Establishment and Analysis of the mRNA Expression Patterns of ABI3-like and Storage Protein Genes during Soybean Seed Development

Abstract 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.

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Amino acid transporter expression and localisation studies in pea (Pisum sativum)

Functional Plant Biology ◽

10.1071/fp07107 ◽

2007 ◽

Vol 34 (11) ◽

pp. 1019 ◽

Cited By ~ 22

Author(s):

Mechthild Tegeder ◽

Qiumin Tan ◽

Aleel K. Grennan ◽

John W. Patrick

Keyword(s):

Amino Acid ◽

Pisum Sativum ◽

Storage Protein ◽

Expression Patterns ◽

Phloem Loading ◽

Transfer Cells ◽

Protein Accumulation ◽

Developmentally Regulated ◽

And Storage ◽

Seed Coats

Expression of the amino acid permeases PsAAP1 and PsAAP2 was analysed in developing pea (Pisum sativum L.) plants. Both transporters were expressed in seed coats and cotyledon epidermal transfer cells and storage parenchyma cells. AAP expression is developmentally regulated and coincides with the onset of storage protein synthesis. Nitrogen was shown to induce AAP expression and AAP transcript levels were upregulated during the photoperiod. Analysis of Arabidopsis thaliana AAP1 promoter activity in pea, using promoter-β-glucuronidase (promotor-GUS) studies, revealed targeting of GUS to seed coats and cotyledon epidermal transfer cells. Expression was found in the nutritious endosperm during the early stages of seed development, whereas GUS staining in embryos was detected from the heart stage onward. In addition, AAP1 expression was observed in the phloem throughout the plant. This finding equally applied to PsAAP1 expression as shown by in situ mRNA hybridisation, which also demonstrated that PsAAP1 expression was localised to companion cells. Overall, PsAAP1 expression patterns and cellular localisation point to a function of the transporter in phloem loading of amino acids for translocation to sinks and in seed loading for development and storage protein accumulation.

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Formation of Storage Protein Components during Soybean Seed Development

Agricultural and Biological Chemistry ◽

10.1080/00021369.1978.10863048 ◽

1978 ◽

Vol 42 (4) ◽

pp. 697-702

Author(s):

Sonoe Ochiai-Yanagi ◽

Chikafusa Fukazawa ◽

Kyuya Harada

Keyword(s):

Seed Development ◽

Storage Protein ◽

Soybean Seed ◽

Protein Components

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A mutant of Arabidopsis which is defective in seed development and storage protein accumulation is a new abi3 allele

The Plant Journal ◽

10.1111/j.1365-313x.1992.00435.x ◽

1992 ◽

Vol 2 (4) ◽

pp. 435-441 ◽

Cited By ~ 109

Author(s):

Eiji Nambara ◽

Satoshi Naito ◽

Peter McCourt

Keyword(s):

Seed Development ◽

Storage Protein ◽

Protein Accumulation ◽

And Storage

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Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development

BMC Genomics ◽

10.1186/s12864-021-07783-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Hengyou Zhang ◽

Zhenbin Hu ◽

Yuming Yang ◽

Xiaoqian Liu ◽

Haiyan Lv ◽

...

Keyword(s):

Seed Development ◽

Temporal Dynamics ◽

Expression Patterns ◽

Critical Time ◽

Soybean Seed ◽

Transcript Abundance ◽

Specific Gene ◽

Oilseed Crop ◽

Seed Formation ◽

Developing Seeds

Abstract Background Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. Results In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. Conclusions Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.

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THE MOLECULAR BIOLOGY OF PEA SEED DEVELOPMENT WITH PARTICULAR REFERENCE TO THE STORAGE PROTEIN GENES

Genetic Engineering of Crop Plants ◽

10.1016/b978-0-408-04779-1.50015-0 ◽

1990 ◽

pp. 127-141 ◽

Cited By ~ 1

Author(s):

DONALD BOULTER ◽

R.R.D. CROY ◽

I. MARTA EVANS ◽

J.A. GATEHOUSE ◽

N. HARRIS ◽

...

Keyword(s):

Molecular Biology ◽

Seed Development ◽

Storage Protein ◽

Storage Protein Genes ◽

Pea Seed

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The developmentally regulated bZIP factor ROM1 modulates transcription from lectin and storage protein genes in bean embryos

The Plant Journal ◽

10.1046/j.1365-313x.1996.10010135.x ◽

1996 ◽

Vol 10 (1) ◽

pp. 135-148 ◽

Cited By ~ 37

Author(s):

Maw-Shenq Chern ◽

Hans Georg Eiben ◽

Mauricio M. Bustos

Keyword(s):

Storage Protein ◽

Developmentally Regulated ◽

Bzip Factor ◽

And Storage ◽

Storage Protein Genes

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Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development

International Journal of Molecular Sciences ◽

10.3390/ijms21207603 ◽

2020 ◽

Vol 21 (20) ◽

pp. 7603

Author(s):

Shuo Sun ◽

Changyu Yi ◽

Jing Ma ◽

Shoudong Wang ◽

Marta Peirats-Llobet ◽

...

Keyword(s):

Gene Expression ◽

Glycine Max ◽

Seed Development ◽

Regulatory Networks ◽

Expression Patterns ◽

Soybean Seed ◽

Endosperm Development ◽

A Genome ◽

Early Seed Development ◽

Spatio Temporal

Soybean (Glycine max) 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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Formation of storage protein componets during soybean seed development.

Agricultural and Biological Chemistry ◽

10.1271/bbb1961.42.697 ◽

1978 ◽

Vol 42 (4) ◽

pp. 697-702 ◽

Cited By ~ 2

Author(s):

Sonoe OCHIAI-YANAGI ◽

Chikafusa FUKAZAWA ◽

Kyuya HARADA

Keyword(s):

Seed Development ◽

Storage Protein ◽

Soybean Seed

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