Molecular Basis to Integrate Microgravity Signals into the Photoperiodic Flowering Pathway in Arabidopsis thaliana under Spaceflight Condition

Understanding the effects of spaceflight on plant flowering regulation is important to setup a life support system for long-term human space exploration. However, the way in which plant flowering is affected by spaceflight remains unclear. Here, we present results from our latest space experiments on the Chinese spacelab Tiangong-2, in which Arabidopsis wild-type and transgenic plants pFT::GFP germinated and grew as normally as their controls on the ground, but the floral initiation under the long-day condition in space was about 20 days later than their controls on the ground. Time-course series of digital images of pFT::GFP plants showed that the expression rhythm of FT in space did not change, but the peak appeared later in comparison with those of their controls on the ground. Whole-genome microarray analysis revealed that approximately 16% of Arabidopsis genes at the flowering stage changed their transcript levels under spaceflight conditions in comparison with their controls on the ground. The GO terms were enriched in DEGs with up-regulation of the response to temperature, wounding, and protein stabilization and down-regulation of the function in circadian rhythm, gibberellins, and mRNA processes. FT and SOC1 could act as hubs to integrate spaceflight stress signals into the photoperiodic flowering pathway in Arabidopsis in space.

Comparative transcriptomics of seven Impatiens species

Impatiens is a genus containing more than 1000 species. Thanks to its size, it is a unique system for studying species diversification in natural populations. This study focused on the characterization of novel transcriptomes from seven Impatiens species originating from Nepal. Leave transcriptome of Impatines balsamina L., I. racemosa DC., I. bicornuta Wall, I. falcifer Hook, I. devendrae Pusalkar, I. scullyi Hook and I. scabrida DC were sequenced and compared. Reads were de novo assembled and aligned to 92 035-226 081 contigs. We identified 14 728 orthology groups shared among all the species and 3 020 which were unique to a single species. In single species, 2536-3009 orthology groups were under selection from which 767 were common for all species. Six of the seven investigated species shared 77% of gene families with I. bicornuta being the most distinct species. Specific gene families involved in response to different environmental stimuli were closely described. Impatiens bicornuta selection profile shared selection on zing finger protein structures and flowering regulation and stress response proteins with the other investigated species. Overall, the study showed substantial similarity in patterns of selections on transcribed genes across the species suggesting similar evolutionary pressures. This suggests that the species group may have evolved via adaptive radiation.

Metabolic Analysis of the Regulatory Mechanism of Sugars on Secondary Flowering in Magnolia

Background: Magnolia is a traditional and important ornamental plant in urban greening, which has been cultivated for about 2,000 years in China for its elegant flower shape and gorgeous flower color. Most varieties of Magnolia bloom once a year in the spring, whereas a few others, such as Magnolia liliiflora Desr. ‘Hongyuanbao’, also bloom for the second time in summer or a little late. Such a twice flowering trait is desirable because of its high ornamental values, but its underlying mechanism remains unclear. Results: To explore the peculiar metabolism twice-flowering in ‘Hongyuanbao’, the chemical metabolites and the relevant genes encoding them in the flower buds during the entire flowering period were analyzed. It appears that there was a significant variation between the metabolic profiles of flower differentiation between the first and secondary flower buds. The sucrose and trehalose metabolic pathways were significantly upregulated during both flowering periods as shown by a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. This was further verified by quantitative real-time polymerase chain reaction analysis which showed that the expression levels of a number of trehalose-6-phosphate synthase (TPS) genes including MlTPS1, MlTPS5, MlTPS6, MlTPS7, and MlTPS9 were substantial increased. To further investigate the potential functional role of sucrose and trehalose in flowering regulation, the leaves of ‘Hongyuanbao’ were sprayed with the sucrose or trehalose solution with a gradient of concentrations including 30 mM, 60 mM, and 90 mM. While both trehalose and sucrose of 60 mM in concentration were able to accelerate the process of flower bud differentiation, their molecular pathways appeared to be different. Sucrose treatment increased the transcription levels of MlTPS5 and MlTPS6, whereas trehalose treatment increased MlTPS1. The expression of a number of flowering-related genes, such as MlFT, MlLFY, and MlSPL was also increased in response to the sprays of sucrose and trehalose. Conclusions: Overall, the findings on the functional roles of sucrose/trehalose and their underlying molecular mechanism in flowering of ‘Hongyuanbao’ improves our current understanding on of the biochemical triggers for flowering in Magnolia and provides a useful tool in Magnolia cultivation and flowering management.

Functional Divergence of AP1 And FUL Genes Related To Flowering Regulation In Upland Cotton (Gossypium Hirsutum L.)

The AP1/FUL transcription factors are important for floral development, but the underlying molecular mechanisms remain unclear. In this study, we cloned and identified two AP1/FUL-like genes, GhAP1.1 and GhFUL2, in upland cotton, which is a commonly cultivated economically valuable crop. Sequence alignments and phylogenetic analyses indicated GhAP1.1 and GhFUL2, which are encoded by genes in the AP1/FUL clade, have conserved N-terminals, but diverse C-terminal domains. A quantitative real-time PCR analysis revealed that GhAP1.1 and GhFUL2 were expressed in the flower and root, and had the opposite expression patterns during different shoot apical meristem stages. The upregulated expression of GhAP1.1 in Arabidopsis and the silencing of GhAP1.1 did not induce significant changes to the flowering time or floral organs, but the transcript levels of the florigen FT gene and the AP1 homolog GhMADS42 increased. The overexpression of GhFUL2 in Arabidopsis delayed flowering and promoted bolting by decreasing the FT and LFY expression levels. Silencing GhFUL2 in cotton dramatically increased the expression of GhFT and GhMADS42 and promoted flowering. Additionally, yeast two-hybrid and bimolecular fluorescence complementation assays indicated that GhAP1.1 can interact with the SVP homolog GhSVP2.2, whereas GhFUL2 can form heterodimers with GhSEP3/GhSEP4 homologs, and GhSVP2.2. Therefore, we proved that the functional divergence of GhAP1.1 and GhFUL2, which involved changes in sequences and expression patterns, influenced the regulation of cotton flower development and plant architecture.

Integrated Methylome and Transcriptome Analyses Reveal the Molecular Mechanism by Which DNA Methylation Regulates Kenaf Flowering

DNA methylation regulates key biological processes in plants. In this study, kenaf seedlings were pretreated with the DNA methylation inhibitor 5-azacytidine (5-azaC) (at concentrations of 0, 100, 200, 400, and 600 μM), and the results showed that pretreatment with 200 μM 5-azaC promoted flowering most effectively. To elucidate the underlying mechanism, phytohormone, adenosine triphosphate (ATP), and starch contents were determined, and genome-wide DNA methylation and transcriptome analyses were performed on anthers pretreated with 200 μM 5-azaC (5-azaC200) or with no 5-azaC (control conditions; 5-azaC0). Biochemical analysis revealed that 5-azaC pretreatment significantly reduced indoleacetic acid (IAA) and gibberellic acid (GA) contents and significantly increased abscisic acid (ABA) and ATP contents. The starch contents significantly increased in response to 200 and 600 μM 5-azaC. Further genome-wide DNA methylation analysis revealed 451 differentially methylated genes (DMGs) with 209 up- and 242 downregulated genes. Transcriptome analysis showed 3,986 differentially expressed genes (DEGs), with 2,171 up- and 1,815 downregulated genes. Integrated genome-wide DNA methylation and transcriptome analyses revealed 72 genes that were both differentially methylated and differentially expressed. These genes, which included ARFs, PP2C, starch synthase, FLC, PIF1, AGL80, and WRKY32, are involved mainly in plant hormone signal transduction, starch and sucrose metabolism, and flowering regulation and may be involved in early flowering. This study serves as a reference and theoretical basis for kenaf production and provides insights into the effects of DNA methylation on plant growth and development.

Transcriptome analysis of flowering regulation by sowing date in Japonica Rice (Oryza sativa L.)

Hybrid japonica cultivars, such as the Yongyou series, have shown high yield potential in the field in both the early and late growing seasons. Moreover, understanding the responses of rice flowering dates to temperature and light is critical for improving yield performance. However, few studies have analyzed flowering genes in high-yielding japonica cultivars. Based on the five sowing date experiments from 2019 to 2020, select the sensitive cultivar Yongyou 538 and the insensitive cultivar Ninggeng 4 and take their flag leaves and panicles for transcriptome analysis. The results showed that compared with sowing date 1 (6/16), after the sowing date was postponed (sowing date 5, 7/9), 4480 and 890 differentially expressed genes (DEGs) were detected in the leaves and panicles in Ninggeng 4, 9275 and 2475 DEGs were detected in the leaves and panicles in Yongyou 538, respectively. KEGG pathway analysis showed that both Ninggeng 4 and Yongyou 538 regulated rice flowering through the plant circadian rhythm and plant hormone signal transduction pathways. Gene expression analysis showed that Os01g0566050 (OsELF3-2), Os01g0182600 (OsGI), Os11g0547000 (OsFKF1), Os06g0275000 (Hd1), and Os09g0513500 (FT-1) were expressed higher and Os02g0771100 (COP1-1) was expressed lower in Yongyou 538 compared with Ninggeng 4 as the climate conditions changed, which may be the key genes that regulate the flowering process with the change of temperature and light resources in sensitive cultivar Yongyou 538 in the late season.

Combined Analysis of MicroRNAs and Target Genes Revealed miR156-SPLs and miR172-AP2 Are Involved in a Delayed Flowering Phenomenon After Chromosome Doubling in Black Goji (Lycium ruthencium)

Polyploidy, which is widely distributed in angiosperms, presents extremely valuable commercial applications in plant growth and reproduction. The flower development process of higher plants is essential for genetic improvement. Nevertheless, the reproduction difference between polyploidy and the polyploid florescence regulatory network from the perspective of microRNA (miRNA) remains to be elucidated. In this study, the autotetraploid of Lycium ruthenicum showed late-flowering traits compared with the progenitor. Combining the association of miRNA and next-generation transcriptome technology, the late-flowering characteristics triggered by chromosome duplication may be caused by the age pathway involved in miR156-SPLs and miR172-AP2, which inhibits the messenger RNA (mRNA) transcripts of FT in the leaves. Subsequently, FT was transferred to the shoot apical meristem (SAM) to inhibit the expression of the flowering integration factor SOC1, which can eventually result in delayed flowering time. Our exploration of the flowering regulation network and the control of the flowering time are vital to the goji producing in the late frost area, which provides a new perspective for exploring the intrinsic molecular mechanism of polyploid and the reproductive development of flowering plants.

Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time

Dendrobium is a semi-shade epiphytic Orchidaceae herb with important ornamental and medicinal value. Parts of the cultivation of Dendrobium germplasm resources, as well as the identification of medicinal components, are more studied, but the functional characterization of the flowering regulation in Dendrobium plants is less reported. Here, six PEBP family genes (DhFT3, DhFT1, DhMFT, DhTFL1b, DhFT2, and DhTFL1a) were identified from the Dendrobium huoshanense genome. The chromosome-level mapping showed that these genes were sequentially distributed on chromosomes 6, 9, 15, and 17. The paralogous gene DhTFL1b corresponded to DhTFL1a, which was determined through tandem duplication. The gene structure and conserved motif of DhPEBP indicated five PEBP genes apart from DhMFT contained four exons and three introns entirely. The phylogeny analysis showed that the PEBP gene family in A. thaliana, O. sativa, Z. mays, S. lycopersicum, and P. equestris were classified into three subclades, FT, TFL, and MFT, which maintained a high homology with D. huoshanense. The conserved domain of the amino acid demonstrated that two highly conserved short motifs (DPDXP and GXHR) embed in DhPEBPs, which may contribute to the conformation of the ligand binding bag. The 86th position of DhFTs was tyrosine (Y), while the 83th and 87th of DhTFL1s belonged to histidine (H), suggesting they should have distinct functions in flowering regulation. The promoter of six DhPEBPs contained several cis-elements related to hormone induction, light response, and abiotic stress, which indicated they could be regulated by the environmental stress and endogenous signaling pathways. The qRT-PCR analysis of DhPEBPs in short-term days induced by GA indicated the gene expressions of all DhFTs were gradually increased, whereas the expression of DhTFL1 was decreased. The results implied that DhPEBPs have various regulatory functions in modulating flowering, which will provide a scientific reference for the flowering regulation of Dendrobium plants.

Functional Divergence of AP1 and FUL Genes Related to Flowering Regulation in Upland Cotton

The AP1/FUL transcription factors are important for floral development, but the underlying molecular mechanisms remain unclear. In this study, we cloned and identified two AP1/FUL-like genes, GhAP1.1 and GhFUL2, in upland cotton, which is a commonly cultivated economically valuable crop. Sequence alignments and phylogenetic analyses indicated GhAP1.1 and GhFUL2, which are encoded by genes in the AP1/FUL clade, have conserved N-terminals, but diverse C-terminal domains. A quantitative real-time PCR analysis revealed that GhAP1.1 and GhFUL2 were expressed in the flower and root, and had the opposite expression patterns during different shoot apical meristem stages. The upregulated expression of GhAP1.1 in Arabidopsis and the silencing of GhAP1.1 did not induce significant changes to the flowering time or floral organs, but the transcript levels of the florigen FT gene and the AP1 homolog GhMADS42 increased. The overexpression of GhFUL2 in Arabidopsis delayed flowering and promoted bolting by decreasing the FT and LFY expression levels. Silencing GhFUL2 in cotton dramatically increased the expression of GhFT and GhMADS42 and promoted flowering. Additionally, yeast two-hybrid and bimolecular fluorescence complementation assays indicated that GhAP1.1 can interact with the SVP homolog GhSVP1, whereas GhFUL2 can form heterodimers with SEP1, SEP4 homologs, and GhSVP1. Therefore, we proved that the functional divergence of GhAP1.1 and GhFUL2, which involved changes in sequences and expression patterns, influenced the regulation of cotton flower development.

Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment

Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (Fragaria × ananassa Duch.) “Benihoppe” were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (PhyB, PIFs, and HY5) and circadian rhythm (FKF1, CCA1, LHY, and CO) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the FaBBX29, one of strawberry’s BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.