scholarly journals Therhg1-a(Rhg1low-copy) nematode resistance source harbors a copia-family retrotransposon within theRhg1-encoded α-SNAP gene

2019 ◽  
Author(s):  
Adam M. Bayless ◽  
Ryan W. Zapotocny ◽  
Shaojie Han ◽  
Derrick J. Grunwald ◽  
Kaela K. Amundson ◽  
...  
Keyword(s):  
Copy Number ◽  
Soybean Cyst Nematode ◽  
Nematode Resistance ◽  
Single Copy ◽  
Protein Abundance ◽  
Genomic Context ◽  
Reading Frame ◽  
Gene Block ◽  
Intron 1 ◽  
Scn Resistance

AbstractSoybean growers widely use theResistance toHeteroderaglycines1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN).Rhg1is a tandemly repeated four gene block. Two classes of SCN resistance-conferringRhg1haplotypes are recognized:rhg1-a(“Peking-type”, low copy number, 3 or fewerRhg1repeats) andrhg1-b(“PI 88788-type”, high copy number, 4 or moreRhg1repeats). Therhg1-aandrhg1-bhaplotypes encode α-SNAP (alpha-SolubleNSFAttachmentProtein) variants α-SNAPRhg1LC and α-SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report thatrhg1-asoybean accessions harbor a copia retrotransposon within theirRhg1 Glyma.18G022500(α-SNAP-encoding) gene. We termed this retrotransposon “RAC”, forRhg1alpha-SNAPcopia. Soybean carries multipleRAC-like retrotransposon sequences. TheRhg1 RACinsertion is in theGlyma.18G022500genes of all truerhg1-ahaplotypes we tested and was not detected in any examinedrhg1-borRhg1WT(single-copy) soybeans.RACis an intact element residing within intron 1, anti-sense to therhg1-a α-SNAPopen reading frame.RAChas intrinsic promoter activities, but overt impacts ofRACon transgenic α-SNAPRhg1LC mRNA and protein abundance were not detected. From the nativerhg1-a RAC+genomic context, elevated α-SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAPRhg1HC (whoserhg1-bdoes not carryRAC). Using a SoySNP50K SNP corresponding withRACpresence, just ∼42% of USDA accessions bearing previously identifiedrhg1-aSoySNP50K SNP signatures harbor theRACinsertion. Subsequent analysis of several of these putativerhg1-aaccessions lackingRACrevealed that none encodedα-SNAPRhg1LC, and thus they are notrhg1-a.rhg1-ahaplotypes are of rising interest, withRhg4, for combating SCN populations that exhibit increased virulence against the widely usedrhg1-bresistance. The present study reveals another unexpected structural feature of manyRhg1loci, and a selectable feature that is predictive ofrhg1-ahaplotypes.

Identification of novel haplotype of a cyst nematode resistance gene, GmSNAP18 in soybean [Glycine max (L.) Merr.]

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Ik-Young Choi ◽  
Prakash Basnet ◽  
Hana Yoo ◽  
Neha Samir Roy ◽  
Rahul Vasudeo Ramekar ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Gene Families ◽  
Nematode Resistance ◽  
Cyst Nematode ◽  
Soybean Breeding ◽  
Resistant Varieties ◽  
Soybean Genotypes ◽  
Glycine Max L ◽  
Scn Resistance

Soybean cyst nematode (SCN) is one of the most damaging pest of soybean. Discovery and characterization of the genes involved in SCN resistance are important in soybean breeding. Soluble NSF attachment protein (SNAP) genes are related to SCN resistance in soybean. SNAP genes include five gene families, and 2 haplotypes of exons 6 and 9 of SNAP18 are considered resistant to the SCN. In present study the haplotypes of GmSNAP18 were surveyed and chacterized in a total of 60 diverse soybean genotypes including Korean cultivars, landraces, and wild-types. The target region of exons 6 and 9 in GmSNAP18 region was amplified and sequenced to examine nucleotide variation. Characterization of 5 haplotypes identified in present study for the GmSNAP18 gene revealed two haplotypes as resistant, 1 as susceptible and two as novel. A total of twelve genotypes showed resistant haplotypes, and 45 cultivars were found susceptible. Interestingly, the two novel haplotypes were present in 3 soybean lines. The information provided here about the haplotypic variation of GmSNAP18 gene can be further explored for soybean breeding to develop resistant varieties.

Identification of the full-length Hs1pro-1 coding sequence and preliminary evaluation of soybean cyst nematode resistance in soybean transformed with Hs1pro-1 cDNA

2007 ◽  
Vol 85 (4) ◽  
pp. 437-441 ◽  
Author(s):  
Michael D. McLean ◽  
Gordon J. Hoover ◽  
Bonnie Bancroft ◽  
Amina Makhmoudova ◽  
Shawn M. Clark ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Soybean Cyst Nematode ◽  
Nematode Resistance ◽  
Cyst Nematode ◽  
Full Length ◽  
Preliminary Evaluation ◽  
Chain Reaction ◽  
Coding Sequence ◽  
Scn Resistance ◽  
Polymerase Chain

The Hs1pro-1 gene reportedly confers resistance to the beet cyst nematode in wild beet and sugar beet. Here, we tested the hypothesis that Hs1pro-1 confers resistance in soybean against the soybean cyst nematode (SCN). The full-length Hs1pro-1 coding sequence, which encodes a predicted polypeptide of 490 amino acids, was first acquired then expressed in ‘Westag’ soybean using a constitutive octopine synthase – mannopine synthase promoter. Thirty T0 lines that successfully expressed the Hs1pro-1 gene, as indicated by both polymerase chain reaction and reverse transcriptase – polymerase chain reaction analyses, were generated. Bioassay of the T1 progeny from these lines revealed that only five T0 lines grew normally and exhibited a high degree of SCN resistance. On average, these T1 transgenic progeny were about 70% more resistant to SCN than susceptible control cultivars. These preliminary data suggest that Hs1pro-1 is a promising candidate for genetically engineering SCN resistance in elite, locally adapted soybean cultivars.

scholarly journals Copy Number Quantification for the Soybean Cyst Nematode Resistance Locus rhg1 in the Soybean Varieties of Taiwan

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1346
Author(s):  
Cheng-Chun Huang ◽  
Jiue-in Yang ◽  
Kuo-Lung Chou ◽  
Chen-Hsiang Lin ◽  
Hao-Xun Chang
Keyword(s):  
Copy Number ◽  
Soybean Cyst Nematode ◽  
Crop Protection ◽  
Nematode Resistance ◽  
The United States ◽  
Cyst Nematode ◽  
Agricultural Product ◽  
Resistance Locus ◽  
Nucleotide Polymorphisms ◽  
Market Needs

Disease resistance is one of the most successful strategies in crop protection. For example, the implementation of PI 88788 type resistance, which contains high copy numbers of Resistance to Heterodera glycines 1 (rhg1) loci, into the commercial soybean varieties of the United States has significantly reduced the yield losses caused by soybean cyst nematode (SCN, H. glycines). Vegetable soybean, or edamame, has become a major exporting agricultural product in Taiwan with an annual revenue over $80 million USD since 2017. Several local varieties have been developed to fulfill the market needs such as the traits of flavor and sweetness. However, it remains unclear if the historical breeding programs ever incorporated rhg1 resistance into the varieties of Taiwan. This study applied the TaqMan qPCR method to measure the fluorescent signals specific to the rhg1 locus on the chromosome 18 of soybean, and the ratio of VIC and FAM signals were analyzed to predict the rhg1 copy number in the 21 soybean varieties of Taiwan. The results indicated the copy number and the single nucleotide polymorphisms of the 21 soybean varieties were identical to the susceptible soybean variety ‘Williams 82’. As importation of soybean will be continuously needed to fulfill the market and because SCN is absent in the soybean fields of Taiwan, lacking rhg1 resistance in the local soybean varieties may put the edamame industry at risk and early implementation of SCN resistance in the breeding program, alongside the application of quarantine regulations, will be the key to maintain the SCN-free status and to sustain the edamame industry in Taiwan.

scholarly journals The soybean Rhg1 amino acid transporter protein becomes abundant along the SCN penetration path and impacts ROS generation

2020 ◽  
Author(s):  
Shaojie Han ◽  
John M. Smith ◽  
Yulin Du ◽  
Andrew F. Bent
Keyword(s):  
Amino Acid ◽  
Soybean Cyst Nematode ◽  
Amino Acid Transporter ◽  
Ros Generation ◽  
Protein Abundance ◽  
Root Cells ◽  
Transporter Protein ◽  
Scn Resistance ◽  
Soybean Resistance ◽  
Acid Transporter

ABSTRACTRhg1 mediates soybean resistance to soybean cyst nematode. Glyma.18G022400, one of three resistance-conferring genes at the complex Rhg1 locus, encodes the putative amino acid transporter AATRhg1 whose mode of action is largely unknown. We discovered that AATRhg1 protein abundance increases 7- to 15-fold throughout root cells penetrated by SCN. These root cells develop increased abundance of vesicles and larger vesicle-like bodies. AATRhg1 was often associated with these vesicles. AATRhg1 abundance remained low in syncytia (plant reprogrammed feeding cells), unlike the Rhg1 α-SNAP protein whose abundance was previously shown to increase in syncytia. In N. benthamiana, if soybean AATRhg1 was present, oxidative stress promoted formation of larger macrovesicles and they contained AATRhg1. AATRhg1 was found to interact with GmRBOHC2, a soybean ortholog of Arabidopsis RBOHD previously found to exhibit upregulated expression upon SCN infection. Reactive oxygen species (ROS) generation was more elevated when AATRhg1 and GmRBOHC2 abundance were co-expressed. These findings suggest that AATRhg1 contributes to SCN resistance along the penetration path as SCN invades the plant, and does so at least in part by interactions with GmRBOHC2 that increase ROS production. The study also shows that Rhg1 resistance functions via at least two spatially and temporally separate modes of action.

scholarly journals A Standard Greenhouse Method for Assessing Soybean Cyst Nematode Resistance in Soybean: SCE08 (Standardized Cyst Evaluation 2008)

2009 ◽  
Vol 10 (1) ◽  
pp. 33 ◽  
Author(s):  
T. L. Niblack ◽  
Gregory L. Tylka ◽  
Prakash Arelli ◽  
Jason Bond ◽  
Brian Diers ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Nematode Resistance ◽  
Cyst Nematode ◽  
Yield Losses ◽  
Resistant Cultivars ◽  
Scn Resistance ◽  
Soybean Cyst Nematode Resistance

The tactic of choice for managing soybean cyst nematode (SCN) in infested fields is the use of resistant cultivars. Because expression of SCN resistance is dependent on the occurrence and frequencies of genes for virulence in SCN populations, labeling of SCN-resistant cultivars can be difficult and, occasionally, highly misleading, leading to unanticipated yield losses. The authors' objective was to offer a set of standards for assessing and labeling SCN-resistant cultivars that would allow farmers to make direct comparisons of cultivars. Accepted for publication 15 March 2009. Published 13 May 2009.

scholarly journals Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode

2014 ◽  
Vol 165 (2) ◽  
pp. 630-647 ◽  
Author(s):  
David E. Cook ◽  
Adam M. Bayless ◽  
Kai Wang ◽  
Xiaoli Guo ◽  
Qijian Song ◽  
...  
Keyword(s):  
Copy Number ◽  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Coding Sequence ◽  
Soybean Resistance ◽  
Methylation Patterns

scholarly journals Arabinanase A from Pseudomonas fluorescens subsp. cellulosa exhibits both an endo- and an exo- mode of action

1997 ◽  
Vol 323 (2) ◽  
pp. 547-555 ◽  
Author(s):  
Vincent A. McKIE ◽  
Gary W. BLACK ◽  
Sarah J. MILLWARD-SADLER ◽  
Geoffrey P. HAZLEWOOD ◽  
Judith I. LAURIE ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Mode Of Action ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Genomic Library ◽  
Glycosyl Hydrolase ◽  
Single Copy ◽  
Terminal Sequence ◽  
Reading Frame ◽  
Significant Release

Pseudomonas fluorescens subsp. cellulosa expressed arabinanase activity when grown on media supplemented with arabinan or arabinose. Arabinanase activity was not induced by the inclusion of other plant structural polysaccharides, and was repressed by the addition of glucose. The majority of the Pseudomonas arabinanase activity was extracellular. Screening of a genomic library of P. fluorescens subsp. cellulosa DNA constructed in Lambda ZAPII, for recombinants that hydrolysed Red-dyed arabinan, identified five arabinan-degrading plaques. Each of the phage contained the same Pseudomonas arabinanase gene, designated arbA, which was present as a single copy in the Pseudomonas genome. The nucleotide sequence of arbA revealed an open reading frame of 1041 bp encoding a protein, designated arabinanase A (ArbA), of Mr 39438. The N-terminal sequence of ArbA exhibited features typical of a prokaryotic signal peptide. Analysis of the primary structure of ArbA indicated that, unlike most Pseudomonas plant cell wall hydrolases, it did not contain linker sequences or have a modular structure, but consisted of a single catalytic domain. Sequence comparison between the Pseudomonas arabinanase and proteins in the SWISS-PROT database showed that ArbA exhibits greatest sequence identity with arabinanase A from Aspergillus niger, placing the enzyme in glycosyl hydrolase Family 43. The significance of the differing substrate specificities of enzymes in Family 43 is discussed. ArbA purifed from a recombinant strain of Escherichia coli had an Mr of 34000 and an N-terminal sequence identical to residues 32–51 of the deduced sequence of ArbA, and hydrolysed linear arabinan, carboxymethylarabinan and arabino-oligosaccharides. The enzyme displayed no activity against other plant structural polysaccharides, including branched sugar beet arabinan. ArbA produced almost exclusively arabinotriose from linear arabinan and appeared to hydrolyse arabino-oligosaccharides by successively releasing arabinotriose. ArbA and the Aspergillus arabinanase mediated a decrease in the viscosity of linear arabinan that was associated with a significant release of reducing sugar. We propose that ArbA is an arabinanase that exhibits both an endo- and an exo- mode of action.

An ubiquitously expressed gene 3.5 kilobases upstream of the glycerol-3-phosphate dehydrogenase gene in mice

1989 ◽  
Vol 9 (3) ◽  
pp. 935-945
Author(s):  
L A Johnston ◽  
M A Kotarski ◽  
D J Jerry ◽  
L P Kozak
Keyword(s):  
Sequence Similarity ◽  
Single Copy ◽  
Transcriptional Unit ◽  
Chromosome 15 ◽  
Glycerol Phosphate ◽  
Reading Frame ◽  
Dehydrogenase Gene ◽  
New Gene ◽  
Or Gene ◽  
Glycerol 3 Phosphate Dehydrogenase

While studying the organization of the mouse glycerol-phosphate dehydrogenase gene (Gdc-1 on chromosome 15), we identified a novel transcriptional unit located only 3.4 kilobases (kb) upstream of the 5' end of the Gdc-1 gene. This gene has been provisionally named D15Kz1. The unusual proximity of these two genes led us to investigate the pattern of expression and sequence characteristics of the new gene for comparison with those of Gdc-1. D15Kz1 was found to have transcripts of 3.2 and 3.4 kb in length. The 3.4-kb transcript was expressed at low levels in all tissues examined, whereas the 3.2-kb transcript was detected only in the cerebral cortex and the brown fat. D15Kz1 and Gdc-1 are not coordinately regulated, as evidenced by the characteristics of their expression in several tissues and in differentiating 3T3-F442A adipocyte cultures. A cDNA sequence of 3,105 bases isolated from an embryonal carcinoma lambda gt10 cDNA library had a large open reading frame of 461 amino acids at one end followed by 1.6 kb of sequence with multiple stop codons. Algorithms used to search the protein and nucleic acid data bases detected no significant sequence similarity to any other protein or gene. Southern blot analysis of genomic DNA using the D15Kz1 cDNA as a probe indicated that D15Kz1 is a single-copy gene in the mouse genome and that it is conserved in humans, rats, and chickens. This conservation of gene sequences suggests that D15Kz1 encodes a protein with an important cellular function.

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.

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