Association of single nucleotide polymorphic sites in candidate genes with aggressiveness and deoxynivalenol production in Fusarium graminearum causing wheat head blight

Fusarium graminearum causes head blight disease in wheat and barley. To help understand the infection process on wheat, we studied global gene expression of F. graminearum in a time series from 24 to 196 h after inoculation, compared with a noninoculated control. The infection was rapid and, after 48 h, over 4,000 fungal genes were expressed. The number of genes expressed increased over time up to 96 h (>8,000 genes), and then declined at the 144- and 192-h post-inoculation time points. After subtraction of genes found expressed on complete medium, during carbon or nitrogen starvation, and on barley, only 355 were found exclusively expressed in wheat, mostly genes with unknown function (72.6%). These genes were mainly found in single-nucleotide polymorphism-enriched islands on the chromosomes, suggesting a higher evolutionary selection pressure. The annotated genes were enriched in functional groups predicted to be involved in allantoin and allantoate transport, detoxification, nitrogen, sulfur and selenium metabolism, secondary metabolism, carbohydrate metabolism, and degradation of polysaccharides and ester compounds. Several putative secreted virulence factors were also found expressed in wheat.

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A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex

PeerJ ◽

10.7717/peerj.2609 ◽

2016 ◽

Vol 4 ◽

pp. e2609 ◽

Cited By ~ 12

Author(s):

Hao Zhang ◽

Balázs Brankovics ◽

Theo A.J. van der Lee ◽

Cees Waalwijk ◽

Anne A.D. van Diepeningen ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Fusarium Graminearum ◽

Species Complex ◽

Simultaneous Detection ◽

Point Mutations ◽

Nucleotide Polymorphism ◽

Head Blight ◽

Single Nucleotide ◽

Allele Specific ◽

Resistant Genotypes

The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.

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Genome wide association study identifies novel single nucleotide polymorphic loci and candidate genes involved in soybean sudden death syndrome resistance

PLoS ONE ◽

10.1371/journal.pone.0212071 ◽

2019 ◽

Vol 14 (2) ◽

pp. e0212071 ◽

Cited By ~ 2

Author(s):

Sivakumar Swaminathan ◽

Anindya Das ◽

Teshale Assefa ◽

Joshua M. Knight ◽

Amilton Ferreira Da Silva ◽

...

Keyword(s):

Sudden Death ◽

Association Study ◽

Candidate Genes ◽

Genome Wide Association Study ◽

Sudden Death Syndrome ◽

Genome Wide Association ◽

Single Nucleotide Polymorphic ◽

Single Nucleotide ◽

Polymorphic Loci ◽

Genome Wide

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Dementia key gene identification with multi-layered SNP-gene-disease network

Bioinformatics ◽

10.1093/bioinformatics/btaa814 ◽

2020 ◽

Vol 36 (Supplement_2) ◽

pp. i831-i839

Author(s):

Dong-gi Lee ◽

Myungjun Kim ◽

Sang Joon Son ◽

Chang Hyung Hong ◽

Hyunjung Shin

Keyword(s):

Candidate Genes ◽

Learning Algorithm ◽

Search Space ◽

Supplementary Information ◽

Gene Identification ◽

Nucleotide Polymorphisms ◽

Disease Network ◽

Single Nucleotide ◽

Key Genes ◽

Significant Attention

Abstract Motivation Recently, various approaches for diagnosing and treating dementia have received significant attention, especially in identifying key genes that are crucial for dementia. If the mutations of such key genes could be tracked, it would be possible to predict the time of onset of dementia and significantly aid in developing drugs to treat dementia. However, gene finding involves tremendous cost, time and effort. To alleviate these problems, research on utilizing computational biology to decrease the search space of candidate genes is actively conducted. In this study, we propose a framework in which diseases, genes and single-nucleotide polymorphisms are represented by a layered network, and key genes are predicted by a machine learning algorithm. The algorithm utilizes a network-based semi-supervised learning model that can be applied to layered data structures. Results The proposed method was applied to a dataset extracted from public databases related to diseases and genes with data collected from 186 patients. A portion of key genes obtained using the proposed method was verified in silico through PubMed literature, and the remaining genes were left as possible candidate genes. Availability and implementation The code for the framework will be available at http://www.alphaminers.net/. Supplementary information Supplementary data are available at Bioinformatics online.

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Screening of Durum Wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.) Italian Cultivars for Susceptibility to Fusarium Head Blight Incited by Fusarium graminearum

Plants ◽

10.3390/plants10010068 ◽

2020 ◽

Vol 10 (1) ◽

pp. 68

Author(s):

Gaetano Bentivenga ◽

Alfio Spina ◽

Karim Ammar ◽

Maria Allegra ◽

Santa Olga Cacciola

Keyword(s):

Durum Wheat ◽

Fusarium Head Blight ◽

Fusarium Graminearum ◽

Triticum Turgidum ◽

Disease Incidence ◽

Morphological Characteristics ◽

Pcr Amplification ◽

Conidial Suspension ◽

Head Blight ◽

Italian Origin

In 2009, a set of 35 cultivars of durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.) of Italian origin was screened for fusarium head blight (FHB) susceptibility at CIMMYT (Mexico) and in the 2019–20 cropping season, 16 of these cultivars, which had been included in the Italian National Plant Variety Register, were tested again in southern and northern Italy. Wheat cultivars were artificially inoculated during anthesis with a conidial suspension of Fusarium graminearum sensu lato using a standard spray inoculation method. Inoculum was a mixture of mono-conidial isolates sourced in the same areas where the trials were performed. Isolates had been characterized on the basis of morphological characteristics and by DNA PCR amplification using a specific primer set and then selected for their virulence and ability to produce mycotoxins. The susceptibility to FHB was rated on the basis of the disease severity, disease incidence and FHB index. Almost all of the tested cultivars were susceptible or very susceptible to FHB with the only exception of “Duprì”, “Tiziana” and “Dylan” which proved to be moderately susceptible. The susceptibility to FHB was inversely correlated with the plant height and flowering biology, the tall and the late heading cultivars being less susceptible.

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Age by Single Nucleotide Polymorphism Interactions on Bronchodilator Response in Asthmatics

Journal of Personalized Medicine ◽

10.3390/jpm11010059 ◽

2021 ◽

Vol 11 (1) ◽

pp. 59

Author(s):

Kirsten Voorhies ◽

Joanne E. Sordillo ◽

Michael McGeachie ◽

Elizabeth Ampleford ◽

Alberta L. Wang ◽

...

Keyword(s):

Candidate Genes ◽

P Value ◽

Genome Wide Association Studies ◽

Genetic Associations ◽

Single Nucleotide ◽

Significance Level ◽

Bronchodilator Response ◽

Genome Wide ◽

A Genome ◽

Β2 Agonists

An unaddressed and important issue is the role age plays in modulating response to short acting β2-agonists in individuals with asthma. The objective of this study was to identify whether age modifies genetic associations of single nucleotide polymorphisms (SNPs) with bronchodilator response (BDR) to β2-agonists. Using three cohorts with a total of 892 subjects, we ran a genome wide interaction study (GWIS) for each cohort to examine SNP by age interactions with BDR. A fixed effect meta-analysis was used to combine the results. In order to determine if previously identified BDR SNPs had an age interaction, we also examined 16 polymorphisms in candidate genes from two published genome wide association studies (GWAS) of BDR. There were no significant SNP by age interactions on BDR using the genome wide significance level of 5 × 10−8. Using a suggestive significance level of 5 × 10−6, three interactions, including one for a SNP within PRAG1 (rs4840337), were significant and replicated at the significance level of 0.05. Considering candidate genes from two previous GWAS of BDR, three SNPs (rs10476900 (near ADRB2) [p-value = 0.009], rs10827492 (CREM) [p-value = 0.02], and rs72646209 (NCOA3) [p-value = 0.02]) had a marginally significant interaction with age on BDR (p < 0.05). Our results suggest age may be an important modifier of genetic associations for BDR in asthma.

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Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

International Journal of Molecular Sciences ◽

10.3390/ijms22073477 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3477

Author(s):

Julia Zaborowska ◽

Bartosz Łabiszak ◽

Annika Perry ◽

Stephen Cavers ◽

Witold Wachowiak

Keyword(s):

Population Structure ◽

Candidate Genes ◽

Genetic Basis ◽

Redox Homeostasis ◽

Snp Markers ◽

Regulation Of Transcription ◽

Single Nucleotide ◽

Homeostasis Regulation ◽

Genomic Regions ◽

Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

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Near-infrared versus visual sorting of Fusarium-damaged kernels in winter wheat

Canadian Journal of Plant Science ◽

10.4141/cjps08053 ◽

2008 ◽

Vol 88 (6) ◽

pp. 1087-1089 ◽

Cited By ~ 14

Author(s):

Stephen N Wegulo ◽

Floyd E Dowell

Keyword(s):

Quality Assurance ◽

Winter Wheat ◽

Fusarium Head Blight ◽

Key Words ◽

Fusarium Graminearum ◽

Near Infrared ◽

Strongly Correlated ◽

Head Blight ◽

Rater Reliability ◽

Key Words Wheat

Fusarium head blight (scab) of wheat, caused by Fusarium graminearum, often results in shriveled and/or discolored kernels, which are referred to as Fusarium-damaged kernels (FDK). FDK is a major grain grading factor and therefore is routinely determined for purposes of quality assurance. Measurement of FDK is usually done visually. Visual sorting can be laborious and is subject to inconsistencies resulting from variability in intra-rater repeatability and/or inter-rater reliability. The ability of a single-kernel near-infrared (SKNIR) system to detect FDK was evaluated by comparing FDK sorted by the system to FDK sorted visually. Visual sorting was strongly correlated with sorting by the SKNIR system (0.89 ≤ r ≤ 0.91); however, the SKNIR system had a wider range of FDK detection and was more consistent. Compared with the SKNIR system, visual raters overestimated FDK in samples with a low percentage of Fusarium-damaged grain and underestimated FDK in samples with a high percentage of Fusarium-damaged grain. Key words: Wheat, Fusarium head blight, Fusarium-damaged kernels, single-kernel near-infrared

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