Abstract Legume plants such as soybean produce two major types of root lateral organs, lateral roots and root nodules. A robust computational framework was developed to predict potential gene regulatory networks (GRNs) associated with root lateral organ development in soybean. A genome-scale expression data set was obtained from soybean root nodules and lateral roots and subjected to biclustering using QUBIC (QUalitative BIClustering algorithm). Biclusters and transcription factor (TF) genes with enriched expression in lateral root tissues were converged using different network inference algorithms to predict high-confidence regulatory modules that were repeatedly retrieved in different methods. The ranked combination of results from all different network inference algorithms into one ensemble solution identified 21 GRN modules of 182 co-regulated genes networks, potentially involved in root lateral organ development stages in soybean. The workflow correctly predicted previously known nodule- and lateral root-associated TFs including the expected hierarchical relationships. The results revealed distinct high-confidence GRN modules associated with early nodule development involving AP2, GRF5 and C3H family TFs, and those associated with nodule maturation involving GRAS, LBD41 and ARR18 family TFs. Knowledge from this work supported by experimental validation in the future is expected to help determine key gene targets for biotechnological strategies to optimize nodule formation and enhance nitrogen fixation.
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This content will become publicly available on May 1, 2025
The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula
The conservation of GOLVEN (GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide encoding genes across plant genomes capable of forming roots or root‐like structures underscores their potential significance in the terrestrial adaptation of plants. This study investigates the function and role of GOLVEN peptide‐coding genes in
- Award ID(s):
- 2217830
- PAR ID:
- 10541087
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 118
- Issue:
- 3
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- 607 to 625
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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