Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat

Abstract Background Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB resistance. Resistance QTL were identified for the durum wheat cv. Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B in a previous study. The objective of this study was to identify the defense mechanisms underlying the resistance of Blackbird and report candidate regulator defense genes and single nucleotide polymorphism (SNP) markers within these genes for high-resolution mapping of resistance QTL reported for the durum wheat cv. Strongfield/Blackbird population. Results Gene network analysis identified five networks significantly (P < 0.05) associated with the resistance to FHB spread (Type II FHB resistance) one of which showed significant correlation with both plant height and relative maturity traits. Two gene networks showed subtle differences between Fusarium graminearum-inoculated and mock-inoculated plants, supporting their involvement in constitutive defense. The candidate regulator genes have been implicated in various layers of plant defense including pathogen recognition (mainly Nucleotide-binding Leucine-rich Repeat proteins), signaling pathways including the abscisic acid and mitogen activated protein (MAP) kinase, and downstream defense genes activation including transcription factors (mostly with dual roles in defense and development), and cell death regulator and cell wall reinforcement genes. The expression of five candidate genes measured by quantitative real-time PCR was correlated with that of RNA-seq, corroborating the technical and analytical accuracy of RNA-sequencing. Conclusions Gene network analysis allowed identification of candidate regulator genes and genes associated with constitutive resistance, those that will not be detected using traditional differential expression analysis. This study also shed light on the association of developmental traits with FHB resistance and partially explained the co-localization of FHB resistance with plant height and maturity QTL reported in several previous studies. It also allowed the identification of candidate hub genes within the interval of three previously reported FHB resistance QTL for the Strongfield/Blackbird population and associated SNPs for future high resolution mapping studies.

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Mapping of FHB resistance QTLs in tetraploid wheat

Genome ◽

10.1139/g06-127 ◽

2006 ◽

Vol 49 (12) ◽

pp. 1586-1593 ◽

Cited By ~ 69

Author(s):

Daryl J. Somers ◽

George Fedak ◽

John Clarke ◽

Wenguang Cao

Keyword(s):

Durum Wheat ◽

Resistance Gene ◽

Triticum Turgidum ◽

Tetraploid Wheat ◽

Epistatic Effect ◽

Resistance Allele ◽

Head Blight ◽

Resistance Qtls ◽

Resistance Qtl ◽

Fhb Resistance

Triticum turgidum L var. durum is known to be particularly susceptible to infection by Fusarium graminearum, the causal agent for Fusarium head blight (FHB), which results in severe yield losses and grain contaminated with mycotoxins. This research was aimed at identifying FHB resistance in tetraploid wheat and mapping the location of FHB resistance genes. A tetraploid cross of durum wheat (‘Strongfield’) × Triticum carthlicum (‘Blackbird’) was used to generate a doubled-haploid (DH) population. This population was evaluated for type II resistance to F. graminearum in replicated greenhouse trials, in which heads were innoculated and the percent of infected spikelets was determined 21 days later. The population was also genotyped with microsatellite markers to construct a map of 424 loci, covering 2 052 cM. The FHB reaction and genotypic data were used to identify FHB resistance quantitative trait loci (QTLs). It was determined that 2 intervals on chromosomes 2BL and 6BS controlled FHB resistance in this tetraploid cross. The FHB resistance allele on chromosome 2BL (r2 = 0.26, logarithm of odds (LOD) = 8.5) was derived from ‘Strongfield’, and the FHB resistance allele on chromosome 6BS (r2 = 0.23, LOD = 6.6) was derived from ‘Blackbird’. Two other loci, on chromosomes 5AS and 2AL, were shown to regulate FHB infection and to have an epistatic effect on the FHB resistance QTL on chromosome 6BS. Further, the FHB resistance QTL peak on chromosome 6BS was clearly coincident with the known FHB resistance gene Fhb2, derived from Sumai 3. The results show that FHB resistance can be expressed in durum wheat, and that T. carthlicum and Triticum aestivum likely share a common FHB resistance gene on chromosome 6BS.

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Mapping of QTL associated with Fusarium head blight in spring wheat RL4137

Czech Journal of Genetics and Plant Breeding ◽

10.17221/70/2008-cjgpb ◽

2009 ◽

Vol 44 (No. 4) ◽

pp. 147-159 ◽

Cited By ~ 9

Author(s):

Srinivasachary ◽

N. Gosman ◽

A. Steed ◽

S. Faure ◽

R. Bayles ◽

...

Keyword(s):

Fusarium Head Blight ◽

Recombinant Inbred Lines ◽

Inbred Lines ◽

Resistant Variety ◽

Resistant Line ◽

Head Blight ◽

Resistance Qtl ◽

Multiple Trials ◽

Fhb Resistance ◽

Positive Effect

Fusarium head blight (FHB) is a destructive disease of wheat worldwide. We aimed to map QTL for FHB resistance in RL4137, a FHB resistant line derived from Frontana using 90 recombinant inbred lines (RIL) from a cross between RL4137 and the moderately FHB resistant variety Timgalen. A total of seven putative FHB resistance QTL (1B, 2B, 3A, 6A, 6B, 7A and 7D) were identified and in all but one instance, the alleles from RL4137 had a positive effect on FHB resistance. The QTL, Qfhs.jic-2band Qfhs.jic-6b contributed by the alleles from RL4137 and Timgalen, respectively were detected in multiple trials. Our study also identified three QTL for plant height (2B, 4A and 5B), two QTL for weight of infected spikelets from infected ears (2B and 6A) and one QTL for “awns” (2B). The QTL mapped on 2B for PH, WIS and awns co-localized with Qfhs.jic-2b. The FHB QTL on 1B and 6B were not associated with PH QTL and that the minor PH QTL on 4A and 5B, did not co-localise with any other FHB resistance QTL.

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Fusarium Head Blight in Durum Wheat: Recent Status, Breeding Directions, and Future Research Prospects

Phytopathology ◽

10.1094/phyto-03-19-0095-rvw ◽

2019 ◽

Vol 109 (10) ◽

pp. 1664-1675 ◽

Cited By ~ 13

Author(s):

Jemanesh K. Haile ◽

Amidou N’Diaye ◽

Sean Walkowiak ◽

Kirby T. Nilsen ◽

John M. Clarke ◽

...

Keyword(s):

Durum Wheat ◽

Fusarium Head Blight ◽

Seed Quality ◽

Association Studies ◽

Tetraploid Wheat ◽

The United States ◽

Genome Wide Association Studies ◽

Head Blight ◽

Food And Feed ◽

Fhb Resistance

Fusarium head blight (FHB) is a major fungal disease affecting wheat production worldwide. Since the early 1990s, FHB, caused primarily by Fusarium graminearum, has become one of the most significant diseases faced by wheat producers in Canada and the United States. The increasing FHB problem is likely due to the increased adoption of conservation tillage practices, expansion of maize production, use of susceptible wheat varieties in rotation, and climate variability. Durum wheat (Triticum turgidum sp. durum) is notorious for its extreme susceptibility to FHB and breeding for resistance is complicated because sources of FHB resistance are rare in the primary gene pool of tetraploid wheat. Losses due to this disease include yield, test weight, seed quality, food and feed quality, and when severe, market access. More importantly, it is the contamination with mycotoxins, such as deoxynivalenol, in Fusarium-infected durum kernels that causes the most serious economic as well as food and feed safety concerns. Several studies and thorough reviews have been published on germplasm development and breeding for FHB resistance and the genetics and genomics of FHB resistance in bread or common wheat (T. aestivum); however, similar reviews have not been conducted in durum wheat. Thus, the aim of this review is to summarize and discuss the recent research efforts to mitigate FHB in durum wheat, including quantitative trait locus mapping, genome-wide association studies, genomic prediction, mutagenesis and characterization of genes and pathways involved in FHB resistance. It also highlights future directions, FHB-resistant germplasm, and the potential role of morphological traits to enhance FHB resistance in durum wheat.

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Historic recombination in a durum wheat breeding panel enables high-resolution mapping of Fusarium head blight resistance quantitative trait loci

Scientific Reports ◽

10.1038/s41598-020-64399-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ehsan Sari ◽

Ron E. Knox ◽

Yuefeng Ruan ◽

Maria Antonia Henriquez ◽

Santosh Kumar ◽

...

Keyword(s):

Quantitative Trait Loci ◽

High Resolution ◽

Durum Wheat ◽

Quantitative Trait ◽

Fusarium Head Blight Resistance ◽

Wheat Breeding ◽

Blight Resistance ◽

Head Blight ◽

High Resolution Mapping ◽

Resolution Mapping

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Gene network analysis: from heart development to cardiac therapy

Thrombosis and Haemostasis ◽

10.1160/th14-06-0483 ◽

2015 ◽

Vol 113 (03) ◽

pp. 521-531 ◽

Cited By ~ 3

Author(s):

Riccardo Bellazzi ◽

Felix Engel ◽

Fulvia Ferrazzi

Keyword(s):

Network Analysis ◽

Heart Development ◽

Gene Networks ◽

Gene Network ◽

Stem Cell Differentiation ◽

Cellular Systems ◽

Expression Data ◽

Temporal Expression ◽

Regulatory Processes ◽

Gene Network Analysis

SummaryNetworks offer a flexible framework to represent and analyse the complex interactions between components of cellular systems. In particular gene networks inferred from expression data can support the identification of novel hypotheses on regulatory processes. In this review we focus on the use of gene network analysis in the study of heart development. Understanding heart development will promote the elucidation of the aetiology of congenital heart disease and thus possibly improve diagnostics. Moreover, it will help to establish cardiac therapies. For example, understanding cardiac differentiation during development will help to guide stem cell differentiation required for cardiac tissue engineering or to enhance endogenous repair mechanisms. We introduce different methodological frameworks to infer networks from expression data such as Boolean and Bayesian networks. Then we present currently available temporal expression data in heart development and discuss the use of network-based approaches in published studies. Collectively, our literature-based analysis indicates that gene network analysis constitutes a promising opportunity to infer therapy-relevant regulatory processes in heart development. However, the use of network-based approaches has so far been limited by the small amount of samples in available datasets. Thus, we propose to acquire high-resolution temporal expression data to improve the mathematical descriptions of regulatory processes obtained with gene network inference methodologies. Especially probabilistic methods that accommodate the intrinsic variability of biological systems have the potential to contribute to a deeper understanding of heart development.

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Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat

Theoretical and Applied Genetics ◽

10.1007/s00122-015-2606-x ◽

2015 ◽

Vol 129 (1) ◽

pp. 31-43 ◽

Cited By ~ 11

Author(s):

Xianwen Zhu ◽

Shaobin Zhong ◽

Shiaoman Chao ◽

Yong Qiang Gu ◽

Shahryar F. Kianian ◽

...

Keyword(s):

Durum Wheat ◽

Fusarium Head Blight ◽

Fusarium Head Blight Resistance ◽

Genomic Region ◽

Blight Resistance ◽

Head Blight ◽

Resistance Qtl

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Identification of novel QTL for resistance to Fusarium head blight in a tetraploid wheat population

Genome ◽

10.1139/gen-2012-0110 ◽

2012 ◽

Vol 55 (12) ◽

pp. 853-864 ◽

Cited By ~ 25

Author(s):

Yuefeng Ruan ◽

André Comeau ◽

François Langevin ◽

Pierre Hucl ◽

John M. Clarke ◽

...

Keyword(s):

Durum Wheat ◽

Fusarium Head Blight ◽

Fusarium Graminearum ◽

Triticum Turgidum ◽

Tetraploid Wheat ◽

Field Trials ◽

Gibberella Zeae ◽

Head Blight ◽

Wheat Population ◽

Fhb Resistance

Most tetraploid durum wheat (Triticum turgidum L var. durum) cultivars are susceptible to Fusarium head blight (FHB). This study reports novel quantitative trait loci (QTL) associated with FHB resistance. A backcross recombinant inbred line (BCRIL) population was developed from the cross BGRC3487/2*DT735, and 160 lines were evaluated for resistance to Fusarium graminearum Schwabe (teleomorph Gibberella zeae (Schwein. Petch) in field trials over 3 years (2008–2010) and to a F. graminearum 3-acetyl-deoxynivalenol (3-ADON) chemotype in greenhouse trials. The population was genotyped with 948 polymorphic loci using DArT and microsatellite markers. Eleven QTL were associated with FHB resistance under field conditions on chromosomes 2A, 3B, 5A, 5B, 7A, and 7B. Two of these, QFhb.usw-3B from BGRC3487 and QFhb.usw-7A2, were consistently detected over environments. The QFhb.usw-3B QTL was in a similar position to a resistance QTL in hexaploid wheat. The combination of the two QTL reduced field index by 53.5%–86.2%. Two QTL for resistance to the 3-ADON chemotype were detected on chromosomes 1B and 4B. Both BGRC3487 and DT735 could provide new sources of FHB resistance and the combination of QTL reported here could be valuable tools in breeding FHB-resistant durum wheat.

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Gene network analysis to determine the effect of hypoxia-associated genes on brain damages and tumorigenesis using an avian model

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00184-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Hamed Kharrati-Koopaee ◽

Esmaeil Ebrahimie ◽

Mohammad Dadpasand ◽

Ali Niazi ◽

Rugang Tian ◽

...

Keyword(s):

Network Analysis ◽

High Altitude ◽

Uv Radiation ◽

Drug Toxicity ◽

Gene Networks ◽

Gene Network ◽

Comparative Genomic ◽

Low Oxygen ◽

Genomic Study ◽

Gene Network Analysis

Abstract Background Hypoxia refers to the condition of low oxygen pressure in the atmosphere and characterization of response to hypoxia as a biological complex puzzle, is challenging. Previously, we carried out a comparative genomic study by whole genome resequencing of highland and lowland Iranian native chickens to identify genomic variants associated with hypoxia conditions. Based on our previous findings, we used chicken as a model and the identified hypoxia-associated genes were converted to human’s orthologs genes to construct the informative gene network. The main goal of this study was to visualize the features of diseases due to hypoxia-associated genes by gene network analysis. Results It was found that hypoxia-associated genes contained several gene networks of disorders such as Parkinson, Alzheimer, cardiomyopathy, drug toxicity, and cancers. We found that biological pathways are involved in mitochondrion dysfunctions including peroxynitrous acid production denoted in brain injuries. Lewy body and neuromelanin were reported as key symptoms in Parkinson disease. Furthermore, calmodulin, and amyloid precursor protein were detected as leader proteins in Alzheimer’s diseases. Dexamethasone was reported as the candidate toxic drug under the hypoxia condition that implicates diabetes, osteoporosis, and neurotoxicity. Our results suggested DNA damages caused by the high doses of UV radiation in high-altitude conditions, were associated with breast cancer, ovarian cancer, and colorectal cancer. Conclusions Our results showed that hypoxia-associated genes were enriched in several gene networks of disorders including Parkinson, Alzheimer, cardiomyopathy, drug toxicity, and different types of cancers. Furthermore, we suggested, UV radiation and low oxygen conditions in high-altitude regions may be responsible for the variety of human diseases.

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Effects of Durum Wheat Cultivars with Different Degrees of FHB Susceptibility Grown Under Different Meteorological Conditions on the Contamination of Regulated, Modified and Emerging Mycotoxins

10.20944/preprints202101.0610.v1 ◽

2021 ◽

Author(s):

Valentina Scarpino ◽

Massimo Blandino

Keyword(s):

Durum Wheat ◽

Meteorological Conditions ◽

Wheat Cultivars ◽

Head Blight ◽

North West ◽

Modified Mycotoxins ◽

Growing Seasons ◽

Condi Tions ◽

Fhb Resistance ◽

Resistant Genotypes

The enhancement of Fusarium head blight (FHB) resistance is one of the best options to reduce mycotoxin contamination in wheat. This study has aimed to verify that the genotypes with high tolerance to deoxynivalenol could guarantee an overall minimization of the sanitary risk, by evaluating the contamination of regulated, modified and emerging mycotoxins on durum wheat cvs with different degrees of FHB susceptibility, grown under different meteorological condi-tions, in 8 growing seasons in North-West Italy. The years which were characterized by frequent and heavy rainfall in spring, were also those with the highest contamination of deoxynivalenol, zearalenone, moniliformin and enniatins. The most FHB resistant genotypes resulted in the lowest contamination of all the mycotoxins but showed the highest deoxyniva-lenol-3-glucoside/deoxynivalenol ratio and moniliformin/deoxynivalenol ratio. An inverse re-lationship between the amount of deoxynivalenol and the deoxyniva-lenol-3-glucoside/deoxynivalenol ratio was recorded for all the cvs and all the years. Converse-ly, the enniatins/deoxynivalenol ratio had a less intense relationship with cv tolerance to FHB. In conclusion, even though the more tolerant cvs, showed higher relative relationships between modified/emerging mycotoxins and native/target mycotoxins than the susceptible ones, they showed lower absolute levels of contamination of both emerging and modified mycotoxins.

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