scholarly journals Combining Targeted Metabolite Analyses and Transcriptomics to Reveal Specific Chemical Composition and Associated Genes in Resistant Soybean Infected with Soybean Cyst Nematode

2020 ◽  
Author(s):  
Xue Shi ◽  
Qiansi Chen ◽  
Shiming Liu ◽  
Jiajun Wang ◽  
Deliang Peng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Cyst Nematode ◽  
Sphingolipid Metabolism ◽  
Resistant Variety ◽  
Biological Processes ◽  
Specific Chemical ◽  
Kegg Pathways ◽  
Before And After

Abstract Background: Soybean cyst nematode Heterodera glycines is one of the most devastating pathogens on soybean and causes severe annual yield loss worldwide. Different soybean varieties exhibit different responses to soybean cyst nematode infection at various levels, such as genomic, transcriptional, proteomic, and metabolomic levels. However, there were not yet any reports on the differential responses of resistant and susceptible soybeans infected with soybean cyst nematode by combining the metabolomic analyses and transcriptomics.Results: In this study, a highly-resistant variety PI 437654 and three susceptible varieties Williams 82, Zhonghuang 13 and Hefeng 47 were used as the test materials to clarify the differences in metabolites and transcriptomics between resistant and susceptible soybeans before and after SCN infection. A local metabolite-calibrated database was used to identify potential differential metabolites, and the differences of metabolites and metabolic pathways were compared between the resistant and susceptible soybean varieties after inoculation with SCN. Totally, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories including the metabolites/pathways overlapped among resistant and susceptible soybeans, specific in susceptible or resistant soybeans, respectively. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specifically differential metabolites such as significantly up-regulated nicotine and down-regulated D-aspartic acid, and their involved KEGG pathways such as tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolisms, sphingolipid metabolism and arginine biosynthesis were significantly changed and abundantly enriched in the resistant soybean, and likely played pivotal roles in defensing against SCN infection. Three key metabolites including N-acetyltranexamic acid, nicotine, and D, L-typotophan, which were found to be significantly up-regulated in the resistant soybean PI437654 infected by SCN, classified into two types and used for combination analyses with the transcriptomic expression profiling. Associated genes were predicted, and suggested their likely biological processes, cellular component, molecular function and involved pathways. Conclusions: Our results not only found out the potential novel metabolites and associated genes in the resistant response of soybean to soybean cyst nematode, but also provided new insights into the interactions between soybean and soybean cyst nematode.

scholarly journals Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xue Shi ◽  
Qiansi Chen ◽  
Shiming Liu ◽  
Jiajun Wang ◽  
Deliang Peng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Sphingolipid Metabolism ◽  
Soybean Variety ◽  
Cyst Nematodes ◽  
Specific Chemical ◽  
Kegg Pathways ◽  
Before And After ◽  
Soybean Cyst Nematodes

Abstract Background Soybean cyst nematode, Heterodera glycines, is one of the most devastating pathogens of soybean and causes severe annual yield losses worldwide. Different soybean varieties exhibit different responses to H. glycines infection at various levels, such as the genomic, transcriptional, proteomic and metabolomic levels. However, there have not yet been any reports of the differential responses of incompatible and compatible soybean varieties infected with H. glycines based on combined metabolomic and transcriptomic analyses. Results In this study, the incompatible soybean variety PI437654 and three compatible soybean varieties, Williams 82, Zhonghuang 13 and Hefeng 47, were used to clarify the differences in metabolites and transcriptomics before and after the infection with HG1.2.3.5.7. A local metabolite-calibrated database was used to identify potentially differential metabolites, and the differences in metabolites and metabolic pathways were compared between the incompatible and compatible soybean varieties after inoculation with HG1.2.3.5.7. In total, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories: metabolites/pathways overlapped in the incompatible and compatible soybeans, and metabolites/pathways specific to either the incompatible or compatible soybean varieties. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specific differential metabolites (such as significantly up-regulated nicotine and down-regulated D-aspartic acid) and their associated KEGG pathways (such as the tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolism, sphingolipid metabolism and arginine biosynthesis) were significantly altered and abundantly enriched in the incompatible soybean variety PI437654, and likely played pivotal roles in defending against HG1.2.3.5.7 infection. Three key metabolites (N-acetyltranexamic acid, nicotine and D,L-tryptophan) found to be significantly up-regulated in the incompatible soybean variety PI437654 infected by HG1.2.3.5.7 were classified into two types and used for combined analyses with the transcriptomic expression profiling. Associated genes were predicted, along with the likely corresponding biological processes, cellular components, molecular functions and pathways. Conclusions Our results not only identified potential novel metabolites and associated genes involved in the incompatible response of PI437654 to soybean cyst nematode HG1.2.3.5.7, but also provided new insights into the interactions between soybeans and soybean cyst nematodes.

scholarly journals Untargeted Metabolomics and Polyamine Profiling in Serum before and after Surgery in Colorectal Cancer Patients

Metabolites ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 487
Author(s):  
Yu Ra Lee ◽  
Ki-Yong An ◽  
Justin Jeon ◽  
Nam Kyu Kim ◽  
Ji Won Lee ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Metabolic Pathways ◽  
Sphingolipid Metabolism ◽  
Proline Metabolism ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Serum Samples ◽  
Physiological Alterations ◽  
Before And After ◽  
Colorectal Cancer Patients

Colorectal cancer is one of the most prevalent cancers in Korea and globally. In this study, we aimed to characterize the differential serum metabolomic profiles between pre-operative and post-operative patients with colorectal cancer. To investigate the significant metabolites and metabolic pathways associated with colorectal cancer, we analyzed serum samples from 68 patients (aged 20–71, mean 57.57 years). Untargeted and targeted metabolomics profiling in patients with colorectal cancer were performed using liquid chromatography-mass spectrometry. Untargeted analysis identified differences in sphingolipid metabolism, steroid biosynthesis, and arginine and proline metabolism in pre- and post-operative patients with colorectal cancer. We then performed quantitative target profiling of polyamines, synthesized from arginine and proline metabolism, to identify potential polyamines that may serve as effective biomarkers for colorectal cancer. Results indicate a significantly reduced serum concentration of putrescine in post-operative patients compared to pre-operative patients. Our metabolomics approach provided insights into the physiological alterations in patients with colorectal cancer after surgery.

scholarly journals Unique transcriptome and gene expression analysis of rice seedling reveals different cadmium response regulatory mechanisms between indica and japonica rice

2020 ◽  
Author(s):  
Shan Tong ◽  
Xin Luo ◽  
Hira Khanzada ◽  
Ghulam Mustafa Wassan ◽  
Licao Cui ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Rice Seedling ◽  
Resistant Variety ◽  
Japonica Rice ◽  
Biological Processes ◽  
Cd Stress ◽  
Metabolic Pathway Analysis ◽  
Improvement Programs ◽  
Rice Improvement ◽  
Different Response

Abstract Background: In general, the Cd content in indica rice is higher than that in japonica. However, the mechanism underlying this discrepancy has not been elucidated. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is highly important for rice improvement programs.Results: In this study, two varieties of rice, japonica 02428 and indica CH891, were continuously exposed to Cd, and seedlings of the two varieties at two critical stages (the 3rd and 5th day) were selected for dynamic gene analysis by the transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differentially expressed genes (DEGs) associated with Cd stress were detected on the 3rd day and 5th day, respectively. Furthermore, we divided these DEGs into three categories: SCR (sensitive variety with Cd-responsive), RCR (resistant variety with Cd-responsive) and CCR (common Cd-responsive). The enriched metabolic pathway analysis of DEGs preferentially expressed in a stage-specific and cultivar-specific manner showed that secondary metabolic processes were enriched in SCR, while protein metabolism and plant hormones were enriched in RCR. The diverted metabolic pathways might be the major reason for the different response mechanisms of Cd in indica and japonica rice.Conclusion: These results provide novel insights regarding the Cd response mechanism in rice seedlings between different varieties, and these important Cd-responsive DEGs were frequently involved in specific biological processes and metabolic pathways that might help to elucidate the mechanisms of the indica and japonica rice Cd response differences.

scholarly journals Increase in Soybean Cyst Nematode Virulence and Reproduction on Resistant Soybean Varieties in Iowa From 2001 to 2015 and the Effects on Soybean Yields

2017 ◽  
Vol 18 (3) ◽  
pp. 146-155 ◽  
Author(s):  
Michael T. McCarville ◽  
Christopher C. Marett ◽  
Mark P. Mullaney ◽  
Gregory D. Gebhart ◽  
Gregory L. Tylka
Keyword(s):  
Soybean Cyst Nematode ◽  
Field Experiments ◽  
Yield Loss ◽  
Plant Introduction ◽  
Cyst Nematode ◽  
Population Densities ◽  
Sources Of Resistance ◽  
Nematode Reproduction ◽  
Soybean Yield ◽  
Pi 88788

Management of the soybean cyst nematode (SCN) relies heavily on use of SCN-resistant soybean varieties to limit nematode reproduction and minimize yield loss. For Iowa, almost all SCN-resistant soybean varieties contain SCN resistance genes from a breeding line named Plant Introduction (PI) 88788. Iowa State University conducts experiments to evaluate numerous SCN-resistant and three to four SCN-susceptible soybean varieties in up to nine field experiments across Iowa each year. Data on SCN population density, virulence (SCN race and HG type), soybean yield, precipitation, and growing degree days from more than 25,000 four-row plots in field experiments conducted from 2001 to 2015 were analyzed to determine how these factors affected SCN reproduction and yield. SCN population densities were positively correlated with temperatures and negatively associated with precipitation during the growing seasons, indicating that SCN reproduction was greatest in hot, dry years. Over the years, virulence of SCN populations on PI 88788 increased in the fields in which the experiments were conducted, resulting in increased end-of-season SCN population densities and reduced yields of SCN-resistant soybean varieties with the PI 88788 source of resistance. These results indicate that soybean yield loss caused by SCN on resistant varieties with the common PI 88788 source of resistance likely will increase as virulence of SCN populations increases unless new sources of resistance become widely available and used in the future.

Yield loss caused by soybean cyst nematode, Heterodera glycines, in Iran

Nematology ◽  
2012 ◽  
Vol 14 (5) ◽  
pp. 589-593 ◽  
Author(s):  
Ramin Heydari ◽  
Zahra Tanha Maafi ◽  
Ebrahim Pourjam
Keyword(s):  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Heterodera Glycines ◽  
Block Design ◽  
Economic Importance ◽  
Cyst Nematode ◽  
Resistant Cultivar ◽  
Reproduction Rate ◽  
Seed Composition ◽  
Second Stage

The soybean cyst nematode, Heterodera glycines, is of major economic importance and widely distributed throughout the world. The effect of H. glycines HG Type 0 on seed yield of susceptible and resistant soybean cultivars was assessed with and without nematicide application in two naturally infested fields in Iran. Soybean cvs BP (susceptible) and DPX (resistant) were arranged in a randomised complete block design and fenamiphos 10G was used in-furrow as a treatment. The population levels of eggs and second-stage juveniles of H. glycines were determined in soil samples collected at planting and harvesting time. Although no above-ground symptoms of nematode infection were visible, mean yield was 48% greater for the resistant cultivar compared with the susceptible cultivar. The yield of cv. BP increased by 16% in plots treated with fenamiphos compared with untreated plots. The resistant cultivar suppressed the reproduction rate of H. glycines. Seed composition, including protein and oil, did not show significant differences between resistant and susceptible cultivars. This is the first demonstration of the yield loss caused by the soybean cyst nematode in Iran.

Effect of Diseases on Soybean Yield in the Top Eight Producing Countries in 2006

2010 ◽  
Vol 11 (1) ◽  
pp. 29 ◽  
Author(s):  
A. Wrather ◽  
G. Shannon ◽  
R. Balardin ◽  
L. Carregal ◽  
R. Escobar ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Total Yield ◽  
Cyst Nematode ◽  
Brown Spot ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Field Surveys ◽  
Glycine Max L ◽  
Systematic Field

The objective of this project was to compile estimates of yield loss in soybean [Glycine max (L.) Merr] to diseases in the top eight soybean-producing countries in 2006. The purpose was to provide information needed by local and world agencies to allocate funds for research and to help scientists focus and coordinate research efforts. Methods used by plant pathologists to estimate yield loss to diseases in these countries included systematic field surveys, cultivar trials, diagnostic clinic records, personal observations, and questionnaires sent to crop consultants and extension staff. The 2006 harvest of soybeans in the top eight soybean-producing countries was reduced an estimated 59.9 million metric tonnes (t) by diseases according to results of the current study. Soybean rust, caused by Phakopsora pachyrhizi, reduced yield in all these countries except Canada in 2006, and the total was more than any other. Next in decreasing order of total yield loss were soybean cyst nematode, brown spot, seedling diseases, anthracnose, and charcoal rot. Accepted for publication 27 October 2009. Published 25 January 2010.

Effect of Soybean Cultivars Moderately Resistant to Soybean Cyst Nematode on SCN Populations and Yield

2008 ◽  
Vol 9 (1) ◽  
pp. 14 ◽  
Author(s):  
Eric A. Adee ◽  
Martin L. Johnson ◽  
Terry L. Niblack
Keyword(s):  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Cyst Nematode ◽  
Yield Potential ◽  
High Yield ◽  
Nematode Reproduction ◽  
Resistant Cultivars ◽  
Soybean Cultivars ◽  
Moderate Resistance ◽  
Moderately Resistant

Spread of soybean cyst nematode Heterodera glycines (SCN) to much of the soybean (Glycine max) growing region in the Midwest has created a persistent and significant annual yield loss for soybean. Host resistance has been the primary means of reducing yield loss to SCN. It is not known how moderately resistant cultivars fit into the management of SCN. Moderately resistant cultivars can have high yield potential, but nematode reproduction is greater than on resistant cultivars. Moderate resistance is defined by a SCN female index (FI) of 10 to 29 in standardized tests, whereas cultivars with an FI < 10 are considered resistant. Two each of SCN-resistant, moderately resistant, and susceptible (FI > 60) cultivars were planted in the same plots for two soybean crops in annual rotation with corn. The SCN population was reduced 80 and 54% by resistant and moderately resistant cultivars, respectively, and increased 189% by the susceptible. Yields of the resistant and moderately resistant were 8.2 and 11.8 bu/acre better, respectively, than for the susceptible. All plots were planted to a susceptible cultivar in the final year of the study, and demonstrated there was a carry-over effect from previous cultivars. Following resistant and moderately resistant cultivars, yields of the susceptible were 6.6 and 4.3 bu/acre above following susceptible cultivars. This study showed that moderately resistant soybean cultivars can be an effective tool for improving profitability of soybean. Accepted for publication 9 April 2008. Published 18 June 2008.

Transgenic soybeans expressing siRNAs specific to a major sperm protein gene suppress Heterodera glycines reproduction

2006 ◽  
Vol 33 (11) ◽  
pp. 991 ◽  
Author(s):  
Ryan M. Steeves ◽  
Tim C. Todd ◽  
Juliane S. Essig ◽  
Harold N. Trick
Keyword(s):  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Heterodera Glycines ◽  
Control Strategies ◽  
Reproductive Potential ◽  
Cyst Nematode ◽  
Root Tissue ◽  
Parasitic Nematodes ◽  
Major Sperm Protein ◽  
Sperm Protein

The soybean cyst nematode (SCN), Heterodera glycines, is the major disease-causing agent limiting soybean production in the USA. The current management strategy to reduce yield loss by SCN involves the deployment of resistant soybean cultivars and rotation to non-host crops. Although this management scheme has shown some success, continued yearly yield loss estimates demonstrate the limitations of these techniques. As a result, new control strategies are needed to complement the existing methods. Reported here is a novel method of SCN control that utilises RNA interference (RNAi). Transgenic soybeans were generated following transformation with an RNAi expression vector containing inverted repeats of a cDNA clone of the major sperm protein (MSP) gene from H. glycines. The accumulation of MSP-specific short interfering RNA (siRNA) molecules were detected by northern blot analysis of transgenic soybeans. T0 plants displaying MSP siRNA accumulation were deployed in a bioassay to evaluate the effects of MSP interfering molecules on H. glycines reproduction. Bioassay data has shown up to a 68% reduction in eggs g–1 root tissue, demonstrating that MSPi transgenic plants significantly reduced the reproductive potential of H. glycines. An additional bioassay evaluating progeny nematodes for maintenance of reproductive suppression indicated that progeny were also impaired in their ability to successfully reproduce, as demonstrated by a 75% reduction in eggs g–1 root tissue. The results of this study demonstrate the efficacy of an RNAi-based strategy for control of the soybean cyst nematode. In addition, these results may have important implications for the control of other plant parasitic nematodes.

Distribution of the Soybean Cyst Nematode, Heterodera glycines, in the United States and Canada: 1954 to 2014

2014 ◽  
Vol 15 (2) ◽  
pp. 85-87 ◽  
Author(s):  
Gregory L. Tylka ◽  
Christopher C. Marett
Keyword(s):  
United States ◽  
North America ◽  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Heterodera Glycines ◽  
The United States ◽  
Cyst Nematode ◽  
The Usa ◽  
Initial Discovery

The soybean cyst nematode (Heterodera glycines) is considered the most damaging pathogen of soybean in the USA and Canada, and causes considerable yield loss in many other soybean-producing countries. It is believed to have been introduced into North America from Asia. The map of the known distribution of H. glycines in the USA and Canada has been updated for 2014. Maps of its known distribution in past years illustrate the spread of the pathogen since its initial discovery in the United States in 1954. Accepted for publication 20 April 2014. Published 27 May 2014.

Sign in / Sign up

Export Citation Format

Share Document