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Differences in metabolite profiles and antioxidant activities between wild and cultivated black soybeans evaluated by a correlation analysis (part II)

ABSTRACT: Non-targeted metabolic profiling of 26 soybean varieties using liquid chromatography-mass spectrometry (LC-MS) including 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), combined with multivariate analysis, revealed significant differences in 25 differential metabolites

ORGANISM(S): Soybean Glycine Max

TISSUE(S): Plant

SUBMITTER: Jiuliang Xu

PROVIDER: ST000766 | MetabolomicsWorkbench | Tue Jul 04 00:00:00 BST 2017

REPOSITORIES: MetabolomicsWorkbench

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Differences in metabolite profiles and antioxidant activities between wild and cultivated black soybeans evaluated by a correlation analysis (part I)

Project description:non-targeted metabolic profiling of 26 soybean varieties using liquid chromatography-mass spectrometry (LC-MS) including 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), combined with multivariate analysis, revealed significant differences in 25 differential metabolites

2017-07-03 | ST000765 | MetabolomicsWorkbench

Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans

Project description:Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development.

2017-06-13 | GSE94366 | GEO

A Comparative Proteome and Phosphoproteome Reveal the Molecular Mechanism of the Difference between Imitative Wild Variety and Cultivated Variety of Dendrobium huoshanense C. Z. Tang et S. J. Cheng

Project description:This project intends to conduct comparative proteomics research on wild and cultivated varieties of Dendrobium huoshanense that are similar in plant shape and in the same growth and development stage through proteomics and protein modification omics combined with the differences in metabolites in Dendrobium huoshanense. Full-scan proteomic data of Dendrobium; compare the protein expression levels of wild and cultivated varieties to find relevant candidate proteins, and perform functional annotation and KEGG analysis of metabolic pathways for candidate proteins with different expressions to further analyze the material basis differences between wild and cultivated varieties Provide research objects of molecular biology.

2022-06-24 | PXD022337 | Pride

Whole-transcriptome RNA sequencing of skin reveals innate immunity differences between wild-type and yellow mutant rainbow trout

Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.

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Identification of differentially expressed genes between developing seeds of different soybean cultivars

2015-04-29 | GSE21598 | GEO

Mellor2012_LipooxygenasePathway

Project description:This model is from the article: Reduction of off-flavor generation in soybean homogenates: a mathematical model. Mellor N , Bligh F , Chandler I , Hodgman C J. Food Sci.2010 Sep; 75(7): R131-8; PMID: 2153556, Abstract: The generation of off-flavors in soybean homogenates such as n-hexanal via the lipoxygenase (LOX) pathway can be a problem in the processed food industry. Previous studies have examined the effect of using soybean varieties missing one or more of the 3 LOX isozymes on n-hexanal generation. A dynamic mathematical model of the soybean LOX pathway using ordinary differential equations was constructed using parameters estimated from existing data with the aim of predicting how n-hexanal generation could be reduced. Time-course simulations of LOX-null beans were run and compared with experimental results. Model L(2), L(3), and L(12) beans were within the range relative to the wild type found experimentally, with L(13) and L(23) beans close to the experimental range. Model L(1) beans produced much more n-hexanal relative to the wild type than those in experiments. Sensitivity analysis indicates that reducing the estimated K(m) parameter for LOX isozyme 3 (L-3) would improve the fit between model predictions and experimental results found in the literature. The model also predicts that increasing L-3 or reducing L-2 levels within beans may reduce n-hexanal generation. PRACTICAL APPLICATION: This work describes the use of mathematics to attempt to quantify the enzyme-catalyzed conversions of compounds in soybean homogenates into undesirable flavors, primarily from the compound n-hexanal. The effect of different soybean genotypes and enzyme kinetic constants was also studied, leading to recommendations on which combinations might minimize off-flavor levels and what further work might be carried out to substantiate these conclusions.

2024-09-02 | BIOMD0000000415 | BioModels

Identification of genes differentially expressed between developing seeds of different soybean varieties

Project description:Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production. Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits. The soybean plants of two soybean varieties Minsoy and Archer and two recombinant inbred lines from the cross that are similar in maturity but differ in yield were grown in St Paul, Minnesota during the summers of 2007 and 2008. In 2007, each line was planted as a single row. In 2008, a randomized complete block (RCB) design was used and each line had 3 replicates planted 1-2 weeks apart. Within each replicate, two rows per line were planted. Seeds were harvested at three developmental stages, namely, seed length = 2 mm, 3.5 mm, and 5-6 mm, which correspond approximately to soybean reproductive stages R4, R5 and early R6, respectively. In 2007 three independent samples were collected for each line and developmental stage. In 2008, two seed samples (one from each row) were collected for each line at each stage within each replicate. The pairs of seed samples were then pooled. Thus, three sets of independent tissue samples were collected for RNA extraction and hybridization on Affymetrix microarrys.

2015-04-29 | E-GEOD-21598 | biostudies-arrayexpress

Gene expression profiles in black soybean sprouts: 0.5 cm long vs 5 cm long

Project description:To explore the mechanism underlying antioxidant activity of extracts from black soybean sprouts 0.5 cm long, Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K was used to compare mRNA expression between the black soybean sprouts 0.5 cm long (n=4) and the black soybean sprouts 5 cm long (n=4). GO term enrichment analysis showed ten up-regulated genes (BE823689.1_567, GMFL01-02-F14-R_381, GMFL01-03-G22-R_364, GMFL01-14-M12-R_553, GMFL01-51-M23-R_265, AW757007.1_297, AW761420.1_260, BI788389.1_501, BQ273202.1_332 and GMFL01-10-I14-F_701) in the 0.5 cm seedlings were associated with response to oxidative stress. qRT-PCR assay confirmed the up-regulation of these ten genes in sprouts 0.5 cm long. In conclusion, these ten genes may contribute to antioxidant activity of sprout extract. Gene expressions in black soybean sprouts were measured using Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K. Four independent experiments were performed in each group using different sprout sample.

2012-08-09 | E-GEOD-40002 | biostudies-arrayexpress

Gene expression profiles in black soybean sprouts: 0.5 cm long vs 5 cm long

2012-08-10 | GSE40002 | GEO

Transcriptome differences analysis between Yersinia pestis 201 wild strain and fyuA mutant strain

Project description:Purpose: In previous studies, we found that the fyuA gene plays an important role in the virulence and pathogenicity of Yersinia pestis strain 201. In order to globally observe which functions of the fyuA gene also affect Y. pestis, we performed RNA-seq on the Y. pestis wild strain 201-WT and mutant strains △fyuA and △fyuAGCAdel, hoping to find their differences at the transcription level, so that better elucidate the effect of fyuA gene on Y. pestis gene transcription. Methods: Total RNA was extracted using the PureLink™ RNA Mini Kit, and then used for creating a cDNA library and deep sequencing. According to the values of Fragments Per Kilobase of Transcript per Million Mapped Reads (FPKM), the ratio of transcript levels between WT and ΔfyuAGCAdel groups was used as the logarithm to the base 2 (twofold change). The differential values of at least a 2-fold were applied to analyze the differential expression of genes according to the Y. pestis 91001 genome annotation. The transcriptome data were verified by qPCR. Results: We found that compared with 201-WT, genes related to siderophore synthesis such as ybtS, ybtX, ybtQ, irp2, irp1, ybtU, ybtT and ybtE were significantly down-regulated at either 26 ℃ or 37 ℃. At 37 ℃, the genes related to type Ⅲ secretion system were significantly up-regulated.

2022-03-22 | GSE198937 | GEO

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