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Research article
Transcriptome Profiling Reveals Spatial-temporal Dynamics of Gene Expression Essential for Soybean Seed Development
Dan Zhang
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6119-9533
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This work is licensed under a CC BY 4.0 License. Read Full License
Background: Seeds are the economic basis of oilseed crops, especially for soybean, thus far the most widely cultivated oilseed crop worldwide. Seed development is accompanied with a multitude of diverse cellular processes and revealing the underlying regulatory activities is critical for seed improvement.
Results: Here, we profiled transcriptomes of developing seeds (20, 25, 30, 40 days after flowering) representing key points of seed development from early to full development. We identified a set of highly-abundant genes and highlighted the importance of these genes to support nutrient accumulation and transcriptional regulation in developing seeds. We identified 8,925 differentially expressed genes that exhibited temporal expression patterns over the course and had expression specificities in distinct tissues including seeds and non-seed tissues (roots, stems, leaves). Genes with specificities to non-seed tissues have tissue-specialized roles while remain relatively low transcript abundance in developing seeds, exhibiting their supportive roles spatially for seed development. Co-expression network analysis identified several under-explored genes in soybean that bridge tissue-specific gene modules.
Conclusions: Our study provides a global view of gene activities and biological processes critical for seed formation in soybean and prioritizes a set of genes for further study. The results shed insight into the mechanism controlling seed development and storage reserves.
Keywords
Soybean, Glycine max, seed development, transcriptome, spatial/temporal gene expression
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- SupplemetalTablesWm82Seeds.xlsx
Supporting information Table S1 Statistics of quality control and alignment for the sequencing reads. Table S2 Information for the 8925 DEGs. Table S3 High abundance genes in developing seeds. Table S4 Expression correlation of 16 genes between qPCR and RNA-Seq
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CURRENT STATUS: Under Review
Version 1
Posted 18 Dec, 2020
No community comments so far
Review #1 received
Received 14 Jan, 2021
Reviewer #2 agreed
On 10 Jan, 2021
Reviewers invited
Invitations sent on 19 Dec, 2020
Reviewer #1 agreed
On 19 Dec, 2020
Editor invited
On 13 Dec, 2020
Editor assigned
On 06 Dec, 2020
Submission checks complete
On 06 Dec, 2020
First submitted
On 05 Dec, 2020
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Transcriptome Profiling Reveals Spatial-temporal Dynamics of Gene Expression Essential for Soybean Seed Development
Dan Zhang
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6119-9533
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 18 Dec, 2020
No community comments so far
Review #1 received
Received 14 Jan, 2021
Reviewer #2 agreed
On 10 Jan, 2021
Reviewers invited
Invitations sent on 19 Dec, 2020
Reviewer #1 agreed
On 19 Dec, 2020
Editor invited
On 13 Dec, 2020
Editor assigned
On 06 Dec, 2020
Submission checks complete
On 06 Dec, 2020
First submitted
On 05 Dec, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Seeds are the economic basis of oilseed crops, especially for soybean, thus far the most widely cultivated oilseed crop worldwide. Seed development is accompanied with a multitude of diverse cellular processes and revealing the underlying regulatory activities is critical for seed improvement.
Results: Here, we profiled transcriptomes of developing seeds (20, 25, 30, 40 days after flowering) representing key points of seed development from early to full development. We identified a set of highly-abundant genes and highlighted the importance of these genes to support nutrient accumulation and transcriptional regulation in developing seeds. We identified 8,925 differentially expressed genes that exhibited temporal expression patterns over the course and had expression specificities in distinct tissues including seeds and non-seed tissues (roots, stems, leaves). Genes with specificities to non-seed tissues have tissue-specialized roles while remain relatively low transcript abundance in developing seeds, exhibiting their supportive roles spatially for seed development. Co-expression network analysis identified several under-explored genes in soybean that bridge tissue-specific gene modules.
Conclusions: Our study provides a global view of gene activities and biological processes critical for seed formation in soybean and prioritizes a set of genes for further study. The results shed insight into the mechanism controlling seed development and storage reserves.
Figure 1
Figure 1
Figure 1
Figure 1
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