Similar Datasets
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 | GSE231885 | 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:Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean.
| PRJNA970057 | ENA
Project description:Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [CHIP-seq]
| PRJNA970062 | ENA
Project description:Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [CUT&Tag]
| PRJNA970063 | ENA
Project description:Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [RNA-seq]
| PRJNA970061 | ENA
Project description:Soybean is a short-day plant that typically flowers earlier when exposed to short-day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome-wide association studies (GWAS) using two re-sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13-3, which encodes a protein homologous to the pseudo-response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13-3 in the natural population, with haplotype H4 (qFT13-3H4) being lost during domestication, while qFT13-3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13-3H1 were located in high-latitude regions. Knockout of qFT13-3 accelerated flowering and maturity time under long-day conditions, indicating that qFT13-3 functions as a flowering inhibitor. Our results also showed that qFT13-3 directly downregulates the expression of GmELF3b-2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13-3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13-3 can be utilized for the breeding of high-yield cultivars with a short maturity time suitable for high latitudes.
| S-EPMC11022795 | biostudies-literature
Project description:In Arabidopsis thaliana, four FAD-dependent lysine-specific histone demethylases (LDL1, LDL2, LDL3, and FLD) are present, bearing both a SWIRM and an amine oxidase domain. In this study, a comparative analysis of gene structure, evolutionary relationships, tissue- and organ-specific expression patterns, physiological roles and target genes for the four Arabidopsis LDL/FLDs is reported. Phylogenetic analysis evidences a different evolutionary history for the four LDL/FLDs, while promoter activity data show that LDL/FLDs are strongly expressed during plant development and embryogenesis, with some gene-specific expression patterns. Furthermore, phenotypical analysis of loss-of-function mutants indicates a role of all four Arabidopsis LDL/FLD genes in the control of flowering time, though for some of them with opposing effects. This study contributes toward a better understanding of the LDL/FLD physiological roles and may provide biotechnological strategies for crop improvement.
| S-EPMC6558185 | biostudies-literature
Project description:Onset of flowering of plants is precisely controlled by extensive environmental factors and internal molecular networks, in which FLOWERING LOCUS T (FT) is a key flowering integrator. In soybean, a typical short-day plant, 11 FT homologues are found in its genome, of which several homologues are functionally diversified in flowering pathways and the others including GmFT3a are yet unknown. In the current study, we characterized GmFT3a, which is located on the same chromosome as the flowering promoters GmFT2a and GmFT5a. Overexpression of GmFT3a significantly promoted flowering of Arabidopsis under the inductive long-day (LD) photoperiod. GmFT3a over-expressed soybean also flowered earlier than the control under LD, but they were not significantly different under inductive short-day (SD) conditions, indicating that GmFT3a acts as a flowering promoter in the non-inductive photoperiod in soybean. Compared with other GmFT homologues, GmFT3a exhibited a slighter effect in flowering promotion than GmFT2a, GmFT5a and GmFT2b under LD conditions. GmFT3a promoted flowering by regulating the expression of downstream flowering-related genes and also affected the expression of other GmFTs. According to the re-sequencing data, the regional distributions of two major haplotypes in 176 soybean varieties were analyzed. The varieties with GmFT3a-Hap2 haplotype matured relatively early, and relative higher expression of GmFT3a was detected in early maturing varieties, implying that Hap2 variation may contribute to the adaptation of soybean to higher latitude regions by increasing expression level of genes in metabolism and signaling pathways. The early flowering germplasm generated by overexpression of GmFT3a has potential to be planted at higher latitudes where non-inductive long day is dominant in the growing season, and GmFT3a can be used to fine-tune soybean flowering and maturity time and improve the geographical adaptation.
| S-EPMC9358591 | biostudies-literature