Network Landscape of Photothermal Flowering in Soybean.
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ABSTRACT:
PROVIDER: PRJNA482870 | ENA |
REPOSITORIES: ENA
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Project description:The project aims at elucidation of global gene expression patterns underlying photothermal flowering of soybean to clarify the molecular mechanisms of photothermal flowering in soybean.
2021-07-25 | GSE117673 | GEO
Project description:In order to identify candidate genes that are involved in soybean flowering transition in response to photoperiods, we performed RNA sequencing analysis under different photoperiod treatments. We identified genes exhibiting daily oscillation patterns under different photoperiod treatments, genes under control of maturity loci (E1, E2, E3 and E5), and genes that constitute the soybean flowering gene network.
2017-07-21 | GSE51007 | GEO
Project description:Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. In vitro and in vivo assays demonstrate that GmJMJ19 and GmJMJ20 bind to histone, but lack histone demethylase activity. Notably, simultaneous mutation of GmJMJ19 and GmJMJ20 causes delayed flowering time. Further transcriptomic, CUT&Tag and ChIP-seq analyses show that GmJMJ19/20 and GmLUX2 primarily co-repress transcription of 168 genes, which are not associated with the alternation of examined histone methylation state. Strikingly, we identify that the direct repression of GmSVP by GmJMJ19/20-GmLUX2 module is independent of the classical EC-E1 pathway. Interestingly, haplotype analyses support the idea that GmJMJ19 might undergo selection during soybean expansion to lower latitude. In summary, our findings reveal a mechanistic insight of GmJMJ19/20-GmLUX2 into flowering time control beyond EC complex in plants and also provide resources for improving soybean adaptability through molecular breeding.
2024-05-05 | GSE231884 | GEO
Project description:Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. In vitro and in vivo assays demonstrate that GmJMJ19 and GmJMJ20 bind to histone, but lack histone demethylase activity. Notably, simultaneous mutation of GmJMJ19 and GmJMJ20 causes delayed flowering time. Further transcriptomic, CUT&Tag and ChIP-seq analyses show that GmJMJ19/20 and GmLUX2 primarily co-repress transcription of 168 genes, which are not associated with the alternation of examined histone methylation state. Strikingly, we identify that the direct repression of GmSVP by GmJMJ19/20-GmLUX2 module is independent of the classical EC-E1 pathway. Interestingly, haplotype analyses support the idea that GmJMJ19 might undergo selection during soybean expansion to lower latitude. In summary, our findings reveal a mechanistic insight of GmJMJ19/20-GmLUX2 into flowering time control beyond EC complex in plants and also provide resources for improving soybean adaptability through molecular breeding.
2024-05-05 | GSE231883 | GEO
Project description:Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. In vitro and in vivo assays demonstrate that GmJMJ19 and GmJMJ20 bind to histone, but lack histone demethylase activity. Notably, simultaneous mutation of GmJMJ19 and GmJMJ20 causes delayed flowering time. Further transcriptomic, CUT&Tag and ChIP-seq analyses show that GmJMJ19/20 and GmLUX2 primarily co-repress transcription of 168 genes, which are not associated with the alternation of examined histone methylation state. Strikingly, we identify that the direct repression of GmSVP by GmJMJ19/20-GmLUX2 module is independent of the classical EC-E1 pathway. Interestingly, haplotype analyses support the idea that GmJMJ19 might undergo selection during soybean expansion to lower latitude. In summary, our findings reveal a mechanistic insight of GmJMJ19/20-GmLUX2 into flowering time control beyond EC complex in plants and also provide resources for improving soybean adaptability through molecular breeding.
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2014-09-11 | E-GEOD-61350 | biostudies-arrayexpress
Project description:Resistance (R) genes are very effective for disease control in plants. Current research shows that R genes predominantly function by inducing a hypersensitive reaction (HR), which results in localized cell death thought to restrict pathogen spread. Some R genes elicit a more atypical response where resistance is not associated with HR or the associated gene expression changes, termed extreme resistance (ER). The molecular regulatory mechanism underlying ER is largely unexplored. One of the few known, naturally occurring, instances of ER is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent strains of soybean mosaic virus (SMV). To discern the regulatory mechanism underlying the Rsv3-mediated ER reaction, we generated a gene regulatory network using transcriptomic data from a time course comparison of SMV-G7-infected resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. We identified putative interactions between transcription factors (TFs) regulating gene expression in hormone regulatory pathways, such as abscisic acid (ABA) and jasmonic acid (JA). This is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. We found significant enrichment for the G-box motif (“CACGTG”) among genes implicated in ABA- and JA-related activities. This motif is specifically recognized by MYC2, which is a master regulator of ABA and JA signaling. Our network identified a MYC2 TF encoded by Glyma.07G051500 as a putative transcriptional regulator whose expression was significantly down-regulated in L29. This correlated with the down-regulation of expression of genes involved in ABA and JA processes. Our results suggest an important function for Glyma.07G051500 in ABA and JA derived defense signaling. Additionally, our regulatory network found other putative TFs with differential expression, such as MYBs and ERFs, which may also be involved in regulating ABA and JA signaling for defense. The regulatory network presented here offers new insights into the regulation of the molecular defense mechanism underlying Rsv3-mediated ER against SMV.
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Project description:The Hydrophobic protein from soybean (HPS) locus is polymorphic among soybean cultivars and copy-number changes in the tandem array at this locus are directly correlated with expression level and seed coat luster phenotypes. Keywords: comparative genomic hybridization
2006-03-21 | GSE3810 | GEO
Project description:Drought-responsive genes in soybean leaves were successfully identified using Affymetrix Soybean Gene 1.0 ST arrays on leaves samples of reproductive-stage soybean plants. R1 soybean plants planted in pots were imposed drought by withholding water for 5 days until the soil moisture content dropped to 5%, and 3rd trifoliates (now at the R2 stage) were collected for expression profiling. Soybean plants were grown in pots. When the plants reached the R1 stage (started flowering), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 5th day of water withholding, when soil moisture content reached 5%. The 3rd trifoliate (counting from shoots), now at the R2 stage, was collected for total RNA extraction, while other 3rd trifoliates of similar chlorophyl index were collected for leaves water content determination to identify the severity of the stress. Total RNA from 3rd trifoliates were used for expression profiling using Affymetrix Soybean Gene 1.0 ST arrays. Four biological repeats per treatment were performed, three biological repeats were chosen for expression profiling.
2012-11-10 | E-GEOD-40604 | biostudies-arrayexpress