ArticlePloS one2013
Using RNA-Seq to profile soybean seed development from fertilization to maturity.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analyses of QTLs Associated with Protein and Oil Contents and Compositions in Soybean [Glycine max (L.) Merr.] Seed.International journal of molecular sciences · 2017Pooled it
- Article
- Targets and strategies to design soybean seed composition traits.The plant genome · 2025Review
- Molecular Network Analysis in Model and Non-Model Legumes: Challenges in Omics Data Interpretation Across Species, with a Focus onPlants (Basel, Switzerland) · 2025Review
- Dissecting the cellular architecture and genetic circuitry of the soybean seed.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Understanding the transition from embryogenesis to seed filling inFrontiers in plant science · 2025Article
- Dissecting the temporal genetic networks programming soybean embryo development from embryonic morphogenesis to post-germination.Plant cell reports · 2024Article
- Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1.Biotechnology for biofuels and bioproducts · 2023Article
- The Late Embryogenesis Abundant Proteins in Soybean: Identification, Expression Analysis, and the Roles of GmLEA4_19 in Drought Stress.International journal of molecular sciences · 2023Article
- Exploration into Natural Variation Genes Associated with Determinate and Capitulum-like Inflorescence inInternational journal of molecular sciences · 2023Article
- Regulatory Effects of ABA and GA on the Expression of Conglutin Genes andInternational journal of molecular sciences · 2023Article
- Transcriptome analysis of ovules offers early developmental clues after fertilization in3 Biotech · 2023Article
- Article
- Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales): evidence for epigenetic patterning during reproduction.Plant reproduction · 2022Article
- Detection of a major QTL and development of KASP markers for seed weight by combining QTL-seq, QTL-mapping and RNA-seq in peanut.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Multi-Omics Techniques for Soybean Molecular Breeding.International journal of molecular sciences · 2022Review
- Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model.Frontiers in plant science · 2022Article
- Dynamic transcriptome analysis suggests the key genes regulating seed development and filling in Tartary buckwheat (Frontiers in genetics · 2022Article
- Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement.Computational and structural biotechnology journal · 2022Article
- Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM.Frontiers in plant science · 2022Article
23 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes encoding storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. More significantly, the power of RNA-Seq to detect genes expressed at low levels revealed hundreds of transcription factors with notable expression in at least one stage of seed development. Results from a second biological replicate demonstrate high reproducibility of these data revealing a comprehensive view of the transciptome of seed development in the cultivar Williams, the reference cultivar for the first soybean genome sequence.
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