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Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

ABSTRACT: To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. BARC-2 (Rj4/Rj4)) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to the seed pack (Seed Pack; Daiki rika Kogyo Co., Ltd., Shiga, Japan) watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61 or its type III secretion mutant BErhcJ. Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 2 and 4 days after inoculation.

ORGANISM(S): Glycine max

PROVIDER: GSE79015 | GEO | 2016/03/09

SECONDARY ACCESSION(S): PRJNA314702

REPOSITORIES: GEO

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Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

Project description:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. BARC-2 (Rj4/Rj4)) were surface-sterilized and germinated at 25 Â°C for 2 days and were transferred to the seed pack (Seed Pack; Daiki rika Kogyo Co., Ltd., Shiga, Japan) watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61 or its type III secretion mutant BErhcJ. Plants were cultivated in a growth chamber at 25Â°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 2 and 4 days after inoculation. Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BErhcJ was measured 2 and 4 days after inoculation. Three independent experiments were performed at each inoculation.

2016-03-09 | E-GEOD-79015 | biostudies-arrayexpress

Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

Project description:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 M-BM-0C for 2 days and were transferred to a plant box (CUL-JAR300; Iwaki, Tokyo, Japan) containing sterile vermiculite watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25M-BM-0C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation. Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment) was measured 8 days after inoculation. Three independent experiments were performed at each inoculation.

2013-09-17 | E-GEOD-38520 | biostudies-arrayexpress

Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

Project description:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to a plant box (CUL-JAR300; Iwaki, Tokyo, Japan) containing sterile vermiculite watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation.

2013-09-17 | GSE38520 | GEO

Glycine max

Project description:Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

| PRJNA314702 | ENA

Glycine max

Project description:Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

| PRJNA168096 | ENA

Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle

Project description:We report the genome-wide transcriptome of soybean seeds across several stages of seed development and the entire life cycle using Illumina high-throughput sequencing technology. Specifically, we profiled whole seeds containing globular-stage, heart-stage, cotyledon-stage, and early maturation-stage embryos. We also profiled dry soybean seeds, and vegetative and reproductive tissues including leaves, roots, stems, seedlings, and floral buds. Illumina sequencing of transcripts from whole seeds at five stages of seed development (globular, heart, cotyledon, early-maturation, dry), and vegetative (leaves, roots, stems, seedlings) and reproductive (floral buds) tissues.

2011-05-10 | E-GEOD-29163 | biostudies-arrayexpress

Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.

Project description:To dissect differences in gene expression profile of soybean roots and root nodules, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and were hydroponically cultivated under controlled conditions with nitrogen free culture solution (Saito et al. 2014). At 19 days after planting, each plant were treated with or without 5 mM nitrate for 24 hours. Roots and nodules from three plants were pooled with three biological replications, and total RNA was extracted.

2018-10-01 | GSE104582 | GEO

Transcriptome analysis reveals GmZF351-affected gene expression in leaf and root.

Project description:GmZF351 has previously been characterized as a seed preferred gene participating mainly in oil accumulation. Here we report that over-expression of GmZF351 confers drought and salt tolerance in transgenic soybean seedlings. When soybean seedlings grew to V1 stage, leaves and roots were cut for RNA sequencing. Transcriptome analysis shows that GmZF351 regulates expression of downstream genes related to abiotic stress process.

2023-06-24 | GSE201762 | GEO

Identification of miRNAs and their target genes in developing seeds of soybean by deep sequencing

Project description:In our study, small RNA library and degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis, and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. Many identified miRNA targets may perform functions in soybean seed development by GO analysis. Additionally, soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3(AtSGS3) was detected as target of the new identified miRNA Soy_25, suggesting presence of feedback control of miRNA biogenesis sample 1: Examination of small RNA in soybean seed sample 2: identification of miRNA targets in soybean seed

2010-11-11 | E-GEOD-25260 | biostudies-arrayexpress

Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle

Project description:We report the genome-wide transcriptome of soybean seeds across several stages of seed development and the entire life cycle using Illumina high-throughput sequencing technology. Specifically, we profiled whole seeds containing globular-stage, heart-stage, cotyledon-stage, early maturation-stage, mid-maturation-stage, and late-maturation-stage embryos. We also profiled dry soybean seeds, and vegetative and reproductive tissues including leaves, roots, stems, seedlings, and floral buds.

2011-05-10 | GSE29163 | GEO

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