scholarly journals Fusarium Populations on Chinese Barley Show a Dramatic Gradient in Mycotoxin Profiles

2008 ◽  
Vol 98 (6) ◽  
pp. 719-727 ◽  
Author(s):  
L. Yang ◽  
T. van der Lee ◽  
X. Yang ◽  
D. Yu ◽  
C. Waalwijk

We report on a large gene bank of Fusarium isolates established by a broad survey conducted in 2005 in which infected barley ears were collected in 23 counties of seven provinces and two municipalities along the Yangtze River in China. In total, 1,894 single spore isolates were obtained. The isolates were characterized at the species level by a newly developed and robust set of diagnostic primers based on single nucleotide polymorphisms (SNPs) among members of the F. graminearum clade. In addition, we determined their chemotype using previously described polymerase chain reaction (PCR) primers. The results showed that in all regions F. asiaticum was the predominant species causing Fusarium head blight (FHB) on barley in China (N = 1,706), while in the upper valleys of the Yangtze River also F. graminearum sensu stricto, F. meridionale, and F. proliferatum were found. Major differences in the chemotypes were found in the F. asiaticum populations, from very high to exclusive nivalenol (NIV) chemotypes in the mountainous upper valleys of the Yangtze River to predominantly deoxynivalenol (DON) chemotypes in the middle and lower valleys. In contrast to the F. asiaticum isolates from three counties in Sichuan province, which were largely NIV producers (278 of 291), F. graminearum isolates from these sampling sites were for the vast majority (27 of 28) DON producers, indicating that despite sharing the same habitat, these sympatric species apparently have unique mycotoxin chemotypes.

2021 ◽  
Vol 7 (12) ◽  
pp. 1076
Author(s):  
Wenbing Gong ◽  
Nan Shen ◽  
Lin Zhang ◽  
Yinbing Bian ◽  
Yang Xiao

Meiotic crossover plays a critical role in generating genetic variations and is a central component of breeding. However, our understanding of crossover in mushroom-forming fungi is limited. Here, in Lentinula edodes, we characterized the chromosome-wide intragenic crossovers, by utilizing the single-nucleotide polymorphisms (SNPs) datasets of an F1 haploid progeny. A total of 884 intragenic crossovers were identified in 110 single-spore isolates, the majority of which were closer to transcript start sites. About 71.5% of the intragenic crossovers were clustered into 65 crossover hotspots. A 10 bp motif (GCTCTCGAAA) was significantly enriched in the hotspot regions. Crossover frequencies around mating-type A (MAT-A) loci were enhanced and formed a hotspot in L. edodes. Genome-wide quantitative trait loci (QTLs) mapping identified sixteen crossover-QTLs, contributing 8.5–29.1% of variations. Most of the detected crossover-QTLs were co-located with crossover hotspots. Both cis- and trans-QTLs contributed to the nonuniformity of crossover along chromosomes. On chr2, we identified a QTL hotspot that regulated local, global crossover variation and crossover hotspot in L. edodes. These findings and observations provide a comprehensive view of the crossover landscape in L. edodes, and advance our understandings of conservation and diversity of meiotic recombination in mushroom-forming fungi.


Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1533-1543
Author(s):  
Michaela M Gutacker ◽  
James C Smoot ◽  
Cristi A Lux Migliaccio ◽  
Stacy M Ricklefs ◽  
Su Hua ◽  
...  

Abstract Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.


2018 ◽  
Vol 108 (1) ◽  
pp. 124-132 ◽  
Author(s):  
Pallavi Sharma ◽  
Manu P. Gangola ◽  
Chen Huang ◽  
H. Randy Kutcher ◽  
Seedhabadee Ganeshan ◽  
...  

An in vitro spike culture method was optimized to evaluate Fusarium head blight (FHB) resistance in wheat (Triticum aestivum) and used to screen a population of ethyl methane sulfonate treated spike culture-derived variants (SCDV). Of the 134 SCDV evaluated, the disease severity score of 47 of the variants was ≤30%. Single nucleotide polymorphisms (SNP) in the UDP-glucosyltransferase (UGT) genes, TaUGT-2B, TaUGT-3B, and TaUGT-EST, differed between AC Nanda (an FHB-susceptible wheat variety) and Sumai-3 (an FHB-resistant wheat cultivar). SNP at 450 and 1,558 bp from the translation initiation site in TaUGT-2B and TaUGT-3B, respectively were negatively correlated with FHB severity in the SCDV population, whereas the SNP in TaUGT-EST was not associated with FHB severity. Fusarium graminearum strain M7-07-1 induced early expression of TaUGT-2B and TaUGT-3B in FHB-resistant SCDV lines, which were associated with deoxynivalenol accumulation and reduced FHB disease progression. At 8 days after inoculation, deoxynivalenol concentration varied from 767 ppm in FHB-resistant variants to 2,576 ppm in FHB-susceptible variants. The FHB-resistant SCDV identified can be used as new sources of FHB resistance in wheat improvement programs.


2011 ◽  
Vol 101 (1) ◽  
pp. 124-134 ◽  
Author(s):  
Liane Rosewich Gale ◽  
Stephen A. Harrison ◽  
Todd J. Ward ◽  
Kerry O'Donnell ◽  
Eugene A. Milus ◽  
...  

U.S. populations of the Fusarium graminearum clade cause head blight on wheat and barley and usually contaminate grain with the trichothecene mycotoxin deoxynivalenol (DON). Recently, however, individual nivalenol (NIV)-type isolates from the United States were described that belonged to either the newly described species F. gerlachii or the genetically distinct Gulf Coast population of F. graminearum sensu stricto (s.s.). Here, we describe the discovery of NIV-type F. graminearum s.s. populations that were found in high proportion (79%) among isolates from small-grain-growing regions of Louisiana. We genotyped 237 isolates from Louisiana with newly developed polymerase chain reaction (PCR) restriction fragment length polymorphism markers and multiplex PCR primers that distinguish among the three trichothecene types: the two DON types (15ADON and 3ADON) and NIV. These isolates were compared with 297 isolates from 11 other U.S. states, predominantly from the Midwest. Using Bayesian-model-based clustering, we discovered a southern Louisiana population of F. graminearum s.s. that was genetically distinct from the previously recognized pathogen population in the Midwest (MW15ADON population). Population membership was correlated with trichothecene type. Most isolates from the southern Louisiana population were of the NIV type, while the majority of the isolates from the Midwest were of the 15ADON type. A smaller proportion of isolates from Louisiana belonged to the previously described Gulf Coast population that was mostly of the 3ADON type. The NIV type was also identified in collections from Arkansas (12%), North Carolina (40%), and Missouri (2%), with the collections from Arkansas and North Carolina being small and unrepresentative. F. asiaticum was detected from the two southern Louisiana parishes Acadia and Alexandria. All identified 41 F. asiaticum isolates were of the NIV type. Greenhouse tests indicated that U.S. NIV types accumulated four times less trichothecene toxin than DON types on inoculated wheat. This is the first report of NIV-type populations of F. graminearum s. s. and F. asiaticum in the United States.


2012 ◽  
Vol 102 (1) ◽  
pp. 128-134 ◽  
Author(s):  
Firas Talas ◽  
Rasha Kalih ◽  
Thomas Miedaner

Fusarium head blight (FHB), caused by Fusarium graminearum sensu stricto (s.s.), causes tremendous annual yield losses in wheat worldwide. Variation of aggressiveness of isolates from individual field populations in terms of FHB infection and deoxynivalenol (DON) concentration in the host are important population parameters reflecting parasitic ability. Our main objective was to estimate the variation of both traits within three populations of F. graminearum s.s., each consisting of 30 single-spore isolates collected from small wheat fields in Germany, and to compare it with 11 isolates of a collection (F. graminearum collection) from four countries. The same isolates were characterized using 19 single-sequence repeat markers. All isolates were spray inoculated on a moderately resistant spring wheat cultivar at two field locations over 2 years (i.e., in four environments). The genotypic proportion of phenotypic variance (σ2G) within populations was significant (P < 0.01) for both traits, and the σ2G × environment interaction was even more important for mean FHB severity. Ranges in mean FHB severity and DON concentration in the host were only slightly smaller for the field populations than for the F. graminearum collection. Both traits were significantly (P < 0.05) correlated within and across populations. A further partitioning of σ2G revealed 72% of σ2G within and 28% of σ2G across populations for both traits. Molecular variance of the three populations was similarly distributed (73.6% within versus 26.4% between populations). In view of this high within-field variation for traits of parasitic ability and selection, neutral molecular markers, multiple resistance genes of different origin should be employed in wheat breeding programs to obtain a long-term stable FHB resistance.


Plant Disease ◽  
2015 ◽  
Vol 99 (1) ◽  
pp. 160-160 ◽  
Author(s):  
J.-H. Wang ◽  
X.-D. Peng ◽  
S.-H. Lin ◽  
A.-B. Wu ◽  
S.-L. Huang

Fusarium head blight (FHB), or scab, caused by Fusarium species, is an economically devastating disease of wheat and other cereal crops worldwide. FHB epidemics in wheat occur frequently in China, especially along the middle and lower reaches of the Yangtze River, including Jiangsu and Shanghai. In 2013, wheat spikes showing clear FHB symptoms were collected from fields in Jiangsu and Shanghai. Symptomatic seeds were surface-sterilized for 1 min with a 5% sodium hypochlorite solution and dipping in 70% ethanol for 30 s, then rinsed three times in sterile distilled water and dried. They were placed onto potato dextrose agar (PDA) and incubated for 3 to 5 days at 28°C in the dark. Fungal colonies displaying morphological characteristics of Fusarium spp. (1,2) were purified by the single-spore technique and characterized at the species level by morphological observations (1,2) and translation elongation factor 1-α (TEF) gene sequencing. The results indicated that members of the Fusarium graminearum clade were predominant on wheat, while the morphological characteristics of 16 isolates were found to be identical to those of F. sacchari (1,2). Colonies on PDA were densely cottony, initially pale but becoming violet with age. The average growth rate was 6 to 8 mm per day at 25°C in the dark. Reverse pigmentation was brownish red to violet-brown. Microconidia, abundant in the aerial mycelium and formed in false heads, were oval to ellipsoidal in shape, primarily zero-septate, measuring 5.7 to 18.8 (average 10.6) μm in length. Macroconidia were slender, three- to five-septate, with a curved apical cell and a poorly developed basal cell, 26.3 to 68.9 (average 44.0) μm in length. No chlamydospores were observed. Two F. sacchari strains (Y37 and S43), isolated from Jiangsu and Shanghai, respectively, were investigated by sequence comparison of their partial TEF gene sequences (Accession Nos. KM233195 and KM233196). BLASTn analysis of the TEF sequences obtained with sequences available in the GenBank database revealed 99.8 and 99.5% sequence identity to F. sacchari (GenBank Accession Nos. JF740708 and JF740709). Pathogenicity tests were conducted by injecting 10 μl of a spore suspension (5 × 105 spores/ml) into wheat florets (20 per isolate of cv. Yangmai16), which were then grown under field conditions in Shanghai. Control plants were inoculated with sterile distilled water. Spikes were harvested and evaluated 14 days post-inoculation. Reddish white mold was observed on inoculated wheat spikes; in addition, spikelets adjacent to the inoculation point and the infected florets were brown. No symptoms were observed on water controls. Koch's postulates were fulfilled by reisolating the pathogen from infected florets and identifying them by TEF gene sequencing. F. sacchari is the cause of an important disease of sugar cane, pokkah boeng (1), and has been reported to produce the mycotoxin beauvericin, which causes toxicosis in human and other animals (3). To our knowledge, this is the first report of F. sacchari causing wheat head blight in China. The report contributes to an improved understanding of the composition of Fusarium species on wheat in the lower reaches of the Yangtze River in China, which will be useful for exploring appropriate disease management strategies in this region. References: (1) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Publishing, Ames, IA, 2006. (2) J. F. Leslie et al. Mycologia 97:718, 2005. (3) A. Moretti et al. Int. J. Food Microbiol. 118:158, 2007.


2000 ◽  
Vol 46 (9) ◽  
pp. 1464-1470 ◽  
Author(s):  
Alla Lishanski

Abstract Background: New methods are required for the exploration of the human genome by discovering sequence variations. This study evaluated the performance of a new method for screening a large number of samples for several DNA polymorphisms. Methods: We used a homogeneous method based on inhibition of spontaneous branch migration by any sequence difference between two molecules of PCR-amplified DNA. A set of four PCR primers is required: a forward primer, either biotinylated or labeled with digoxigenin, and two reverse primers that share a priming domain but have different “tail” sequences at their 5′ ends. After PCR amplification, denaturation and reannealing of the single DNA strands produce doubly labeled cruciform structures, which dissociate by strand exchange. The presence of two different alleles in a sample causes complete inhibition of dissociation, and the association of biotin and digoxigenin is homogeneously detected using luminescent oxygen channeling immunoassay. Results: The 90 samples of the Human Variation Panel (Coriell Cell Repositories) were screened for nine known single-nucleotide polymorphisms (SNPs) and one 5-bp deletion. The average signal-to-background ratio varied from ∼10 to 20. The frequency of the predominant allele for different SNPs varied from 51% to 88% overall. For some SNPs, it varied among the nine ethnic groups, e.g., 25–85% (average, 51%) for one SNP. The average heterozygosity varied from 0.17 to 0.54 and as much as 0.2–0.9 (average, 0.54) for one of the SNPs. Conclusion: The method allows simple and rapid screening of a large number of samples for the presence of multiple alleles.


Genetics ◽  
2003 ◽  
Vol 163 (3) ◽  
pp. 1123-1134 ◽  
Author(s):  
Y L Zhu ◽  
Q J Song ◽  
D L Hyten ◽  
C P Van Tassell ◽  
L K Matukumalli ◽  
...  

Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the &gt;76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency &gt;0.10) SNPs, were identified.


2017 ◽  
Vol 48 (3) ◽  
pp. 127-141 ◽  
Author(s):  
Mohammed Baqur S. Al-Shuhaib ◽  
Rawan A. Al-Fihan ◽  
Ali A. Al-Qutbi ◽  
Tahreer M. Al-Thuwaini

Abstract This study was conducted to describe the genetic polymorphism within the bovine diacylglycerol acyltransferase 2 (DGAT2) gene and 5′-UTR of butyrophilin (BTN) gene by several in vitro tools, as well as to predict their consequences using several in silico tools. After withdrawing blood, extracting DNA, and designing specific polymerase chain reaction (PCR) primers, single-stranded conformation polymorphism (SSCP) and PCR experiments were performed. Each different SSCP set was sequenced and analyzed. Two genotypes were detected with two alleles. Concerning DGAT2, the AA genotype was the most common, and seven single nucleotide polymorphisms (SNPs) were found in the AB genotype while four SNPs were found in the AA genotype. The only coding SNP (p.Ala7Val) was found in the AB genotype. Concerning BTN, the AB genotype was the most common, and twenty-two novel SNPs were detected in the AB genotype, while six SNPs were observed in the AA genotype. The effect of the observed coding and noncoding SNPs was computationally analyzed. It was shown that the coding SNP, p.Ala7Val, was predicted to have functional consequences on the DGAT2 protein structure and function. Several outcomes were deduced from several noncoding SNPs in both genetic fragments studied. This study determines the pattern of polymorphism within the DGAT2 and BTN genes to conceive their consequences within Holstein breed.


2004 ◽  
Vol 40 ◽  
pp. 157-167 ◽  
Author(s):  
Maria Nilsson ◽  
Karin Dahlman-Wright ◽  
Jan-Åke Gustafsson

For several decades, it has been known that oestrogens are essential for human health. The discovery that there are two oestrogen receptors (ERs), ERalpha and ERbeta, has facilitated our understanding of how the hormone exerts its physiological effects. The ERs belong to the family of ligand-activated nuclear receptors, which act by modulating the expression of target genes. Studies of ER-knockout (ERKO) mice have been instrumental in defining the relevance of a given receptor subtype in a certain tissue. Phenotypes displayed by ERKO mice suggest diseases in which dysfunctional ERs might be involved in aetiology and pathology. Association between single-nucleotide polymorphisms (SNPs) in ER genes and disease have been demonstrated in several cases. Selective ER modulators (SERMs), which are selective with regard to their effects in a certain cell type, already exist. Since oestrogen has effects in many tissues, the goal with a SERM is to provide beneficial effects in one target tissue while avoiding side effects in others. Refined SERMs will, in the future, provide improved therapeutic strategies for existing and novel indications.


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