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Next Generation Sequencing Quantitative Analysis of soybean seeds Transcriptomes

ABSTRACT: To investigate the regulatory mechanisms of GmNFYA in salt stress, leaves and roots of transgenic plants and JACK plants were collected for RNA extraction and sequencing. Clean reads of RNA-sequencing were mapped to soybean genome and genes that had a 2 fold increase or 50% decrease, compared to JACK, were defined as differential expressed genes (DEGs).

ORGANISM(S): Glycine max

PROVIDER: GSE173640 | GEO | 2021/05/01

REPOSITORIES: GEO

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Next Generation Sequencing Quantitative Analysis of soybean seeds Transcriptomes

Project description:To investigate the regulatory mechanisms of GmZF392, GmZF351 and GmNFYA in oil accumulation, seeds at H3 stage of transgenic plants and JACK plants were collected for RNA extraction and sequencing. Before sequencing, qPCR showed that expression of GmZF392, GmZF351 and GmNFYA increased to about 10, 109 and 7 times respectively compared to JACK. Clean reads of RNA-sequencing were mapped to soybean genome and genes that had a 1.5 fold increase or 50% decrease, compared to JACK, were defined as differential expressed genes (DEGs).

2021-04-02 | GSE171304 | GEO

Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (ChIP-seq dataset)

Project description:Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.

2019-07-22 | GSE133573 | GEO

Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (RNA-seq dataset)

2019-07-22 | GSE133574 | GEO

Expression profiling of soybean genes in response to drought (reproductive stage)

2012-11-10 | GSE40604 | GEO

Quantitative proteomics reveals an important role of GsCBRLK in salt stress response of soybean

Project description:Salinity is one of the serious environmental constraints stresses limiting crop plants growth and yield. We have previously reported that GsCBRLK functions as a positive regulator of plant tolerance to salt stress. In order to investigate the physiological and molecular mechanisms underlying the salinity tolerance regulated by GsCBRLK, the gene was overexpressed in soybean plants. Here we examined the salt-responsive proteomes of the GsCBRLK overexpression soybean and wild typeWT plants using iTRAQ-based proteomic approach to elucidate investigate the global effects and potentialssible downstream targets of GsCBRLK protein. A total of 941 proteins showed significant changes in protein abundance in soybean leaves, and 574 of the NaCl-regulated proteins were GsCBRLK-dependent. Among the identified proteins, four protein changes in both the two genotypes after NaCl treatment were validated using Western blot analysis. The iIdentification of the salt-reponsive proteins has revealed the involvement of GsCBRLK protein in the enhancement of ROS scavenging and photosynthesis capacity in soybean plants, which was corrobarated with the physiological effects of GsCBRLK overexpression. More importantly, the proteomic data has suggested the regulatory function of GsCBRLK in salt signal transduction pathway mediated by Ca2+/CaM. These findings have contributed to our knowledge of plant GsCBRLK mediated salt tolerance mechanisms mediated by GsCBRLK.

2016-05-23 | PXD002851 | Pride

Transcriptomics Analyses of soybean leaves and roots sample during water-deficit

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2015-04-26 | GSE49537 | GEO

Expression profiling of soybean genes in response to drought (vegetative stage)

Project description:Drought-responsive genes in soybean leaves were successfully obtained using soybean gene 1.0 ST array. Leaf samples from the vegetative stage of soybean plants were used.

2012-04-03 | GSE29663 | GEO

Expression profiling of soybean genes in response to drought (reproductive stage)

Project description:Drought-responsive genes in soybean leaves were successfully identified using Affymetrix Soybean Gene 1.0 ST arrays on leaves samples of reproductive-stage soybean plants. R1 soybean plants planted in pots were imposed drought by withholding water for 5 days until the soil moisture content dropped to 5%, and 3rd trifoliates (now at the R2 stage) were collected for expression profiling. Soybean plants were grown in pots. When the plants reached the R1 stage (started flowering), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 5th day of water withholding, when soil moisture content reached 5%. The 3rd trifoliate (counting from shoots), now at the R2 stage, was collected for total RNA extraction, while other 3rd trifoliates of similar chlorophyl index were collected for leaves water content determination to identify the severity of the stress. Total RNA from 3rd trifoliates were used for expression profiling using Affymetrix Soybean Gene 1.0 ST arrays. Four biological repeats per treatment were performed, three biological repeats were chosen for expression profiling.

2012-11-10 | E-GEOD-40604 | biostudies-arrayexpress

Transcriptional response to soybean aphid infestation in susceptible and resistant soybean plants

Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. We used microarrays to characterize the soybean plant's transcriptional defense against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured trancript levels in leaves after one and seven days of aphid infestation.

2012-01-31 | GSE35427 | GEO

Transcriptional response to long-term soybean aphid infestation in susceptible and resistant soybean plants

Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. Aphids do not normally kill their host and colonize plants for long periods of time, up to several months in soybean. However, our knowledge of plant responses to long-term aphid colonization is very limited. We used microarrays to characterize the soybean plant's transcriptional response against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured transcript levels in leaves after 21 days of aphid infestation.

2018-06-15 | GSE115790 | GEO

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