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Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by 35S:GmAGL15

ABSTRACT: A soybean ortholog of the Arabidopsis MADS-domain transcription factor (called GmAGL15) enhanced somatic embryogenesis from immature cotyledon explants of soybean when expressed via the 35S promoter compared to non transgenic tissue (cultivar Jack). To better understand how this occurs an expression microarray experiment was performed. publication: Q. Zheng and S.E. Perry. (2014). Alterations in the transcriptome of soybean in response to enhance somatic embryogenesis promoted by orthologs of AGAMOUS-Like 15 and AGAMOUS-Like 18. Plant Physiology, in press. Comparison of transcriptomes of non-transgenic tissue to 35S:GmAGL15 tissue at the time of explant preparation (0 days) and 3 and 7 days after induction of somatic embryogenesis by placement on medium containing 2,4-D.

ORGANISM(S): Glycine max

SUBMITTER: Sharyn Perry

PROVIDER: E-GEOD-54523 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by 35S:GmAGL15

Project description:A soybean ortholog of the Arabidopsis MADS-domain transcription factor (called GmAGL15) enhanced somatic embryogenesis from immature cotyledon explants of soybean when expressed via the 35S promoter compared to non transgenic tissue (cultivar Jack). To better understand how this occurs an expression microarray experiment was performed. publication: Q. Zheng and S.E. Perry. (2014). Alterations in the transcriptome of soybean in response to enhance somatic embryogenesis promoted by orthologs of AGAMOUS-Like 15 and AGAMOUS-Like 18. Plant Physiology, in press.

2014-01-30 | GSE54523 | GEO

Gene expression in response to AGL15 during somatic embryogenesis

Project description:Transcript accumulation was measured using the Affymetrix Arabidopsis ATH1 Genome Array [ATH1-121501] to document changes in response to the MADS-domain transcription factor AGAMOUS-Like 15 during somatic embryogenesis. A somatic embryo system was used where mature seed is allowed to complete germination in liquid MS media containing 2,4-D and seedlings produce somatic embryos from the shoot apical meristem (SAM) region. The frequency with which these embryos are produced directly correlates with AGL15 accumulation. Experiment Overall Design: Wild type Arabidopsis (Columbia ecotype) with normal amounts of AGL15 were compared to (1) 35S:AGL15 that constitutively expresses AGL15 and produces more somatic embryos from the shoot apical region than wild type and (2) agl15 agl18 double loss-of-function mutants that produce less somatic embryos from the shoot apical region than wild type.

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Project description:Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by 35S:GmAGL15

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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.

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Expression profiling of soybean genes in response to drought

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2012-11-10 | E-GEOD-40627 | biostudies-arrayexpress

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

Gene expression in response to AGL15 during somatic embryogenesis

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Transcriptional response to cotton worm feeding in resistant and susceptible soybean lines

Project description:The interaction between soybean and its destructive insect (cotton worm) is complicated. In this paper, the timecourse of induced responses to cotton worm were characterized in two soybean lines, suggesting complex results with different timepoints of peak induced resistance in resistant (WX) and susceptible (NN) soybean lines. To get a better understanding of induced resistant mechanisms of soybean against herbivory, two sets of transcriptome profiles of WX and NN at their peak induced resistant timepoints were compared by microarrays The common phenomenon was that no matter in resistant or susceptible line, there always exist a peak level of induced resistance timepoint. Here we are aimed to focus on transcriptional changes induced by insect feeding at the peak timepoints (5 dai and 24 hai) in WX and NN, three biological replicates were used for each of the four treatments (WX treated (WX-T) and control (WX-CK); NN treated (NN-T) and control (NN-CK) ) with three biological replicates.

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