Soybean gene co‐expression network analysis identifies two co‐regulated gene modules associated with nodule formation and development

Piya, Sarbottam; Pantalone, Vincent R.; Zadegan, Sobhan Bahrami; Shipp, Sarah; Lakhssassi, Naoufal; Knizia, Dounya; Krishnan, Hari B.; Meksem, Khalid; Hewezi, Tarek

doi:10.1111/mpp.13327

Cited by 4 publications

(2 citation statements)

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“…For expression profiling of the candidate genes, the publicly available RNA-seq datasets were used. Description and accession number of these RNA-seq datasets were provided in Piya et al. (2023) .…”

Section: Methodsmentioning

confidence: 99%

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Overexpression of soybean GmNAC19 and GmGRAB1 enhances root growth and water-deficit stress tolerance in soybean

et al. 2023

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Soybean (Glycine max) is an important crop in agricultural production where water shortage limits yields in soybean. Root system plays important roles in water-limited environments, but the underlying mechanisms are largely unknown. In our previous study, we produced a RNA-seq dataset generated from roots of soybean at three different growth stages (20-, 30-, and 44-day-old plants). In the present study, we performed a transcriptome analysis of the RNA-seq data to select candidate genes with probable association with root growth and development. Candidate genes were functionally examined in soybean by overexpression of individual genes using intact soybean composite plants with transgenic hairy roots. Root growth and biomass in the transgenic composite plants were significantly increased by overexpression of the GmNAC19 and GmGRAB1 transcriptional factors, showing up to 1.8-fold increase in root length and/or 1.7-fold increase in root fresh/dry weight. Furthermore, greenhouse-grown transgenic composite plants had significantly higher seed yield by about 2-fold than control plants. Expression profiling in different developmental stages and tissues showed that GmNAC19 and GmGRAB1 were most highly expressed in roots, displaying a distinct root-preferential expression. Moreover, we found that under water-deficit conditions, overexpression of GmNAC19 enhanced water stress tolerance in transgenic composite plants. Taken together, these results provide further insights into the agricultural potential of these genes for development of soybean cultivars with improved root growth and enhanced tolerance to water-deficit conditions.

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Section: Methodsmentioning

confidence: 99%

“…Heatmap plot was created by the PhytoMine tool ( https://phytozome.jgi.doe.gov ) presented at the Phytozome v12 website ( https://phytozome.jgi.doe.gov ). Gene expression analysis and heatmap plot construction were performed as described in Piya et al. (2023) .…”

Section: Methodsmentioning

confidence: 99%

Overexpression of soybean GmNAC19 and GmGRAB1 enhances root growth and water-deficit stress tolerance in soybean

et al. 2023

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Soybean gene co‐expression network analysis identifies two co‐regulated gene modules associated with nodule formation and development

Piya

Pantalone

Zadegan

et al. 2023

Molecular Plant Pathology

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Gene co‐expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait‐associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co‐expression network analysis. Two nodule‐specific modules (NSM‐1 and NSM‐2, containing 304 and 203 genes, respectively) were identified. The NSM‐1 gene promoters were significantly enriched in cis‐binding elements for ERF, MYB, and C2H2‐type zinc transcription factors, whereas NSM‐2 gene promoters were enriched in cis‐binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co‐expressed genes. The co‐expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co‐expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co‐expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.

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Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation

Tan

et al. 2023

Agronomy

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Ormosia is a genus of the Fabaceae family that shows a distinct evolutionary history due to its typical Asian-American tropical disjunction distribution pattern. However, both its phylogeny and biogeographic mechanisms have not been fully resolved. In addition, Ormosia species have great economic and ecological potential in the wood and handicraft (using their attractive seeds) industries, reforestation, and folk medicine (due to their flavonoids, alkaloids, and terpenoids), making them highly valuable in research, especially from a genomic perspective. We report the genome assemblies of two common Ormosia species, Ormosia emarginata and Ormosia semicastrata, in South China, using both long and short sequencing reads. The genome assemblies of O. emarginata and O. semicastrata comprised 90 contigs with a total length of 1,420,917,605 bp and 63 contigs with a total length of 1,511,766,959 bp, respectively. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment revealed 97.0% and 98.3% completeness of the O. emarginata and O. semicastrata assemblies, respectively. The assemblies contain 48,599 and 52,067 protein-coding genes, respectively. Phylogenetic analyses using 1032 single-copy genes with 19 species indicated that they are closely related to Lupinus albus. We investigated genes related to plant hormones, signaling, the circadian rhythm, transcription factors, and secondary metabolites derived from the whole genome and tandem and proximal duplications, indicating that these duplications should play important roles in the growth, development, and defense of Ormosia species. To our knowledge, our study is the first report on Ormosia genome assemblies. This information will facilitate phylogenetic and biogeographic analyses and species breeding in the future.

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Soybean gene co‐expression network analysis identifies two co‐regulated gene modules associated with nodule formation and development

Cited by 4 publications

References 48 publications

Overexpression of soybean GmNAC19 and GmGRAB1 enhances root growth and water-deficit stress tolerance in soybean

Overexpression of soybean GmNAC19 and GmGRAB1 enhances root growth and water-deficit stress tolerance in soybean

Soybean gene co‐expression network analysis identifies two co‐regulated gene modules associated with nodule formation and development

Genome Assemblies of Two Ormosia Species: Gene Duplication Related to Their Evolutionary Adaptation

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