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. 2023 Jan 15;24(2):1699.
doi: 10.3390/ijms24021699.

The Integrated mRNA and miRNA Approach Reveals Potential Regulators of Flowering Time in Arundina graminifolia

Sagheer Ahmad  1 , Chuqiao Lu  1 , Jie Gao  1 , Yonglu Wei  1 , Qi Xie  1 , Jianpeng Jin  1 , Genfa Zhu  1   2 , Fengxi Yang  1   2
Affiliations

The Integrated mRNA and miRNA Approach Reveals Potential Regulators of Flowering Time in Arundina graminifolia

Sagheer Ahmad et al. Int J Mol Sci. .

Abstract

Orchids are among the most precious flowers in the world. Regulation of flowering time is one of the most important targets to enhance their ornamental value. The beauty of Arundina graminifolia is its year-round flowering, although the molecular mechanism of this flowering ability remains masked. Therefore, we performed a comprehensive assessment to integrate transcriptome and miRNA sequencing to disentangle the genetic regulation of flowering in this valuable species. Clustering analyses provided a set of molecular regulators of floral transition and floral morphogenesis. We mined candidate floral homeotic genes, including FCA, FPA, GI, FT, FLC, AP2, SOC1, SVP, GI, TCP, and CO, which were targeted by a variety of miRNAs. MiR11091 targeted the highest number of genes, including candidate regulators of phase transition and hormonal control. The conserved miR156-miR172 pathway of floral time regulation was evident in our data, and we found important targets of these miRNAs in the transcriptome. Moreover, endogenous hormone levels were determined to decipher the hormonal control of floral buds in A. graminifolia. The qRT-PCR analysis of floral and hormonal integrators validated the transcriptome expression. Therefore, miRNA-mediated mining of candidate genes with hormonal regulation forms the basis for comprehending the complex regulatory network of perpetual flowering in precious orchids. The findings of this study can do a great deal to broaden the breeding programs for flowering time manipulation of orchids.

Keywords: bamboo orchid; floral integrators; hormones; micro RNA; multi-omics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The process of plant production and material selection for sequencing (a); the miRNA distribution according to mRNA targets (b); comparison of up- and down-regulated miRNAs among nine samples (blue bars show upregulation and red bars show downregulation)(c); overall distribution of miRNAs along with their predicted mRNA targets (blue target color shows upregulated and orange color shows downregulated genes) (d); and the annotation statistics of mRNA for KEGG, KOG and GO annotations (e).
Figure 2
Figure 2
miRNA with the highest mRNA targets. (a) heatmap of all the important genes targeted by miR11091; (b) clustering analysis of biological processes regulated by miR11091-mediated transcripts.
Figure 3
Figure 3
Major miRNA families for flower regulation. (a) heatmap of genes targeted by each miRNA family; (b) gene distribution for each miRNA family, color bands show biological process enrichment of target genes, node shapes show the stage-specific high expression of target genes; (c) relative abundance of biological process shown by all gene targets of miRNA families (ABA: Abscisic Acid; Aux: Auxin; C: Carpel; FD: Flower Development; GA: Gibberellic acid; CK: Cytokinin; Eth: Ethylene; SA: Salicylic Acid; JA: Jasmonic Acid; V—R: Vegetative to Reproductive phase change; Suc: Sucrose; PD: Pollen Development; AD: Anther Development; SAM: Shoot Apical Meristem; BR: Brassinosteroid; T.V--R: Timing of Vegetative to Reproductive phase change; PTG: Pollen Tube Growth; FOI: Floral Organ Initiation; CF: Carpel Formation; PM: Pollen Maturity; PS: Pollen Sterility; R.V--: Rate of Vegetative phase change; FWD: Floral Whorl Development; FOM: Floral Organ Maturation; AP: Acceptance of Pollen; PTC: Pollen Tube Reception; PSD: Pollen Sperm Cell Differentiation; FOD: Flower Organ Development; Organ Boundary Specification; ID: Inflorescence Determination; T.OF: Timing of Organ Formation; FMD: Floral Meristem Development; FMI: Floral Meristem Identity; St: Strigolactone; CD: Carpel Development).
Figure 4
Figure 4
Tissue-specific expression of miRNA targets and hormone concentrations. (a) clustering of miRNA targets with their maximum expressions to a particular tissue type. Colored circles show the occurrence of same miRNA for multiple targets (row names show the gene ID, common name and biological process abbreviation, the full abbreviation can be seen in the legend of Figure 3c) (some genes have multiple targets, which are placed separate under headings A-F); (b) relative concentrations of different plant hormones in five stages of flower development.
Figure 5
Figure 5
The qRT-PCR analysis of selected candidate mRNAs.
Figure 6
Figure 6
Overview of candidate miRNA targets with their expression intensities and model of miR256-miR172 mediated control of flowering time. The gene colors correspond to pathway colors at the top.
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