide ◽  
Single Nucleotide ◽  
Insecticide Exposure ◽  
Genomic Response

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis -regulatory networks. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

scholarly journals Transcript Assembly and Quantification by RNA-Seq Reveals Significant Differences in Gene Expression and Genetic Variants in Mosquitoes of the Culex pipiens (Diptera: Culicidae) Complex

2020 ◽  
Author(s):  
David S Kang ◽  
Sungshil Kim ◽  
Michael A Cotten ◽  
Cheolho Sim
Keyword(s):  
Gene Expression ◽  
Culex Pipiens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Culex Pipiens Quinquefasciatus ◽  
Niche Differences ◽  
Differential Gene ◽  
Culex Pipiens Molestus ◽  
Transcript Assembly ◽  
Blood Meals

Abstract The taxonomy of Culex pipiens complex of mosquitoes is still debated, but in North America it is generally regarded to include Culex pipiens pipiens, Culex pipiens molestus, and Culex quinquefasciatus (or Culex pipiens quinquefasciatus). Although these mosquitoes have very similar morphometry, they each have unique life strategies specifically adapted to their ecological niche. Differences include the capability for overwintering diapause, bloodmeal preference, mating behaviors, and reliance on blood meals to produce eggs. Here, we used RNA-seq transcriptome analysis to investigate the differential gene expression and nucleotide polymorphisms that may link to the divergent traits specifically between Cx. pipiens pipiens and Cx. pipiens molestus.

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