Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development
Soybean (<i>Glycine max</i>) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and qua...
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| Format: | Article |
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/20/7603 |
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| author | Shuo Sun Changyu Yi Jing Ma Shoudong Wang Marta Peirats-Llobet Mathew G. Lewsey James Whelan Huixia Shou |
| author_facet | Shuo Sun Changyu Yi Jing Ma Shoudong Wang Marta Peirats-Llobet Mathew G. Lewsey James Whelan Huixia Shou |
| author_sort | Shuo Sun |
| collection | DOAJ |
| description | Soybean (<i>Glycine max</i>) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:37:11Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-30c10148db6d45bb9a472a0d1c7c1b7d2023-11-20T17:07:40ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012120760310.3390/ijms21207603Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed DevelopmentShuo Sun0Changyu Yi1Jing Ma2Shoudong Wang3Marta Peirats-Llobet4Mathew G. Lewsey5James Whelan6Huixia Shou7State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, ChinaAustralian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, AustraliaState Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, ChinaKey Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, ChinaAustralian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, AustraliaDepartment of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, AustraliaState Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, ChinaState Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, ChinaSoybean (<i>Glycine max</i>) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.https://www.mdpi.com/1422-0067/21/20/7603<i>Glycine max</i>seed developmenttranscriptomeRNA-sequencing (RNA-seq)tissue specifictranscription factor (TF) |
| spellingShingle | Shuo Sun Changyu Yi Jing Ma Shoudong Wang Marta Peirats-Llobet Mathew G. Lewsey James Whelan Huixia Shou Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development International Journal of Molecular Sciences <i>Glycine max</i> seed development transcriptome RNA-sequencing (RNA-seq) tissue specific transcription factor (TF) |
| title | Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development |
| title_full | Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development |
| title_fullStr | Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development |
| title_full_unstemmed | Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development |
| title_short | Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (<i>Glycine max</i>) Tissues during Early Seed Development |
| title_sort | analysis of spatio temporal transcriptome profiles of soybean i glycine max i tissues during early seed development |
| topic | <i>Glycine max</i> seed development transcriptome RNA-sequencing (RNA-seq) tissue specific transcription factor (TF) |
| url | https://www.mdpi.com/1422-0067/21/20/7603 |
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