scholarly journals Functional Screening Yields a New β-1,4-Endoglucanase Gene from Heterodera glycines that May be the Product of Recent Gene Duplication

2001 ◽  
Vol 14 (1) ◽  
pp. 63-71 ◽  
Author(s):  
Yitang Yan ◽  
Geert Smant ◽  
Eric Davis
Keyword(s):  
Gene Duplication ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Gene Clusters ◽  
Genomic Clone ◽  
Functional Screening ◽  
Cellulolytic Activity ◽  
Endoglucanase Gene ◽  
Recent Gene Duplication ◽  
Flanking Regions

Clones with secreted cellulolytic activity were identified when a cDNA library constructed from poly A(+) RNA of preparasitic second-stage juveniles of Heterodera glycines, the soybean cyst nematode, was expressed in the Escherichia coli SOLR strain and overlaid with a carboxymethylcellulose (CMC) substrate. Twenty CMC-degrading clones were analyzed, and all were either identical or strongly similar to a β-1,4-endoglucanase gene (HG-eng-2), previously isolated from H. glycines. A subgroup of identical “HG-eng-2-like” clones had considerable differences in the 5′ untranslated region compared with HG-eng-2 and were designated HG-eng-3. One H. glycines genomic clone contained HG-eng-2 and HG-eng-3 full-length genes, separated by a distance of approximately 8 kb, and a second genomic clone contained two copies of HG-eng-2, separated by approximately 6.5 kb, suggesting the presence of endoglucanase gene clusters in H. glycines. The HG-eng-2 and HG-eng-3 genes were in opposite transcriptional orientation, with considerable nucleotide differences in their 5′ flanking regions. The highly conserved nucleotide sequence in the introns and exons and their close proximity within the genome suggest that HG-eng-2 and HG-eng-3 are the products of recent gene duplication and inversion.

scholarly journals Weeds Hosting the Soybean Cyst Nematode (Heterodera glycines Ichinohe): Management Implications in Agroecological Systems

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 146
Author(s):  
Leonardo F. Rocha ◽  
Karla L. Gage ◽  
Mirian F. Pimentel ◽  
Jason P. Bond ◽  
Ahmad M. Fakhoury
Keyword(s):  
Weed Management ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Integrated Management ◽  
Cropping System ◽  
Cyst Nematode ◽  
Weed Species ◽  
Initial Inoculum ◽  
Herbicide Resistant ◽  
Sites Of Action

The soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is a major soybean-yield-limiting soil-borne pathogen, especially in the Midwestern US. Weed management is recommended for SCN integrated management, since some weed species have been reported to be hosts for SCN. The increase in the occurrence of resistance to herbicides complicates weed management and may further direct ecological–evolutionary (eco–evo) feedbacks in plant–pathogen complexes, including interactions between host plants and SCN. In this review, we summarize weed species reported to be hosts of SCN in the US and outline potential weed–SCN management interactions. Plants from 23 families have been reported to host SCN, with Fabaceae including most host species. Out of 116 weeds hosts, 14 species have known herbicide-resistant biotypes to 8 herbicide sites of action. Factors influencing the ability of weeds to host SCN are environmental and edaphic conditions, SCN initial inoculum, weed population levels, and variations in susceptibility of weed biotypes to SCN within a population. The association of SCN on weeds with relatively little fitness cost incurred by the latter may decrease the competitive ability of the crop and increase weed reproduction when SCN is present, feeding back into the probability of selecting for herbicide-resistant weed biotypes. Therefore, proper management of weed hosts of SCN should be a focus of integrated pest management (IPM) strategies to prevent further eco–evo feedbacks in the cropping system.

Efficacy of the fungi Hirsutella minnesotensis and H. rhossiliensis from liquid culture for control of the soybean cyst nematode Heterodera glycines

Nematology ◽  
2005 ◽  
Vol 7 (1) ◽  
pp. 149-157 ◽  
Author(s):  
Shufen Liu ◽  
Senyu Chen
Keyword(s):  
Heat Treatment ◽  
Population Density ◽  
Soybean Cyst Nematode ◽  
Liquid Culture ◽  
Heterodera Glycines ◽  
Nematode Population ◽  
Solid Culture ◽  
Nematode Population Density ◽  
Biological Control Potential ◽  
Shoot Weight

AbstractHirsutella minnesotensis and H. rhossiliensis are endoparasites of nematodes, and their biological control potential against Heterodera glycines when cultured and applied on corn grits has been reported. In this study, the potential of liquid cultures of the two fungi was evaluated in two glasshouse experiments. Both liquid culture at 0.2, 0.4 and 0.8 g of fresh mycelium/300 cm3 soil (per pot) and solid culture at 1% (corn grits: soil, w/w) reduced nematode egg population densities in both autoclaved and unheated soils as compared with soil-only control or corn-grits control. However, the liquid culture at 0.2–0.8 g of mycelium/pot appeared to be more effective in reducing the nematode population than the solid culture of 1%. Hirsutella rhossiliensis resulted in lower nematode population density than H. minnesotensis only in unheated soil in one experiment. The soil heat treatment generally increased the nematode population density but did not affect percentage reduction of the nematode population density as compared with respective controls, except that reduction by H. rhossiliensis was greater in unheated soil than heat-treated soil in one experiment. Percentage of second-stage juveniles (J2) parasitised by fungi at the end of the experiment (60 days after planting) was generally higher with H. minnesotensis than with H. rhossiliensis. The percentage parasitism was positively correlated with initial fungal inoculation level. The soil heat treatment increased fungal parasitism in one experiment but not in the other. Plant growth was unaffected by treatments except that the soil heat treatment increased plant shoot weight as compared with unheated soil in one experiment.

AAC Richard Soybean

2022 ◽  
Author(s):  
Kangfu Yu ◽  
Lorna Woodrow ◽  
M. Chun Shi
Keyword(s):  
Glycine Max ◽  
Research And Development ◽  
Soybean Cyst Nematode ◽  
Protein Concentration ◽  
Heterodera Glycines ◽  
Cyst Nematode ◽  
Processing Quality ◽  
Food Grade ◽  
High Protein Concentration ◽  
Glycine Max L

AAC Richard is a food grade soybean [Glycine max (L.) Merr] cultivar with yellow hilum, high protein concentration, and good processing quality for foreign and domestic soymilk, tofu, and miso markets. It has resistance to SCN (soybean cyst nematode) (Heterodera Glycines Ichinohe). AAC Richard was developed at the Agriculture and Agri-Food Canada (AAFC) Harrow Research and Development Centre (Harrow-RDC), Harrow, Ontario and is adapted to areas of southwest Ontario with 3100 or more crop heat units and has a relative maturity of 2.3 (MG 2.3).

Response of soybean genotypes from Northeast China to Heterodera glycines races 4 and 5, and characterisation of rhg1 and Rhg4 genes for soybean resistance

Nematology ◽  
2021 ◽  
pp. 1-13
Author(s):  
Minghui Huang ◽  
Ruifeng Qin ◽  
Chunjie Li ◽  
Mingze Wang ◽  
Ye Jiang ◽  
...  
Keyword(s):  
Northeast China ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Pcr Amplification ◽  
Molecular Characteristics ◽  
Breeding Lines ◽  
Soybean Genotypes ◽  
The Usa ◽  
Local Breeding ◽  
Scn Resistance

Summary Soybean cyst nematode (SCN, Heterodera glycines) is a devastating plant-parasitic nematode worldwide. Two SCN races, race 4 (HG Type 1.2.3.5.6.7) and race 5 (HG Type 2.5.7), with increased virulence were previously identified in Northeast China. To obtain new resistance sources to these SCN populations, the response of 62 genotypes, including 51 local varieties and breeding lines, and 11 indicator lines for SCN race and HG Type identification, were evaluated. Four new primers in the regions of two loci of GmSHMT08 (Rhg4) and GmSNAP18 (rhg1) were designed for PCR amplification and subsequent sequencing to characterise haplotypes instead of genome resequencing. Results indicated three haplotypes among 51 local genotypes; there were 26 lines in Haplotype I carrying both the rhg1-a and Rhg4-a resistant loci as in ‘Peking’, 13 lines in Haplotype II containing only the resistant rhg1-a locus but Rhg4-b susceptible loci, and 12 lines in Haplotype III with rhg1-c and Rhg4-b susceptible loci. Interestingly, there was no ‘PI 88788’-type resistance identified in Northeast China, although it accounts for 90% of sources in the USA. Two local breeding lines in Haplotype I displayed resistance to both SCN races. The resistance lines carried higher copy number (>1) of the tandem duplication at the rhg1 locus compared with susceptible lines (⩽1). The combination of the two microsatellite markers, Sat_162 on Chr 8 and 590 on Chr 18, distinguished the three haplotypes and predicted the resistance/susceptibility for SCN race 5. The knowledge of the phenotypes and molecular characteristics of 51 local breeding lines in Northeast China will accelerate the utilisation of sources for broad-based SCN resistance and marker-assisted selection.

scholarly journals Taxonomic Resolution of the Nematophagous Fungal Isolate ARF18 via Genome Sequencing

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Sandeep Sharma ◽  
Alex Z. Zaccaron ◽  
John B. Ridenour ◽  
Amy Bradshaw ◽  
Terry L. Kirkpatrick ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Novel Species ◽  
Biological Control Agent ◽  
Draft Genome ◽  
Control Agent ◽  
Nematophagous Fungus ◽  
Cyst Nematode ◽  
Fungal Isolate ◽  
Taxonomic Resolution

ABSTRACT The taxonomically uncharacterized nematophagous fungus ARF18, which parasitizes cysts, juveniles, and adults of the soybean cyst nematode (Heterodera glycines), was proposed as a nematode biological control agent in 1991. A 46.3-Mb draft genome sequence of this fungus is presented, and a tentative taxonomic identification as a novel species of Brachyphoris is proposed.

scholarly journals The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes

2018 ◽  
Author(s):  
Rick Masonbrink ◽  
Tom R. Maier ◽  
Usha Muppiral ◽  
Arun S. Seetharam ◽  
Etienne Lord ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Control Strategies ◽  
Cyst Nematode ◽  
Effective Control ◽  
Evolutionary Mechanisms ◽  
Long Read ◽  
Soybean Plants ◽  
Parasitism Genes ◽  
Nematode Genomes

AbstractHeterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulentH. glycinespopulations. The parasitic success ofH. glycinesrelies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted byH. glycinesinto host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. Here, we use PacBio long-read technology to assemble aH. glycinesgenome of 738 contigs into 123Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7Mb), and horizontal gene transfer events (151 genes). Using previously published effector sequences, the newly generatedH. glycinesgenome, and comparisons to other nematode genomes, we investigate the evolutionary mechanisms responsible for the emergence and diversification of effector genes.

scholarly journals Discovery and Biosynthesis of Natural Products from New Zealand Soil Metagenome Libraries

2021 ◽  
Author(s):  
◽  
Luke Stevenson
Keyword(s):  
Natural Products ◽  
New Zealand ◽  
Heterologous Expression ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Coli Strain ◽  
Functional Screening ◽  
Functional Difference ◽  
Biosynthetic Pathways ◽  
New Members

<p>Antibiotic discovery rates dramatically declined following the “golden age” of the 1940’s to the 1960’s. The platforms that underpinned that age of discovery rested upon laboratory cultivation of a small clade of bacteria, the actinomycetes, primarily isolated from soil environments. Fermentation extracts of these isolated bacteria have provided the majority of antibiotics and anticancer small molecules still used today. By applying modern genetic analysis techniques to these same environmental sources that have previously yielded such success, we can uncover new biosynthetic pathways, and bioactive compounds. The work described in this thesis investigated New Zealand soil metagenomes for this purpose.  Four large metagenome libraries were constructed from the microbiomes of diverse soil environments. These were then interrogated by a functional screening approach in a knockout Escherichia coli strain, to recover a large collection of the biosynthetic gene clusters responsible for bacterial secondary metabolite production. Using different modes of bioinformatic analysis, these gene clusters were demonstrated to have both phylogenetic divergence, and functional difference from bacterial biosynthesis pathways previously discovered from culture based studies.  Two additional biosynthetic pathways were recovered from one of these metagenome libraries, and in each case found to have novel genetic features. These gene clusters were further studied by heterologous expression within Streptomyces albus production hosts. One of these gene clusters produced small aromatic polyketide compounds, the structure of one of which was solved by chemical analytic techniques, and found to be a new chemical entity.  The second gene cluster was demonstrated to have similarity to known aureolic acid biosynthesis gene clusters – a class of potent anticancer natural products. Heterologous expression resulted in the production of many metabolites, two of which were characterised and found to be new members of this chemical class.  The research in this thesis both validates the use of metagenomic analysis for future natural product discovery efforts, and adds to a growing body of evidence that understudied clades of bacteria have an untapped biosynthetic potential that can be accessed by metagenomic methods.</p>

Characterization of Virulence Phenotypes of Soybean Cyst Nematode (Heterodera glycines) Populations in North Dakota

2021 ◽  
Author(s):  
Intiaz Amin Chowdhury ◽  
Guiping Yan ◽  
Addison Plaisance ◽  
sam markell
Keyword(s):  
North Dakota ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
The United States ◽  
Cyst Nematode ◽  
Sources Of Resistance ◽  
Resistance Sources ◽  
First Time ◽  
Primary Strategy

Soybean cyst nematode (SCN; Heterodera glycines) continues to be the greatest threat to soybean production in the United States. Since host resistance is the primary strategy used to control SCN, knowledge of SCN virulence phenotypes (HG types) is necessary for choosing sources of resistance for SCN management. To characterize SCN virulence phenotypes in North Dakota (ND), a total of 419 soybean fields across 22 counties were sampled during 2015, 2016, and 2017. SCN was detected in 42% of the fields sampled and population densities in these samples ranged from 30 to 92,800 eggs and juveniles per 100 cm3 of soil. The SCN populations from some of the infested fields were virulence phenotyped with seven soybean indicator lines and a susceptible check (Barnes) using the HG type tests. Overall, 73 SCN field populations were successfully virulence phenotyped. The HG types detected in ND were HG type 0 (frequency rate: 36%), 7 (27%), 2.5.7 (19%), 5.7 (11%), 1.2.5.7 (4%), and 2.7 (2%). However, prior to this study only HG type 0 was detected in ND. The designation of each of the HG types detected was then validated in this study by repeating the HG type tests for thirty-three arbitrarily selected samples. This research for the first time reports several new HG types detected in ND and confirms that the virulence of SCN populations is shifting and overcoming resistance, highlighting the necessity of utilization of different resistance sources, rotation of resistance sources, and identification of novel resistance sources for SCN management in ND.

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