ArticleGenome biology2024
Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
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- Distinct Mg²⁺ responses and species-specific transcriptional regulation of the magnesium transporter MGR2 in Saccharum officinarum and Saccharum spontaneum.BMC plant biology · 2026Article
- Insights into glandular trichome biology from analysis of organ-specific gene expression programmes in cannabis, hop and tomato.The Plant journal : for cell and molecular biology · 2026Article
- Identification of miRNAs Responsive to a Defined Period of Iron Deficiency and Resupply inPlants (Basel, Switzerland) · 2026Article
- Cell wall invertase improves grain nutrition via regulating sugar and hormone metabolism gene expression in transgenic soybean.Annals of botany · 2026Article
- QTL mapping for hundred-seed weight in soybean using high-density SLAF-seq technology.BMC plant biology · 2025Article
- Comprehensive genome-wide identification and analysis of MYB transcription factors related to abiotic and biotic stress regulation in rice.Scientific reports · 2025Article
- Single-Cell Omics in Legumes: Research Trends and Applications.Plants (Basel, Switzerland) · 2025Review
- Review
- Functional Genomics: From Soybean to Legume.International journal of molecular sciences · 2025Review
- The Resistance Mechanisms of Anilinopyrimidine Fungicide Pyrimethanil inJournal of fungi (Basel, Switzerland) · 2025Article
- Transcriptome sequencing revealed the regulation of stem internode length associated with mechanical harvesting in three tea varieties.Frontiers in plant science · 2025Article
- Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean.Genome biology · 2024Article
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13 authors.
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Abstract
backgroundTranscription factors (TFs) bind regulatory genomic regions to orchestrate spatio-temporal expression of target genes. Global dissection of the cistrome is critical for elucidating transcriptional networks underlying complex agronomic traits in crops.
resultsHere, we generate a comprehensive genome-wide binding map for 148 TFs using DNA affinity purification sequencing in soybean. We find TF binding sites (TFBSs) exhibit elevated chromatin accessibility and contain more rare alleles than other genomic regions. Intriguingly, the methylation variations at TFBSs partially contribute to expression bias among whole genome duplication paralogs. Furthermore, we construct a soybean gene regulatory network (SoyGRN) by integrating TF-target interactions with diverse datasets encompassing gene expression, TFBS motifs, chromatin accessibility, and evolutionarily conserved regulation. SoyGRN comprises 2.44 million genome-wide interactions among 3188 TFs and 51,665 target genes. We successfully identify key TFs governing seed coat color and oil content and prioritize candidate genes within quantitative trait loci associated with various agronomic traits using SoyGRN. To accelerate utilization of SoyGRN, we develop an interactive webserver ( www.soytfbase.cn ) for soybean community to explore functional TFs involved in trait regulation.
conclusionsOverall, our study unravels intricate landscape of TF-target interactions in soybean and provides a valuable resource for dissecting key regulators for control of agronomic traits to accelerate soybean improvement.
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